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+++ b/ENCSR000ENZ/cherimoya.fold_2.log @@ -0,0 +1,21 @@ +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 36.823938608169556 4.87580132484436 1377.02880859375 1.1191234588623047 2051.186767578125 0.320197731256485 0.40913302 9.176267623901367 True +1 5802 32.0857720375061 0.5594689846038818 1399.795654296875 1.0330250263214111 1584.4639892578125 0.4904451370239258 0.5172186 6.937195777893066 True +2 8703 32.05281090736389 0.5516369342803955 1287.584228515625 1.481353998184204 1529.4970703125 0.504663348197937 0.5311144 3.5438919067382812 True +3 11604 31.98695182800293 1.223961353302002 897.8517456054688 1.3584871292114258 1510.377685546875 0.5074305534362793 0.5413574 2.5147440433502197 True +4 14505 31.967685222625732 0.5260703563690186 1163.250732421875 1.2052812576293945 1482.6717529296875 0.5170060396194458 0.5570615 1.8376268148422241 True +5 17406 31.980326890945435 0.5478017330169678 1089.4515380859375 1.4810857772827148 1467.3226318359375 0.5225826501846313 0.5656959 1.7244163751602173 True +6 20307 31.952041149139404 0.554224967956543 1477.06201171875 1.5094940662384033 1457.8524169921875 0.5260118842124939 0.5741096 1.3805750608444214 True +7 23208 31.981167554855347 0.544248104095459 1222.494384765625 1.571123719215393 1449.7763671875 0.5284664034843445 0.5811085 1.3086161613464355 True +8 26109 31.987602710723877 0.5776090621948242 1025.5750732421875 1.2767622470855713 1441.3309326171875 0.5286080241203308 0.5930621 1.1818164587020874 True +9 29010 32.05443525314331 0.5550136566162109 936.513427734375 0.9124107360839844 1425.1409912109375 0.5359499454498291 0.60303694 1.1379673480987549 True +10 31911 32.58296060562134 0.5479171276092529 844.5692749023438 1.2435061931610107 1416.1370849609375 0.5390558838844299 0.6149299 1.0146762132644653 True +11 34812 32.03452777862549 0.5565433502197266 1030.1173095703125 0.8182365894317627 1401.6727294921875 0.5437860488891602 0.623064 0.9578788876533508 True +12 37713 31.985242128372192 0.5324623584747314 1136.149169921875 0.8637850880622864 1393.3851318359375 0.5450092554092407 0.6358243 0.8925687074661255 True +13 40614 31.417863130569458 0.543250322341919 983.486083984375 1.037872076034546 1383.914794921875 0.5479173064231873 0.6485875 0.8391196727752686 True +14 43515 31.415305614471436 0.62380051612854 1026.3631591796875 0.8378802537918091 1369.8443603515625 0.5551320314407349 0.66180867 0.8124599456787109 True +15 46416 31.483826398849487 0.5464386940002441 1018.4213256835938 0.7917494773864746 1365.2945556640625 0.5543783903121948 0.67193496 0.7885796427726746 True +16 49317 31.46100926399231 0.5482509136199951 1241.3775634765625 0.832405686378479 1359.3612060546875 0.5562788844108582 0.6784864 0.7724279165267944 True +17 52218 31.5270893573761 0.5501019954681396 1041.8277587890625 0.8028740882873535 1366.131591796875 0.5526578426361084 0.6823513 0.7639548778533936 True +18 55119 31.470991373062134 0.5397348403930664 833.579833984375 0.6592925786972046 1364.240478515625 0.5537410974502563 0.684026 0.763831377029419 True +19 58020 31.548731088638306 0.5379292964935303 1104.716064453125 0.5882836580276489 1363.72412109375 0.5545561909675598 0.6828083 0.7642475962638855 False diff --git a/ENCSR000ENZ/cherimoya.fold_2.performance.tsv b/ENCSR000ENZ/cherimoya.fold_2.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..441079adeea7e02b84f61dfa8bf5e2d9ed1f12d8 --- /dev/null +++ b/ENCSR000ENZ/cherimoya.fold_2.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +1364.240478515625 0.27012646198272705 0.5537410974502563 0.2907203733921051 0.6840260028839111 0.6468825936317444 0.763831377029419 \ No newline at end of file diff --git a/ENCSR000ENZ/cherimoya.fold_3.evaluate.json b/ENCSR000ENZ/cherimoya.fold_3.evaluate.json 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0.3574976921081543 190.97488403320312 0.1932857483625412 0.8767661 0.36757567524909973 True +13 29582 23.837228059768677 0.4529106616973877 175.4378204345703 0.3743295967578888 190.66383361816406 0.19415044784545898 0.8780841 0.36055418848991394 True +14 31695 23.874745845794678 34.2505407333374 168.17510986328125 0.2768093943595886 189.96334838867188 0.19615016877651215 0.8804419 0.3482649624347687 True +15 33808 23.3619441986084 0.44817566871643066 218.31466674804688 0.32950228452682495 189.82461547851562 0.19646787643432617 