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0.6266986131668091 191.1612548828125 0.1894501894712448 0.69426084 0.4747006297111511 True +6 20440 32.18695902824402 0.4972045421600342 165.2374267578125 0.3999229967594147 190.915283203125 0.190864697098732 0.6974602 0.466102659702301 True +7 23360 32.19170022010803 0.5025396347045898 171.56358337402344 0.6543596982955933 190.60784912109375 0.19226190447807312 0.7030269 0.4305437505245209 True +8 26280 31.79849648475647 0.4960215091705322 122.01728057861328 0.4967624247074127 190.1934814453125 0.19472037255764008 0.7076512 0.41508665680885315 True +9 29200 31.551477193832397 0.4922494888305664 150.53390502929688 0.5173699855804443 190.1583709716797 0.19466489553451538 0.71149427 0.40117207169532776 True +10 32120 31.580033540725708 0.4981827735900879 161.95965576171875 0.42053163051605225 189.8264923095703 0.1967935711145401 0.7156562 0.3908422589302063 True +11 35040 31.581331491470337 0.49048376083374023 125.57228088378906 0.5604991912841797 189.5411376953125 0.19837148487567902 0.720656 0.3805754482746124 True +12 37960 31.546882152557373 1.6192882061004639 162.6666259765625 0.6977497339248657 189.26718139648438 0.20002423226833344 0.72775036 0.36868757009506226 True +13 40880 31.689728498458862 0.48484206199645996 175.04769897460938 0.49101436138153076 189.0426788330078 0.20182090997695923 0.7312282 0.3599778711795807 True +14 43800 31.639513969421387 0.49248480796813965 155.43701171875 0.332342267036438 188.8368682861328 0.20374628901481628 0.73829085 0.34957510232925415 True +15 46720 31.591198205947876 0.5014090538024902 126.6109619140625 0.40857911109924316 188.754638671875 0.20387370884418488 0.74256194 0.346829354763031 True +16 49640 31.56977128982544 2.089693546295166 166.66282653808594 0.34550940990448 188.75665283203125 0.20341238379478455 0.7481808 0.3455396294593811 True +17 52560 31.656389236450195 0.4868357181549072 157.29026794433594 0.320041298866272 188.74510192871094 0.20414628088474274 0.7493038 0.346448689699173 True +18 55480 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MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2785 35.38153791427612 3.532156467437744 150.85726928710938 0.8408509492874146 213.4651336669922 0.1267135739326477 0.5510134 3.0899786949157715 True +1 5570 34.73432111740112 28.33311176300049 177.1638946533203 0.5911493301391602 206.57284545898438 0.17219622433185577 0.6554275 0.9290598630905151 True +2 8355 30.77388286590576 7.092920303344727 166.3817596435547 0.5926591753959656 205.03811645507812 0.17851470410823822 0.6767293 0.5138227939605713 True +3 11140 30.87140679359436 35.56194543838501 174.53717041015625 0.7805446982383728 203.9290008544922 0.18461447954177856 0.6869176 0.5604792237281799 True +4 13925 30.913048028945923 0.8497753143310547 164.2420196533203 0.6289970874786377 203.55393981933594 0.18638509511947632 0.6993302 0.6230925917625427 True +5 16710 30.832400798797607 0.5847916603088379 162.17868041992188 0.6542060375213623 203.3466339111328 0.18711477518081665 0.7029588 0.6331853270530701 True +6 19495 31.860793828964233 0.5656592845916748 133.0065155029297 0.5488916635513306 203.31065368652344 0.18755538761615753 0.70508635 0.6376510262489319 True +7 22280 32.34282159805298 27.916252374649048 143.80165100097656 0.47649452090263367 202.845458984375 0.19058364629745483 0.70597595 0.6229262948036194 True +8 25065 30.76236081123352 27.171443700790405 138.67080688476562 0.5175997614860535 202.81539916992188 0.19042497873306274 0.71268713 0.5728873610496521 True +9 27850 31.800822496414185 0.571326494216919 164.14028930664062 0.2709110379219055 202.49301147460938 0.19302423298358917 0.7161203 0.5387101173400879 True +10 30635 30.221853971481323 0.5636188983917236 125.91617584228516 0.5760400295257568 202.30934143066406 0.19367237389087677 0.72078675 0.4832777678966522 True +11 33420 30.695749044418335 0.5659523010253906 167.60134887695312 0.5028790235519409 201.8738250732422 0.19654083251953125 0.72281253 0.4634009003639221 True +12 36205 30.19142198562622 0.576087236404419 154.8804473876953 0.32624876499176025 201.63616943359375 0.19840756058692932 0.73146695 0.4409562349319458 True +13 38990 