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0000000000000000000000000000000000000000..ab0865c9dd720600e272e7a57001cfc0a197a4a6 --- /dev/null +++ b/ENCSR128GBN/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": ["ENCFF622EZO.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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diff --git a/ENCSR137FWW/cherimoya.fold_4.evaluate.json b/ENCSR137FWW/cherimoya.fold_4.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..c5d7e99d552aa5c85d641eb2af474bd63dad853f --- /dev/null +++ b/ENCSR137FWW/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, + 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0.19549337029457092 647.7247924804688 0.415754497051239 0.86037904 0.22357457876205444 True +17 49662 29.976117372512817 0.6853115558624268 548.8856201171875 0.22163482010364532 647.3418579101562 0.4156314730644226 0.86230636 0.21972902119159698 True +18 52421 29.828043699264526 0.5457072257995605 570.321533203125 0.13388988375663757 648.0750732421875 0.41522735357284546 0.8629692 0.21923530101776123 True +19 55180 29.677733421325684 0.5313684940338135 470.58599853515625 0.24110789597034454 648.97509765625 0.4132702648639679 0.8600021 0.22043907642364502 False diff --git a/ENCSR417LPB/cherimoya.fold_3.performance.tsv b/ENCSR417LPB/cherimoya.fold_3.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..0da1f08b0d5fd441ddf252892036a1b6e176b276 --- /dev/null +++ b/ENCSR417LPB/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +648.0750732421875 0.37404918670654297 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0000000000000000000000000000000000000000..905f20fcb253df81a7d08c7555c184528978bd93 --- /dev/null +++ b/ENCSR417LPB/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": ["ENCFF422FNO.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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102.82865905761719 0.3944806456565857 145.86920166015625 0.22599071264266968 0.7611284 0.3140469491481781 True +17 49392 30.342320203781128 0.7325372695922852 106.16273498535156 0.3480221629142761 146.01864624023438 0.224457249045372 0.7638733 0.30987754464149475 True +18 52136 30.35318374633789 0.8457849025726318 108.03764343261719 0.2911915183067322 145.99256896972656 0.22519513964653015 0.7641174 0.3075959086418152 True +19 54880 30.379381895065308 0.7374827861785889 95.01345825195312 0.1695190966129303 145.88595581054688 0.2260473370552063 0.7638942 0.30685338377952576 False diff --git a/ENCSR511GQA/cherimoya.fold_2.fit.json b/ENCSR511GQA/cherimoya.fold_2.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..254672ccf2a74aaa7a91b1c6977bbf35537a549e --- /dev/null +++ b/ENCSR511GQA/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, 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40390 32.23758268356323 0.6040134429931641 97.0293197631836 0.285203218460083 128.87728881835938 0.2048284113407135 0.7044369 0.3334721624851227 True +14 43275 32.227123737335205 0.6025376319885254 110.8595199584961 0.36430686712265015 128.59259033203125 0.2067740559577942 0.71199673 0.31088754534721375 True +15 46160 32.231478691101074 0.6154124736785889 87.98970031738281 0.31350183486938477 128.41238403320312 0.20784179866313934 0.72017014 0.2959815263748169 True +16 49045 32.527090072631836 0.6066057682037354 100.77081298828125 0.3319908082485199 128.38717651367188 0.208069309592247 0.72461325 0.2869738042354584 True +17 51930 32.2314453125 0.6082885265350342 110.04051208496094 0.3494153618812561 128.40133666992188 0.20766089856624603 0.7277952 0.2814716696739197 True +18 54815 32.25225043296814 0.6167926788330078 108.46559143066406 0.38290971517562866 128.4066619873047 0.20768055319786072 0.7278375 0.2789033353328705 True +19 57700 32.244160413742065 1.4196124076843262 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0.24467585980892181 0.79993224 0.5042503476142883 True +11 33000 29.95062780380249 1.70676589012146 174.12294006347656 0.5014582872390747 208.30274963378906 0.24561239778995514 0.80332243 0.4670756757259369 True +12 35750 29.91042160987854 1.8139126300811768 122.86812591552734 0.25323718786239624 207.94781494140625 0.2479221522808075 0.8035605 0.44428014755249023 True +13 38500 29.90751886367798 1.6905896663665771 178.04478454589844 0.46648308634757996 207.6050567626953 0.24895049631595612 0.80801433 0.4165571331977844 True +14 41250 29.82603645324707 1.5219981670379639 167.93368530273438 0.5950479507446289 207.027099609375 0.2516374886035919 0.81362617 0.393160879611969 True +15 44000 29.88494634628296 2.309107542037964 184.19349670410156 0.6034922003746033 206.81138610839844 0.2525911033153534 0.8170246 0.37261560559272766 True +16 46750 29.83925461769104 1.5279686450958252 190.47129821777344 0.41256940364837646 206.78028869628906 0.25327035784721375 0.821873 0.35819628834724426 True +17 49500 29.986920833587646 2.0794193744659424 223.68692016601562 0.33456939458847046 206.7683563232422 0.2533794939517975 0.8230884 0.3501449227333069 True +18 52250 29.939684629440308 1.511521816253662 160.13710021972656 0.22888685762882233 206.91871643066406 0.25263071060180664 0.82319105 0.34839993715286255 True +19 55000 29.922410488128662 1.704662561416626 151.74850463867188 0.4196354150772095 206.80169677734375 0.25371265411376953 0.8222545 0.35062408447265625 False diff --git a/ENCSR550UWM/cherimoya.fold_0.performance.tsv b/ENCSR550UWM/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..45d6b7a6fa94da2d0d46d142a9cd97a4153e3f59 --- /dev/null +++ b/ENCSR550UWM/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +206.91871643066406 0.5286707282066345 0.25263068079948425 0.0554145872592926 0.8231910467147827 0.7623738646507263 0.34839993715286255 \ No newline at end of file diff --git a/ENCSR550UWM/cherimoya.fold_1.fit.json b/ENCSR550UWM/cherimoya.fold_1.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..0bb5630eccae8e93cc6c94da2dad38498be2d56a --- /dev/null +++ b/ENCSR550UWM/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", 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0000000000000000000000000000000000000000..048f141965ccc9045b5cabe2fb37dfb59cae892b --- /dev/null +++ b/ENCSR789FJF/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, + 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True +12 37323 32.103338956832886 1.414567470550537 209.62203979492188 0.5386217832565308 232.65838623046875 0.28072109818458557 0.6484734 0.5605211853981018 True +13 40194 32.139886140823364 0.6263453960418701 189.74383544921875 0.46694400906562805 232.00958251953125 0.2835792303085327 0.6623291 0.5229408144950867 True +14 43065 32.10821318626404 0.6293354034423828 183.70941162109375 0.6073885560035706 231.6876220703125 0.2849750816822052 0.6731632 0.48880621790885925 True +15 45936 32.127809047698975 0.6211075782775879 167.2041778564453 0.6646595001220703 231.01763916015625 0.28838929533958435 0.6797855 0.47116079926490784 True +16 48807 32.12033033370972 0.6293683052062988 179.52679443359375 0.30668219923973083 230.89096069335938 0.2886762320995331 0.6868591 0.463378369808197 True +17 51678 32.09239220619202 0.6311960220336914 183.54531860351562 0.32202041149139404 230.7051544189453 0.289465069770813 0.69059324 0.46010416746139526 True +18 54549 32.09581184387207 0.6271705627441406 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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 2783 35.453476667404175 2.7127132415771484 213.60475158691406 1.2556018829345703 308.9189453125 0.14640037715435028 0.49962947 2.7208001613616943 True +1 5566 30.538906812667847 1.5681087970733643 208.5413818359375 0.8450077772140503 299.5208435058594 0.18555115163326263 0.54843044 1.5116016864776611 True +2 8349 30.546048641204834 0.617922306060791 190.3995819091797 0.7937633991241455 296.00732421875 0.1969364732503891 0.571493 0.9522007703781128 True +3 11132 30.583864212036133 0.7147824764251709 230.15277099609375 0.9735499024391174 293.85345458984375 0.20434656739234924 0.5992068 0.7960008382797241 True +4 13915 30.295106410980225 3.086611747741699 169.25698852539062 0.7780708074569702 292.98626708984375 0.20684416592121124 0.6168929 0.7718011736869812 True +5 16698 29.956782341003418 0.5911910533905029 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0.21992193162441254 0.6685245 0.6045554876327515 True +12 36179 29.950237274169922 0.6295793056488037 211.91375732421875 0.8122107982635498 288.95758056640625 