0.88410336 0.3400510549545288 True +16 35921 23.58465576171875 0.43345165252685547 162.01181030273438 0.30807363986968994 189.82513427734375 0.1961645632982254 0.88462675 0.3352901339530945 True +17 38034 23.267772674560547 0.4330463409423828 171.99871826171875 0.27823448181152344 190.12484741210938 0.1952202171087265 0.88396657 0.33394405245780945 False +18 40147 24.093586921691895 0.4294247627258301 124.32559204101562 0.46471935510635376 189.98841857910156 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0000000000000000000000000000000000000000..228d24288d2e9a3aa9d278878a2e3dbac13eb6fa --- /dev/null +++ b/ENCSR097AMI/cherimoya.fold_4.fit.json @@ -0,0 +1 @@ +{"n_filters": 128, "name": "cherimoya.fold_4", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF507XGA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git 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0000000000000000000000000000000000000000..91a7670830e71d17c61b4a6b56d9f6f8cd11d81e --- /dev/null +++ b/ENCSR648GDP/cherimoya.fold_0.fit.json @@ -0,0 +1 @@ +{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "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 new file mode 100644 index 0000000000000000000000000000000000000000..9f02a11a125d8a23ba0b3acbf6e07bfbc9668cc0 --- /dev/null +++ b/ENCSR648GDP/cherimoya.fold_0.log @@ -0,0 +1,21 @@ +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 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0000000000000000000000000000000000000000..76131aa751b4ec9792ab3a69745d77ab9040f175 --- /dev/null +++ b/ENCSR648GDP/cherimoya.fold_3.fit.json @@ -0,0 +1 @@ +{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "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 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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 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0000000000000000000000000000000000000000..c316a26e40d3cf91c9af63b4463073211e2df26f --- /dev/null +++ b/ENCSR813CKU/cherimoya.fold_1.evaluate.json @@ -0,0 +1,77 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr12", + "chr17" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" + ], + "expansion": 2, + "in_window": 2114, + "loci": [ + "train_peaks.fold_1.bed", + "valid_peaks.fold_1.bed" + ], + "lw_lr": 0.001, + "lw_momentum": 0.9, + "lw_wd": 0.0, + "max_epochs": 20, + "max_jitter": 0, + "model": "cherimoya.fold_1.torch", + "muon_lr": 0.025, + "muon_wd": 0.03, + "n_filters": 128, + "n_layers": 9, + "n_warmup_epochs": 2, + "name": "cherimoya.fold_1", + "negative_ratio": 0.25, + "negatives": [ + "train_nonpeaks.fold_1.bed", + "valid_nonpeaks.fold_1.bed" + ], + "num_workers": 1, + "out_window": 1000, + 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false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "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 new file mode 100644 index 0000000000000000000000000000000000000000..cdbba66175f58663e329da8fd9a5e5dff2cc0bd4 --- /dev/null +++ b/ENCSR813CKU/cherimoya.fold_1.log @@ -0,0 +1,21 @@ +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 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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 new file mode 100644 index 0000000000000000000000000000000000000000..5a5e256294850f4d30109a2f0bfe7d32777cb432 --- /dev/null +++ b/ENCSR813CKU/cherimoya.fold_1.performance.tsv @@ -0,0 +1,2 @@ +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.fit.json b/ENCSR813CKU/cherimoya.fold_2.fit.json new file mode 100644 index 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diff --git a/ENCSR813CKU/cherimoya.fold_2.log b/ENCSR813CKU/cherimoya.fold_2.log new file mode 100644 index 0000000000000000000000000000000000000000..d871d72b6a86344368c95ea5ec3d0ac41fbd09c1 --- /dev/null +++ b/ENCSR813CKU/cherimoya.fold_2.log @@ -0,0 +1,21 @@ +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 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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 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0000000000000000000000000000000000000000..080a9ae81bd63f5b4111d9392170888df17453f4 --- /dev/null +++ b/ENCSR945JJB/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", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "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 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