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Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2725 34.151594161987305 3.9025869369506836 184.13067626953125 0.522003173828125 342.94427490234375 0.14097514748573303 0.68992156 4.688179969787598 True +1 5450 30.42440390586853 1.1645073890686035 235.14117431640625 0.7135612368583679 310.2414855957031 0.1946502923965454 0.7705781 1.8242144584655762 True +2 8175 30.39309072494507 0.7366349697113037 238.69461059570312 0.6185353398323059 304.8887023925781 0.19953440129756927 0.7925913 1.352402687072754 True +3 10900 30.448157787322998 0.7408106327056885 231.2490234375 0.6135579943656921 299.6768798828125 0.20658797025680542 0.80229646 0.8889645338058472 True +4 13625 30.311321020126343 0.6977043151855469 277.4901123046875 0.584162712097168 298.01251220703125 0.20832979679107666 0.8184595 0.6980072855949402 True +5 16350 30.278886795043945 0.7011127471923828 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0.23111797869205475 0.8660098 0.44083172082901 True +12 35425 30.499956607818604 0.706153392791748 271.4010009765625 0.5007250308990479 284.96038818359375 0.23329663276672363 0.8684957 0.4196945130825043 True +13 38150 30.516380786895752 1.241208791732788 241.56863403320312 0.47068876028060913 284.21417236328125 0.2347710132598877 0.8741926 0.39398783445358276 True +14 40875 30.473281621932983 0.8128659725189209 189.4756317138672 0.2827330231666565 283.33544921875 0.23636122047901154 0.8785578 0.3718416392803192 True +15 43600 30.44230580329895 1.0188918113708496 210.15554809570312 0.45887404680252075 281.99761962890625 0.23843146860599518 0.8831802 0.3501846194267273 True +16 46325 30.41007351875305 1.2201776504516602 150.70916748046875 0.21050885319709778 281.2674255371094 0.23889315128326416 0.8853497 0.3337022662162781 True +17 49050 30.58640766143799 20.384246349334717 172.19369506835938 0.39305680990219116 281.4863586425781 0.2382364124059677 0.8879679 0.32526662945747375 True +18 51775 30.568104028701782 24.85631561279297 219.03875732421875 0.25605103373527527 281.68536376953125 0.23764054477214813 0.8854767 0.32405027747154236 False +19 54500 30.669790267944336 1.2012042999267578 138.88551330566406 0.21051621437072754 281.9331970214844 0.2371632158756256 0.8848896 0.3250923752784729 False diff --git a/ENCSR134BSY/cherimoya.fold_2.fit.json b/ENCSR134BSY/cherimoya.fold_2.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..bc2a090468027a6120b9807d914338372a8b25d4 --- /dev/null +++ b/ENCSR134BSY/cherimoya.fold_2.fit.json @@ -0,0 +1 @@ +{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", 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0.5348827838897705 174.5308837890625 0.39970579743385315 256.36737060546875 0.2068142592906952 0.8316388 0.4605626165866852 True +8 26181 32.36528158187866 0.542241096496582 232.0313720703125 0.4187200665473938 255.19918823242188 0.2095058411359787 0.83713573 0.42491915822029114 True +9 29090 32.360084772109985 0.5339679718017578 167.3277587890625 0.3384818732738495 254.8221435546875 0.2098701000213623 0.84125435 0.4117595851421356 True +10 31999 32.35277271270752 0.996955156326294 180.4427947998047 0.45354077219963074 253.54090881347656 0.2126452475786209 0.8499604 0.37787824869155884 True +11 34908 32.43926930427551 0.5388615131378174 209.08621215820312 0.2606126666069031 252.59815979003906 0.21389521658420563 0.856009 0.35384368896484375 True +12 37817 32.43720984458923 0.5503292083740234 222.19256591796875 0.33878093957901 252.24424743652344 0.21469902992248535 0.86001635 0.34068629145622253 True +13 40726 32.42165231704712 0.5387775897979736 