30.276462078094482 0.5601789951324463 142.87387084960938 0.38231906294822693 201.62637329101562 0.19804991781711578 0.73992676 0.4082290232181549 True +14 41775 30.462371110916138 23.60525941848755 147.16986083984375 0.3197447657585144 201.28956604003906 0.20020298659801483 0.7467129 0.3870908319950104 True +15 44560 32.163466453552246 0.5747568607330322 153.54739379882812 0.4625774621963501 201.18685913085938 0.20048081874847412 0.75222784 0.3702990710735321 True +16 47345 30.17652463912964 0.5648784637451172 112.37918090820312 0.33722466230392456 201.23257446289062 0.19977271556854248 0.7553122 0.36406317353248596 True +17 50130 30.178073167800903 0.5553410053253174 143.6448974609375 0.19103729724884033 201.17686462402344 0.20021681487560272 0.7541206 0.36534833908081055 False +18 52915 30.17628526687622 0.5586831569671631 156.28305053710938 0.3367537260055542 201.35580444335938 0.19866709411144257 0.75454295 0.3698301911354065 False +19 55700 30.429019927978516 38.04214358329773 135.98916625976562 0.3959960341453552 201.2498779296875 0.19957435131072998 0.7533126 0.37479063868522644 False diff --git a/ENCSR062DXC/cherimoya.fold_3.performance.tsv b/ENCSR062DXC/cherimoya.fold_3.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..0e6666a4d4ef05abdbe766473a1a02972220f2b8 --- /dev/null +++ b/ENCSR062DXC/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +201.23257446289062 0.5508912801742554 0.19977271556854248 0.04785427451133728 0.7553122043609619 0.7160179615020752 0.36406317353248596 \ No newline at end of file diff --git a/ENCSR062DXC/cherimoya.fold_4.evaluate.json b/ENCSR062DXC/cherimoya.fold_4.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..f7a8c0094628461435ee9dca1acd25afde622d49 --- /dev/null +++ b/ENCSR062DXC/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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+12 37570 32.11288595199585 0.6175038814544678 188.80557250976562 0.41561171412467957 267.2733154296875 0.24556052684783936 0.6596449 0.6008232235908508 True +13 40460 34.65166616439819 23.315112113952637 200.38418579101562 0.6286775469779968 266.89947509765625 0.24718645215034485 0.66862917 0.5751665234565735 True +14 43350 32.07823848724365 0.6540217399597168 237.035888671875 0.5710592269897461 266.44476318359375 0.24995577335357666 0.6785297 0.5467444658279419 True +15 46240 32.10434007644653 0.6043634414672852 172.22628784179688 0.6025151014328003 266.3923034667969 0.24913379549980164 0.68312395 0.52409827709198 True +16 49130 31.98854088783264 0.6025431156158447 231.34010314941406 0.3516480028629303 266.4451904296875 0.24863973259925842 0.6853976 0.5239225029945374 True +17 52020 32.37527060508728 8.16625714302063 212.9249725341797 0.44683244824409485 266.5393981933594 0.2481248825788498 0.68723476 0.5242040157318115 True +18 54910 32.03292107582092 28.41397738456726 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37492 31.343963861465454 0.6147403717041016 648.4835815429688 1.06680166721344 918.8753051757812 0.5716931819915771 0.5650004 1.0804213285446167 True +13 40376 31.38671350479126 1.5094141960144043 790.56591796875 0.6694071292877197 912.2701416015625 0.5744712352752686 0.5818745 0.9910628795623779 True +14 43260 31.448797702789307 0.5654315948486328 695.4096069335938 1.1069695949554443 904.4771728515625 0.5783893465995789 0.59681386 0.9044855237007141 True +15 46144 31.455656051635742 0.5749955177307129 821.1948852539062 0.8121556639671326 899.760498046875 0.5797382593154907 0.611036 0.8262292146682739 True +16 49028 31.4968159198761 0.5699996948242188 531.829345703125 0.6678425073623657 893.583740234375 0.5852952599525452 0.62271273 0.7749153971672058 True +17 51912 31.45119857788086 0.5700533390045166 650.0372924804688 0.7006967067718506 895.1664428710938 0.5814908742904663 0.62839663 0.7412157654762268 True +18 54796 31.406753540039062 0.5731239318847656 925.9988403320312 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"num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR420HOT/cherimoya.fold_0.fit.json b/ENCSR420HOT/cherimoya.fold_0.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..22ed0801c6cbcfc3002b4d77ec1df25e48e0c99f --- /dev/null +++ b/ENCSR420HOT/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", 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b/ENCSR420HOT/cherimoya.fold_1.