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0.15735097229480743 0.7478653 1.3197001218795776 True +3 7736 21.304003953933716 0.38214540481567383 202.2150115966797 0.3961330056190491 209.8649139404297 0.1603691577911377 0.7669916 0.8087561130523682 True +4 9670 21.313782930374146 9.584722757339478 145.27780151367188 0.6311467885971069 207.4176483154297 0.1650901585817337 0.77141917 0.7080750465393066 True +5 11604 21.526824712753296 0.40080976486206055 241.86428833007812 0.6229422092437744 205.9541778564453 0.16827698051929474 0.78610086 0.6496716737747192 True +6 13538 21.328052759170532 15.671534299850464 182.6682586669922 0.4135113060474396 204.89466857910156 0.17025181651115417 0.80705553 0.5356792211532593 True +7 15472 21.350109338760376 0.4056425094604492 210.12258911132812 0.6299154162406921 203.93553161621094 0.1727220118045807 0.81636167 0.5018178224563599 True +8 17406 21.44642424583435 1.7323391437530518 146.86471557617188 0.33051931858062744 203.0780029296875 0.17440442740917206 0.82583433 0.45004144310951233 True +9 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0.4228746294975281 558.505126953125 0.398867666721344 0.6380613 0.46096786856651306 True +12 35191 29.345475912094116 0.5581398010253906 470.19635009765625 0.3630325496196747 556.9335327148438 0.4016926884651184 0.6480557 0.44817614555358887 True +13 37898 29.319990634918213 0.5578982830047607 436.531982421875 0.397601455450058 555.3323974609375 0.4049094021320343 0.6577457 0.42637747526168823 True +14 40605 29.38408350944519 0.5585281848907471 441.6883850097656 0.3252045214176178 554.68212890625 0.40462610125541687 0.67046964 0.3986777067184448 True +15 43312 29.374523162841797 0.5592479705810547 472.47198486328125 0.2374137043952942 553.50830078125 0.40745311975479126 0.6794654 0.36783596873283386 True +16 46019 29.452784299850464 0.5587701797485352 432.1021423339844 0.23977874219417572 553.401611328125 0.4070867896080017 0.6858064 0.3489682376384735 True +17 48726 29.35116696357727 0.5602896213531494 489.5611267089844 0.15596888959407806 553.5094604492188 0.40636932849884033 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at end of file diff --git a/ENCSR745CGG/cherimoya.fold_4.fit.json b/ENCSR745CGG/cherimoya.fold_4.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..f88a29020cf3f4d22bbfdef0ed6bf27d9e5ab620 --- /dev/null +++ b/ENCSR745CGG/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": ["ENCFF031ANP.bigWig"], 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0000000000000000000000000000000000000000..7699c21e499570a23f6139d220968ce161e5e1cf --- /dev/null +++ b/ENCSR762FCX/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": ["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 new file mode 100644 index 0000000000000000000000000000000000000000..11d01553ea766445f7617a7bc440d6a35a699323 --- /dev/null +++ b/ENCSR762FCX/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 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 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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 new file mode 100644 index 0000000000000000000000000000000000000000..6caff7697175732fd3c354abfa678a721aa664f3 --- /dev/null +++ b/ENCSR762FCX/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse 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index 0000000000000000000000000000000000000000..15a62bebc1aa9edc8124f8674665629bea16106f --- /dev/null +++ b/ENCSR762FCX/cherimoya.fold_1.fit.json @@ -0,0 +1 @@ +{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "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_2.evaluate.json b/ENCSR762FCX/cherimoya.fold_2.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..b953878b8fc1a5d245344e3fb1bbec79e78939b6 --- /dev/null +++ b/ENCSR762FCX/cherimoya.fold_2.evaluate.json @@ -0,0 +1,76 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr22", + "chr7" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" + ], + "expansion": 2, + "in_window": 2114, + "loci": [ + "train_peaks.fold_2.bed", + "valid_peaks.fold_2.bed" + ], + "lw_lr": 0.001, + "lw_momentum": 0.9, + "lw_wd": 0.0, + "max_epochs": 20, + "max_jitter": 0, + "model": "cherimoya.fold_2.torch", + "muon_lr": 0.025, + "muon_wd": 0.03, + "n_filters": 128, + "n_layers": 9, + "n_warmup_epochs": 2, + "name": "cherimoya.fold_2", + "negative_ratio": 0.25, + "negatives": [ + "train_nonpeaks.fold_2.bed", + "valid_nonpeaks.fold_2.bed" + ], + "num_workers": 1, + "out_window": 1000, + "performance_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 new file mode 100644 index 0000000000000000000000000000000000000000..c7eca5155e76416ca18b636a67520f1be8cce33d --- /dev/null +++ b/ENCSR762FCX/cherimoya.fold_2.fit.json @@ -0,0 +1 @@ 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