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of file diff --git a/ENCSR076YBB/cherimoya.fold_0.fit.json b/ENCSR076YBB/cherimoya.fold_0.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..b0f8a1c6cf083f7680a331ed99252ab98c290a73 --- /dev/null +++ b/ENCSR076YBB/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": 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0000000000000000000000000000000000000000..2e129489f15d0f32914b83f5320e2b67d7daf71f --- /dev/null +++ b/ENCSR076YBB/cherimoya.fold_2.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +182.90956115722656 0.540979266166687 0.23817573487758636 0.050957731902599335 0.7054022550582886 0.6745656132698059 0.41392436623573303 \ No newline at end of file diff --git a/ENCSR076YBB/cherimoya.fold_3.evaluate.json b/ENCSR076YBB/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..dd60695f18a27ca4064ff93eb4c1e775129d4135 --- /dev/null +++ b/ENCSR076YBB/cherimoya.fold_3.evaluate.json @@ -0,0 +1,75 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr6", + "chr21" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + 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0.5820108652114868 231.35955810546875 0.22984007000923157 0.78274345 0.453151673078537 True +17 49986 30.228166103363037 0.5340898036956787 194.46649169921875 0.41785791516304016 231.22752380371094 0.23042838275432587 0.78303194 0.44590136408805847 True +18 52763 30.221638679504395 0.5313732624053955 188.76776123046875 0.3710499405860901 231.29225158691406 0.23052489757537842 0.78225505 0.443967342376709 False +19 55540 30.21271562576294 0.5212268829345703 151.48944091796875 0.4682803750038147 231.4437255859375 0.2296021729707718 0.7803888 0.4475642144680023 False diff --git a/ENCSR457ILW/cherimoya.fold_0.performance.tsv b/ENCSR457ILW/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..00df5771f2656f6058819b839167cdf2139c06cb --- /dev/null +++ b/ENCSR457ILW/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +231.22752380371094 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of file diff --git a/ENCSR457ILW/cherimoya.fold_1.log b/ENCSR457ILW/cherimoya.fold_1.log new file mode 100644 index 0000000000000000000000000000000000000000..2278247bafa848d74f84ce95df08bdba3eccef61 --- /dev/null +++ b/ENCSR457ILW/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 2742 34.872846364974976 3.6360206604003906 178.36631774902344 0.7061331868171692 281.6355285644531 0.14818784594535828 0.6312613 3.5714962482452393 True +1 5484 30.476975917816162 1.1532416343688965 220.52005004882812 0.6901569366455078 268.70245361328125 0.20758377015590668 0.71412575 1.4486409425735474 True +2 8226 30.51745104789734 0.7386486530303955 182.8670654296875 0.7988866567611694 265.1416931152344 0.2177116423845291 0.73984814 0.7814412713050842 True +3 10968 30.440760374069214 0.7750682830810547 175.96815490722656 0.739244818687439 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0.7426636219024658 164.76927185058594 0.3291790783405304 257.7216796875 0.24481257796287537 0.8062815 0.4454180896282196 True +17 49356 29.90448307991028 1.1598849296569824 191.50747680664062 0.2955152988433838 257.6301574707031 0.24605631828308105 0.80748975 0.4428402781486511 True +18 52098 29.925081253051758 0.7819802761077881 161.3748779296875 0.34251147508621216 257.6486511230469 0.24608422815799713 0.8086443 0.44537636637687683 True +19 54840 29.997009992599487 0.7402756214141846 179.1627655029297 0.5547264218330383 257.7000732421875 0.2458367496728897 0.80768806 0.44715356826782227 False diff --git a/ENCSR457ILW/cherimoya.fold_1.performance.tsv b/ENCSR457ILW/cherimoya.fold_1.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..15b056c86bb1e2046de08710e957afcab8c53bea --- /dev/null +++ b/ENCSR457ILW/cherimoya.fold_1.