0.22126740217208862 0.67375135 0.5991177558898926 True +13 38962 29.916494846343994 0.6203176975250244 197.82763671875 0.6467616558074951 288.67425537109375 0.22174622118473053 0.6793617 0.5811830163002014 True +14 41745 29.915711879730225 1.6289737224578857 215.84176635742188 0.7187613248825073 288.48138427734375 0.22245216369628906 0.6874143 0.569202184677124 True +15 44528 30.003698587417603 0.6206352710723877 202.77435302734375 0.877522885799408 288.3528747558594 0.2227916419506073 0.69223386 0.5618513822555542 True +16 47311 29.903906106948853 0.6001086235046387 192.15093994140625 0.5932161211967468 288.0244445800781 0.2242102026939392 0.69598466 0.5551542043685913 True +17 50094 29.895732402801514 0.637092113494873 215.89813232421875 0.5804283618927002 288.04736328125 0.22420445084571838 0.6955858 0.5681519508361816 False 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0.9074064493179321 266.9922790527344 0.19791173934936523 0.58551383 0.797723114490509 True +6 20223 31.059746026992798 0.5246365070343018 232.85430908203125 1.0709068775177002 266.2217102050781 0.2012227475643158 0.5884501 0.7690116167068481 True +7 23112 31.064486026763916 0.6288771629333496 235.42776489257812 1.007894515991211 265.9130859375 0.20233465731143951 0.60083956 0.7372137904167175 True +8 26001 31.077691316604614 0.5680665969848633 217.6825714111328 0.9140164852142334 265.3514404296875 0.20498675107955933 0.6059545 0.7521728277206421 True +9 28890 31.086934566497803 0.5188145637512207 183.52053833007812 0.8283843994140625 264.92132568359375 0.2063600718975067 0.6116282 0.7134711742401123 True +10 31779 31.11788773536682 1.8403329849243164 203.70806884765625 0.8011735677719116 264.6640930175781 0.20752456784248352 0.6192885 0.7212352752685547 True +11 34668 31.150973796844482 0.542017936706543 196.9974365234375 0.9220924377441406 264.5482177734375 0.20778381824493408 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36504 30.209434032440186 0.5646092891693115 176.40184020996094 0.7779576778411865 276.262451171875 0.20752833783626556 0.6611198 0.6179597973823547 True +13 39312 30.31609606742859 0.5845119953155518 202.36253356933594 0.6345229744911194 276.2403869628906 0.2070520520210266 0.6663149 0.614531397819519 True +14 42120 30.267616748809814 0.5692365169525146 192.08016967773438 0.7450278401374817 276.0877990722656 0.20728912949562073 0.67160213 0.596096932888031 True +15 44928 30.29750156402588 0.5843806266784668 202.59275817871094 0.7841296792030334 275.8856506347656 0.20830444991588593 0.6770174 0.5850862860679626 True +16 47736 30.27552318572998 0.5822749137878418 194.15670776367188 0.8354265093803406 275.67608642578125 0.20888112485408783 0.6773837 0.5758939385414124 True +17 50544 30.364299535751343 0.8298509120941162 200.34951782226562 0.5775316953659058 275.98187255859375 0.20770876109600067 0.6792134 0.582217276096344 True +18 53352 30.440903902053833 0.5843234062194824 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b/ENCSR971MMF/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": ["ENCFF272CCY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR971MMF/cherimoya.fold_4.log b/ENCSR971MMF/cherimoya.fold_4.log new file mode 100644 index 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0.86410046 0.21192814409732819 True +17 50976 30.603577375411987 0.5904674530029297 236.17776489257812 0.15840518474578857 269.7368469238281 0.21283583343029022 0.8628226 0.20984533429145813 False +18 53808 30.67182469367981 0.5811927318572998 225.34112548828125 0.2061648964881897 269.51715087890625 0.21334081888198853 0.862222 0.21349070966243744 False +19 56640 30.634082317352295 0.6009018421173096 284.50616455078125 0.18485739827156067 269.5481872558594 0.21361593902111053 0.86158633 0.2145349681377411 False diff --git a/ENCSR971MMF/cherimoya.fold_4.performance.tsv b/ENCSR971MMF/cherimoya.fold_4.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..4c155f2f7443bfeb10e187e213788bbca754c892 --- /dev/null +++ b/ENCSR971MMF/cherimoya.fold_4.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +269.43902587890625 0.5294126272201538 0.21359169483184814 0.06418660283088684 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