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newline at end of file diff --git a/ENCSR082PDJ/cherimoya.fold_2.evaluate.json b/ENCSR082PDJ/cherimoya.fold_2.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..f06f9946f4252cb804299a801a04094d96c351d8 --- /dev/null +++ b/ENCSR082PDJ/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", + 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192.16183471679688 0.5830851793289185 259.9167785644531 0.23112215101718903 0.6901403 0.5271297693252563 True +5 16530 30.135557651519775 0.6713855266571045 197.27975463867188 0.6682279706001282 259.2725524902344 0.23417985439300537 0.6927232 0.5183658003807068 True +6 19285 30.179007291793823 2.4743728637695312 167.05409240722656 0.5934879779815674 258.66925048828125 0.23710006475448608 0.6963386 0.5231314301490784 True +7 22040 30.24544072151184 0.6702909469604492 175.4369354248047 0.826528012752533 258.3659362792969 0.23807281255722046 0.70166826 0.5323662161827087 True +8 24795 30.240667819976807 0.6658728122711182 177.57362365722656 0.819401741027832 258.0757751464844 0.23918917775154114 0.7096574 0.5174277424812317 True +9 27550 30.145351886749268 0.6558492183685303 162.58737182617188 0.7630202770233154 257.5020446777344 0.2414252758026123 0.7134283 0.479678750038147 True +10 30305 30.22106170654297 0.6834850311279297 194.3524169921875 0.4380756616592407 257.11163330078125 0.24316968023777008 0.71820384 0.47059133648872375 True +11 33060 30.20067262649536 0.6702709197998047 195.6318359375 0.47925475239753723 256.24835205078125 0.2468334287405014 0.72630405 0.4463285207748413 True +12 35815 30.488929986953735 1.8988351821899414 191.17037963867188 0.7150021195411682 256.0428771972656 0.2475631684064865 0.7343502 0.41969218850135803 True +13 38570 30.166165590286255 0.6815927028656006 197.521728515625 0.3607754111289978 255.4613494873047 0.25009629130363464 0.7392418 0.41265350580215454 True +14 41325 30.111517906188965 0.6755352020263672 189.00311279296875 0.31931787729263306 255.31503295898438 0.2504270672798157 0.74797946 0.4021669626235962 True +15 44080 30.153897523880005 0.6799261569976807 203.29754638671875 0.3327895998954773 255.1192626953125 0.2510082423686981 0.75272894 0.3913682997226715 True +16 46835 30.156565189361572 0.667264461517334 192.75527954101562 0.4511367976665497 255.37405395507812 0.249475359916687 0.7597471 0.3841739892959595 True +17 49590 30.100425481796265 0.6695516109466553 200.70166015625 0.3812043368816376 255.25572204589844 0.2506292462348938 0.7609869 0.38480067253112793 True +18 52345 30.147494554519653 0.6575088500976562 171.93508911132812 0.23161166906356812 254.97067260742188 0.2520686089992523 0.7592631 0.39100179076194763 False +19 55100 30.1359760761261 0.6746985912322998 179.11068725585938 0.25563502311706543 255.04058837890625 0.2516672611236572 0.7595066 0.39379337430000305 False diff --git a/ENCSR106RBR/cherimoya.fold_1.performance.tsv b/ENCSR106RBR/cherimoya.fold_1.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..70b0b761906e0d712b121c2bcb8b6c6a2164534e --- /dev/null +++ b/ENCSR106RBR/cherimoya.fold_1.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +255.25572204589844 0.5145676136016846 0.2506292462348938 0.06681715697050095 0.7609869241714478 0.7227747440338135 0.38480067253112793 \ No newline at end of file diff --git a/ENCSR106RBR/cherimoya.fold_2.evaluate.json b/ENCSR106RBR/cherimoya.fold_2.