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse 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0000000000000000000000000000000000000000..8ad80c1be3f762397a5afb1af2d9938205e80828 --- /dev/null +++ b/ENCSR457ILW/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": ["ENCFF405IRH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR457ILW/cherimoya.fold_2.log b/ENCSR457ILW/cherimoya.fold_2.log new file mode 100644 index 0000000000000000000000000000000000000000..c38c66c869b86677bc000d380455394d10ec1dfe --- /dev/null +++ b/ENCSR457ILW/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 2898 38.423882246017456 3.982494354248047 206.8461151123047 0.8461979627609253 260.25006103515625 0.1424180269241333 0.6105442 2.9923787117004395 True +1 5796 32.266408920288086 0.6402325630187988 186.84286499023438 1.1900955438613892 248.57147216796875 0.19859176874160767 0.6897447 1.597287654876709 True +2 8694 32.251526832580566 1.5819542407989502 167.2410430908203 0.5293213129043579 245.04367065429688 0.21102795004844666 0.7093386 0.9215191602706909 True +3 11592 32.276939868927 0.5335707664489746 194.72763061523438 0.792697012424469 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0.5375382900238037 224.0723876953125 0.3798891603946686 238.50466918945312 0.2377581000328064 0.7797933 0.45410388708114624 True +17 52164 31.619734048843384 0.5313718318939209 217.35595703125 0.326545774936676 238.54200744628906 0.23799768090248108 0.78195435 0.44983506202697754 True +18 55062 31.682032585144043 0.5408921241760254 192.09352111816406 0.3847072720527649 238.53631591796875 0.23788177967071533 0.78232396 0.4523977041244507 True +19 57960 31.592505931854248 0.5339155197143555 180.42276000976562 0.36013299226760864 238.64503479003906 0.23735693097114563 0.78152215 0.4542780816555023 False diff --git a/ENCSR457ILW/cherimoya.fold_2.performance.tsv b/ENCSR457ILW/cherimoya.fold_2.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..3840d921c9f568662164254c4a7b451bc2472bb8 --- /dev/null +++ b/ENCSR457ILW/cherimoya.fold_2.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +238.53631591796875 0.525105893611908 0.23788177967071533 0.06485214829444885 0.782323956489563 0.7440676093101501 0.4523977041244507 \ No newline at end of file diff --git a/ENCSR457ILW/cherimoya.fold_3.evaluate.json b/ENCSR457ILW/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..cbadceaf45611d51a5482fbee2d1a78b760de7af --- /dev/null +++ b/ENCSR457ILW/cherimoya.fold_3.evaluate.json @@ -0,0 +1,75 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr6", + "chr21" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" + ], + "expansion": 2, + "in_window": 2114, + "loci": [ + "train_peaks.fold_3.bed", + "valid_peaks.fold_3.bed" + ], + "lw_lr": 0.001, + "lw_momentum": 0.9, + "lw_wd": 0.0, + "max_epochs": 20, + "max_jitter": 0, + "model": 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index 0000000000000000000000000000000000000000..2640fef4130e8f498c08aae29bdc35e6f35ab150 --- /dev/null +++ b/ENCSR457ILW/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": ["ENCFF405IRH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff 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0000000000000000000000000000000000000000..807b1d65e292a5aacef40b95724828d2b1251ac7 --- /dev/null +++ b/ENCSR637ZLM/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": ["ENCFF144PIF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file 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0000000000000000000000000000000000000000..7e5105a4d12d4d83b7abb856b80a6c735d4d7ca3 --- /dev/null +++ b/ENCSR941DTJ/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": ["ENCFF131SQK.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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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 new file mode 100644 index 0000000000000000000000000000000000000000..d97bdc2ecea3b9525dd7a5e6f9fdedc613adca48 --- /dev/null +++ b/ENCSR964WHY/cherimoya.fold_4.performance.tsv @@ -0,0 +1,2 @@ +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