234.788330078125 0.22264669835567474 251.10105895996094 0.21744094789028168 0.86304474 0.3249139189720154 True +14 43635 32.440354347229004 0.5325424671173096 177.63754272460938 0.2607607841491699 250.37709045410156 0.21825948357582092 0.8656964 0.31456300616264343 True +15 46544 32.458831787109375 0.5247790813446045 233.40542602539062 0.2884191572666168 250.2930450439453 0.21846719086170197 0.8705404 0.3028471767902374 True +16 49453 32.38774251937866 1.2376136779785156 192.0396728515625 0.3025864362716675 249.32496643066406 0.22050487995147705 0.87242764 0.2924911677837372 True +17 52362 32.482518672943115 0.5419979095458984 208.43869018554688 0.17764067649841309 249.8711700439453 0.21997347474098206 0.87345976 0.2888903319835663 True +18 55271 32.43690061569214 0.5277481079101562 153.364013671875 0.1929943561553955 249.9200439453125 0.2199935019016266 0.8724984 0.2884783446788788 False +19 58180 32.44397473335266 0.5226261615753174 147.49485778808594 0.20129220187664032 249.8652801513672 0.22034038603305817 0.8735784 0.28947940468788147 True diff --git a/ENCSR134BSY/cherimoya.fold_3.performance.tsv b/ENCSR134BSY/cherimoya.fold_3.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..e0322fb667ea98c0983e783a412f76f29fe5d471 --- /dev/null +++ b/ENCSR134BSY/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +250.34027099609375 0.5356976985931396 0.21949593722820282 0.06342422217130661 0.8646211624145508 0.7982994318008423 0.33523982763290405 \ No newline at end of file diff --git a/ENCSR134BSY/cherimoya.fold_4.evaluate.json b/ENCSR134BSY/cherimoya.fold_4.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..a4d6bff1b9994bfd77703532fea6814ff0658159 --- /dev/null +++ b/ENCSR134BSY/cherimoya.fold_4.evaluate.json @@ -0,0 +1,75 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr10", + "chr18" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" + ], + "expansion": 2, + "in_window": 2114, + "loci": [ + "train_peaks.fold_4.bed", + "valid_peaks.fold_4.bed" + ], + "lw_lr": 0.001, + "lw_momentum": 0.9, + "lw_wd": 0.0, + "max_epochs": 20, + "max_jitter": 0, + "model": "cherimoya.fold_4.torch", + "muon_lr": 0.025, + "muon_wd": 0.03, + "n_filters": 128, + "n_layers": 9, + "n_warmup_epochs": 2, + "name": "cherimoya.fold_4", + "negative_ratio": 0.25, + "negatives": [ + "train_nonpeaks.fold_4.bed", + "valid_nonpeaks.fold_4.bed" + ], + "num_workers": 1, + "out_window": 1000, + "performance_filename": "cherimoya.fold_4.performance.tsv", + "random_state": null, + "residual_scale": 0.15, + "reverse_complement": false, + "reverse_complement_average": false, + "sequences": "hg38.fa", + "signals": [ + "ENCFF517EIH.bigWig" + ], + "skip": false, + "summits": false, + "training_chroms": [ + "chr1", + "chr2", + "chr3", + "chr4", + "chr5", + "chr6", + "chr8", + "chr9", + "chr11", + "chr12", + "chr14", + "chr15", + "chr16", + "chr20", + "chr22", + "chrY" + ], + "validation_chroms": [ + "chr10", + "chr18" + ], + "verbose": true +} \ No newline at end of file diff --git a/ENCSR134BSY/cherimoya.fold_4.performance.tsv b/ENCSR134BSY/cherimoya.fold_4.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..badbcb03a14c96fc66f52716ca45ca6290e12d03 --- /dev/null +++ b/ENCSR134BSY/cherimoya.fold_4.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +205.17318725585938 0.5584061741828918 0.1914346069097519 0.05349152535200119 0.8651641607284546 0.7797526717185974 0.23713399469852448 \ No newline at end of file diff --git a/ENCSR139PLJ/cherimoya.fold_2.evaluate.json b/ENCSR139PLJ/cherimoya.fold_2.evaluate.json new file mode 100644 index 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