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..3702354db8b5e5c7662d4b364ea2789d201a9e4f --- /dev/null +++ b/ENCSR106RBR/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": 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b/ENCSR106RBR/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": ["ENCFF045KEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR106RBR/cherimoya.fold_2.log b/ENCSR106RBR/cherimoya.fold_2.log new file mode 100644 index 0000000000000000000000000000000000000000..22c7211a625dbbb969dd9c70d13609b66a2ce05c --- /dev/null +++ b/ENCSR106RBR/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 2912 37.17389988899231 3.9797935485839844 167.31646728515625 0.6839104890823364 257.699951171875 0.155486062169075 0.48598093 2.9087729454040527 True +1 5824 32.47227644920349 0.5726094245910645 211.41287231445312 0.7104066610336304 245.80215454101562 0.2129216492176056 0.60591507 1.0761340856552124 True +2 8736 32.43924260139465 0.5122725963592529 193.51840209960938 0.7256734371185303 243.5325469970703 0.2189653068780899 0.6329311 0.5955008268356323 True +3 11648 32.46146607398987 0.5386779308319092 177.99681091308594 0.8795602917671204 242.36520385742188 0.2232140302658081 0.64026123 0.5562801957130432 True +4 14560 32.08673620223999 0.511589765548706 169.71929931640625 0.7481688261032104 241.3438720703125 0.22869306802749634 0.6443202 0.5817424058914185 True +5 17472 31.85094380378723 0.5023801326751709 187.54299926757812 0.5782490372657776 241.3515167236328 0.22815962135791779 0.6498299 0.5965369939804077 True +6 20384 31.855295658111572 0.5028698444366455 181.2571563720703 0.525891900062561 240.7298126220703 0.23121728003025055 0.65348077 0.6241613030433655 True +7 23296 31.866652965545654 0.508901834487915 156.76129150390625 0.5044710040092468 240.14508056640625 0.23400139808654785 0.6585677 0.6411905288696289 True +8 26208 31.818727254867554 0.4994783401489258 201.29415893554688 0.8125445246696472 239.98614501953125 0.23549264669418335 0.66350734 0.5827091336250305 True +9 29120 31.802559852600098 0.5040333271026611 212.0532989501953 0.564957857131958 239.55136108398438 0.23724091053009033 0.6679403 0.562773585319519 True +10 32032 31.883716583251953 0.4855620861053467 185.21055603027344 0.5875037908554077 239.13699340820312 0.23871156573295593 0.6744166 0.5333630442619324 True +11 34944 31.94636821746826 15.633396863937378 186.18637084960938 0.44493043422698975 238.6887969970703 0.24086330831050873 0.67926794 0.4992121458053589 True +12 37856 32.00089621543884 14.373074054718018 183.0007781982422 0.38569456338882446 238.41795349121094 0.24124163389205933 0.68720704 0.4767806828022003 True +13 40768 32.03850531578064 1.0371477603912354 178.529052734375 0.4753146469593048 237.8711700439453 0.24388980865478516 0.6942606 0.4431458115577698 True +14 43680 31.935035467147827 0.5084481239318848 174.77806091308594 0.46170371770858765 237.57986450195312 0.24489973485469818 0.70158976 0.4220823049545288 True +15 46592 31.899011373519897 0.5029754638671875 197.16049194335938 0.36781251430511475 237.48641967773438 0.24550274014472961 0.706919 0.4024573564529419 True +16 49504 31.984299182891846 0.5017249584197998 184.9762420654297 0.3086825907230377 237.1871795654297 0.24701587855815887 0.71129125 0.3963128924369812 True +17 52416 31.884854793548584 0.5060973167419434 217.64535522460938 0.42880427837371826 237.31764221191406 0.24605786800384521 0.7149493 0.3962721824645996 True +18 55328 31.769349336624146 1.7846252918243408 215.659912109375 0.2568260729312897 237.57315063476562 0.24472396075725555 0.7139214 0.4033799469470978 False +19 58240 31.915941953659058 17.314345598220825 137.9851837158203 0.3309667110443115 237.532470703125 0.245170459151268 0.7155881 0.4072324335575104 True diff --git a/ENCSR106RBR/cherimoya.fold_2.performance.tsv b/ENCSR106RBR/cherimoya.fold_2.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..c8fb19e42c02e8bb7b7b6fbe817e387d52e1c0ff --- /dev/null +++ b/ENCSR106RBR/cherimoya.fold_2.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +237.532470703125 0.5213837027549744 0.245170459151268 0.06315303593873978 0.7155880928039551 0.668106198310852 0.4072324335575104 \ No newline at end of file diff --git a/ENCSR106RBR/cherimoya.fold_3.evaluate.json b/ENCSR106RBR/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..bed660563c64309e207232888904d1c6894fadd2 --- /dev/null +++ b/ENCSR106RBR/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": "cherimoya.fold_3.torch", + "muon_lr": 0.025, + "muon_wd": 0.03, + "n_filters": 128, + "n_layers": 9, + "n_warmup_epochs": 2, + "name": 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b/ENCSR106RBR/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": ["ENCFF045KEF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR106RBR/cherimoya.fold_3.log b/ENCSR106RBR/cherimoya.fold_3.log new file mode 100644 index 0000000000000000000000000000000000000000..f8e9f79ee8a060ac9707e63b60fc5118c188dc27 --- /dev/null +++ b/ENCSR106RBR/cherimoya.fold_3.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 2766 38.33952713012695 4.041626691818237 197.74166870117188 0.8677603602409363 271.7477111816406 0.14934876561164856 0.49451658 3.0954160690307617 True +1 5532 30.837297916412354 0.5964548587799072 222.069091796875 0.909373939037323 259.7004089355469 0.20945653319358826 0.6076697 1.2083032131195068 True +2 8298 30.86240029335022 0.6524901390075684 183.2929229736328 0.6781946420669556 256.7730712890625 0.2196105271577835 0.6318489 0.7394782900810242 True +3 11064 30.62969660758972 0.5753540992736816 190.37005615234375 0.841118574142456 255.82778930664062 0.22273088991641998 0.6370789 0.6395250558853149 True +4 13830 30.28114628791809 0.5884718894958496 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newline at end of file diff --git a/ENCSR141IUS/cherimoya.fold_0.evaluate.json b/ENCSR141IUS/cherimoya.fold_0.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..703f4ce82ff17401948479eec297ec583cbec10e --- /dev/null +++ b/ENCSR141IUS/cherimoya.fold_0.evaluate.json @@ -0,0 +1,78 @@ +{ + "adam_lr": 0.001, + "adam_wd": 0.0, + "batch_size": 64, + "chroms": [ + "chr8", + "chr20" + ], + "controls": null, + "device": "cuda", + "dtype": "bfloat16", + "early_stopping": 20, + "exclusion_lists": [ + "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz" + ], + "expansion": 2, + "in_window": 2114, + "loci": [ + "train_peaks.fold_0.bed", + "valid_peaks.fold_0.bed" + ], + "lw_lr": 0.001, + "lw_momentum": 0.9, + "lw_wd": 0.0, + "max_epochs": 20, + "max_jitter": 0, + "model": "cherimoya.fold_0.torch", + "muon_lr": 0.025, + "muon_wd": 0.03, + "n_filters": 128, + "n_layers": 9, + "n_warmup_epochs": 2, + "name": "cherimoya.fold_0", + 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diff --git a/ENCSR306BHE/cherimoya.fold_3.performance.tsv b/ENCSR306BHE/cherimoya.fold_3.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5f48b14c247fb29e49509cbf177bb3cdcadc9904 --- /dev/null +++ b/ENCSR306BHE/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +909.3954467773438 0.2918933928012848 0.4972250759601593 0.2525729537010193 0.8145690560340881 0.7876662611961365 0.26580363512039185 \ No newline at end of file diff --git a/ENCSR306BHE/cherimoya.fold_4.evaluate.json b/ENCSR306BHE/cherimoya.fold_4.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..2a52feceb98884cad919f3afc9d1ca4c392096b5 --- /dev/null +++ b/ENCSR306BHE/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": 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29.683576345443726 0.6228227615356445 173.84471130371094 0.2697855532169342 262.5788269042969 0.2157997190952301 0.8393558 0.37244394421577454 True +13 38612 29.75660800933838 0.6231815814971924 256.4035339355469 0.19301742315292358 261.37115478515625 0.21845503151416779 0.84326917 0.34529048204421997 True +14 41370 29.711443185806274 0.631525993347168 223.0817108154297 0.5521673560142517 260.1048583984375 0.22032995522022247 0.84953296 0.3236030042171478 True +15 44128 29.678820848464966 1.9271538257598877 223.9356231689453 0.2173958718776703 260.2248840332031 0.2193853259086609 0.8541038 0.30684125423431396 True +16 46886 29.710891246795654 0.6226615905761719 270.9646301269531 0.2789011597633362 259.2607421875 0.22200395166873932 0.858527 0.29042214155197144 True +17 49644 29.648555994033813 0.607703685760498 190.3528594970703 0.25899720191955566 259.4098815917969 0.22073712944984436 0.8586023 0.2867627739906311 True +18 52402 29.62883949279785 0.6021878719329834 217.08920288085938 0.16920751333236694 259.679443359375 0.2206822633743286 0.85744655 0.28665605187416077 False +19 55160 29.628028869628906 0.5812602043151855 175.65777587890625 0.2708727717399597 260.0123596191406 0.2195560783147812 0.85772383 0.2890876531600952 False diff --git a/ENCSR442GKD/cherimoya.fold_0.performance.tsv b/ENCSR442GKD/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..9bd5627ba25a4dc435383b7f57f52eea984ff035 --- /dev/null +++ b/ENCSR442GKD/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +259.4098815917969 0.5380845665931702 0.22073712944984436 0.06294448673725128 0.8586022853851318 0.7990933060646057 0.2867627739906311 \ No newline at end of file diff --git a/ENCSR442GKD/cherimoya.fold_1.evaluate.json b/ENCSR442GKD/cherimoya.fold_1.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..5868169821b93ad8fadf00da38fb157aa7442bdb --- /dev/null +++ b/ENCSR442GKD/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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Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2697 34.33150506019592 4.307103395462036 182.59986877441406 0.5170491337776184 379.234375 0.168264701962471 0.66967815 4.521982192993164 True +1 5394 29.62762212753296 0.7358872890472412 262.9713439941406 0.5437461137771606 347.4978942871094 0.21443723142147064 0.75527376 2.048445224761963 True +2 8091 29.411670446395874 0.7247231006622314 273.8294982910156 0.5469580292701721 343.03204345703125 0.21674196422100067 0.7422018 1.4712713956832886 False +3 10788 29.044608116149902 0.7044427394866943 298.6732177734375 0.47382059693336487 332.97015380859375 0.22636394202709198 0.7809412 1.0160729885101318 True +4 13485 29.095191478729248 0.7151494026184082 201.55123901367188 0.4054657220840454 329.5471496582031 0.23195387423038483 0.7935309 0.8535144329071045 True +5 16182 29.023343801498413 0.6918675899505615 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0.8462992 0.49166184663772583 True +12 35061 29.03348445892334 0.6936047077178955 258.2894592285156 0.39288514852523804 314.422119140625 0.24802446365356445 0.8547804 0.4369693398475647 True +13 37758 28.973565578460693 0.7010245323181152 215.7909393310547 0.3365636169910431 313.4083557128906 0.24792325496673584 0.8622739 0.3988654911518097 True +14 40455 29.106000900268555 0.7135379314422607 221.65293884277344 0.314562052488327 311.5631103515625 0.2506744861602783 0.86636394 0.3837887644767761 True +15 43152 29.07149600982666 1.3639724254608154 205.84544372558594 0.2838521897792816 310.93896484375 0.2513848543167114 0.8704546 0.3578249514102936 True +16 45849 29.05206561088562 2.1685335636138916 296.24688720703125 0.24678337574005127 309.6276550292969 0.2532229721546173 0.87497157 0.34488674998283386 True +17 48546 29.059650659561157 0.7143020629882812 180.02218627929688 0.25372451543807983 310.1327819824219 0.2515822649002075 0.8743356 0.33902373909950256 False +18 51243 29.140383005142212 0.7158722877502441 233.91246032714844 0.3588774502277374 309.8505554199219 0.2527881860733032 0.8739524 0.3412005305290222 False +19 53940 29.092687606811523 0.7150921821594238 223.47715759277344 0.17405059933662415 310.4583740234375 0.25101423263549805 0.87391824 0.3414759635925293 False diff --git a/ENCSR442GKD/cherimoya.fold_1.performance.tsv b/ENCSR442GKD/cherimoya.fold_1.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..43dca18662758dcacdae72cfd879dccc8bc2a65a --- /dev/null +++ b/ENCSR442GKD/cherimoya.fold_1.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +309.6276550292969 0.5142970681190491 0.2532229721546173 0.07802886515855789 0.8749715685844421 0.8440071940422058 0.34488674998283386 \ No newline at end of file diff --git a/ENCSR442GKD/cherimoya.fold_2.evaluate.json b/ENCSR442GKD/cherimoya.fold_2.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..3e505200dd9ffafbbaa6d6412add9af65fdf226e --- /dev/null +++ b/ENCSR442GKD/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, + 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"early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF991GDC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR442GKD/cherimoya.fold_2.log b/ENCSR442GKD/cherimoya.fold_2.log new file mode 100644 index 0000000000000000000000000000000000000000..e332b6022d198beccad9dcb678d5d897c857c1d7 --- /dev/null +++ b/ENCSR442GKD/cherimoya.fold_2.log @@ -0,0 +1,21 @@ +Epoch Iteration Training 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0.47769537568092346 289.0232849121094 0.21472765505313873 0.7919418 0.6299863457679749 True +6 20153 31.079939126968384 0.5808045864105225 300.3422546386719 0.5337694883346558 286.3138732910156 0.21768803894519806 0.8037621 0.565406084060669 True +7 23032 30.896743774414062 0.5817365646362305 220.91265869140625 0.5326197147369385 285.7810363769531 0.21730364859104156 0.8085229 0.5401657819747925 True +8 25911 30.941447973251343 1.4306085109710693 207.76939392089844 0.39655113220214844 283.29656982421875 0.22234633564949036 0.8187214 0.47399264574050903 True +9 28790 30.99927020072937 1.0201020240783691 145.6434326171875 0.2811568081378937 282.3519592285156 0.22308018803596497 0.8225523 0.4783056676387787 True +10 31669 30.946330785751343 0.5714194774627686 262.4501037597656 0.4949836730957031 280.9185791015625 0.2255549132823944 0.83031654 0.42910483479499817 True +11 34548 30.976814031600952 0.5690968036651611 279.46380615234375 0.5001986026763916 280.426025390625 0.2259507030248642 0.8334762 0.39971625804901123 True +12 37427 31.00836992263794 0.5598313808441162 255.5193634033203 0.48604536056518555 279.43255615234375 0.2281903475522995 0.8378586 0.38964149355888367 True +13 40306 31.020239114761353 0.5558657646179199 234.87774658203125 0.4471547603607178 278.66357421875 0.22921037673950195 0.8429873 0.3594433665275574 True +14 43185 30.97210955619812 0.5499465465545654 273.4026794433594 0.1908586323261261 277.6815185546875 0.23021264374256134 0.84870404 0.3334129750728607 True +15 46064 31.027528047561646 0.5677664279937744 228.9478759765625 0.37872159481048584 276.948974609375 0.23086832463741302 0.8528544 0.318562775850296 True +16 48943 31.180210828781128 0.5654089450836182 196.51844787597656 0.2931019067764282 276.1424865722656 0.2321971207857132 0.8551229 0.3094150424003601 True +17 51822 31.068874835968018 0.5800027847290039 258.642333984375 0.23739206790924072 276.76629638671875 0.22987999022006989 0.85828173 0.3041626811027527 True +18 54701 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0.2039322853088379 0.817 0.3724520206451416 True +12 36296 30.770358324050903 0.6335408687591553 245.65147399902344 0.4683440029621124 237.78749084472656 0.20533035695552826 0.8233075 0.33697593212127686 True +13 39088 30.63564443588257 0.6219987869262695 272.66455078125 0.32364213466644287 236.81634521484375 0.20738062262535095 0.8305773 0.31544870138168335 True +14 41880 30.091894149780273 0.6303493976593018 223.55343627929688 0.34408795833587646 236.47352600097656 0.20687216520309448 0.8344243 0.2965472340583801 True +15 44672 30.15551519393921 0.621912956237793 189.28419494628906 0.3088156580924988 236.29771423339844 0.20660121738910675 0.84116143 0.27876800298690796 True +16 47464 30.025245189666748 0.6190109252929688 206.55355834960938 0.19825540482997894 236.07301330566406 0.20819073915481567 0.84592515 0.268789678812027 True +17 50256 30.064050436019897 0.6206917762756348 192.42550659179688 0.23118376731872559 236.3121337890625 0.2066563367843628 0.84644485 0.2676020860671997 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