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5b5bb09ebda247047b44dae17dc55a289d8053c6 --- /dev/null +++ b/ENCSR420HOT/cherimoya.fold_1.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +447.34130859375 0.46346306800842285 0.2837522029876709 0.11311869323253632 0.8924232721328735 0.8616697192192078 0.2977924346923828 \ No newline at end of file diff --git a/ENCSR420HOT/cherimoya.fold_2.log b/ENCSR420HOT/cherimoya.fold_2.log new file mode 100644 index 0000000000000000000000000000000000000000..0f084166696bfabdc5d9403e88effd127009b146 --- /dev/null +++ b/ENCSR420HOT/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 2887 36.724063873291016 4.043926954269409 373.55084228515625 0.5229448080062866 452.7323913574219 0.1968565583229065 0.7232465 3.9438555240631104 True +1 5774 31.743184089660645 1.8580477237701416 334.23309326171875 0.3396579623222351 420.88525390625 0.2396698147058487 0.8003483 0.9436640739440918 True +2 8661 32.14371633529663 0.5666220188140869 349.84832763671875 0.45400863885879517 415.28936767578125 0.2465730756521225 0.8146306 0.7357478141784668 True +3 11548 32.108601331710815 0.5887453556060791 311.8153076171875 0.2596215605735779 412.31463623046875 0.2513028383255005 0.82308006 0.5544826984405518 True +4 14435 32.104878664016724 0.5682981014251709 223.36141967773438 0.20761993527412415 411.0728454589844 0.252949982881546 0.8289308 0.46576404571533203 True +5 17322 32.08289432525635 0.5594406127929688 281.91436767578125 0.5196924805641174 409.90673828125 0.25368303060531616 0.8359705 0.4034779667854309 True +6 20209 32.12815451622009 0.5645749568939209 341.2351379394531 0.4080827832221985 409.010498046875 0.25545838475227356 0.83701223 0.426318883895874 True +7 23096 32.06321954727173 0.9554932117462158 301.566650390625 0.29018235206604004 408.0528869628906 0.25765520334243774 0.8462744 0.39969298243522644 True +8 25983 32.082698822021484 0.5710797309875488 334.272216796875 0.3798571228981018 408.0945129394531 0.25730466842651367 0.84966767 0.39424240589141846 True +9 28870 32.07685422897339 0.5745441913604736 387.6566162109375 0.3515622615814209 407.117431640625 0.2591278851032257 0.8557218 0.3693353533744812 True +10 31757 32.095388412475586 0.5631880760192871 254.89199829101562 0.2712840437889099 405.4618835449219 0.2623229920864105 0.85967964 0.34890493750572205 True +11 34644 32.104506969451904 12.092059850692749 347.3355712890625 0.23305043578147888 405.53955078125 0.26244303584098816 0.86261 0.3348570466041565 True +12 37531 32.1869101524353 0.7546026706695557 314.69244384765625 0.36000871658325195 404.9906005859375 0.262164831161499 0.86514395 0.3193095922470093 True +13 40418 32.121304750442505 0.6041462421417236 326.0148620605469 0.1804889440536499 404.0636291503906 0.26383912563323975 0.8672802 0.30643701553344727 True +14 43305 32.11353778839111 0.560887336730957 312.4202880859375 0.16346171498298645 403.9112243652344 0.2649214565753937 0.8705298 0.2991054952144623 True +15 46192 32.1245641708374 0.57126784324646 315.70147705078125 0.270375519990921 403.17242431640625 0.26580914855003357 0.8729103 0.29007673263549805 True +16 49079 32.107115030288696 0.5693764686584473 330.2690124511719 0.25191545486450195 403.9022521972656 0.2642994523048401 0.87258923 0.28707578778266907 False +17 51966 32.12152934074402 0.5704402923583984 346.904052734375 0.18873487412929535 404.1204528808594 0.26429128646850586 0.87170315 0.2887662351131439 False +18 54853 32.13098907470703 0.5749433040618896 372.8163146972656 0.1985154002904892 404.47979736328125 0.2628810405731201 0.86988497 0.2942987084388733 False +19 57740 32.161092042922974 0.5722415447235107 287.478759765625 0.19021835923194885 404.3238525390625 0.26414504647254944 0.86720544 0.29778215289115906 False diff --git a/ENCSR420HOT/cherimoya.fold_3.evaluate.json b/ENCSR420HOT/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..e65d2f260ba16468683099f8e752ffe79244e9ed --- /dev/null +++ b/ENCSR420HOT/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": "cherimoya.fold_3", + "negative_ratio": 0.25, + "negatives": [ + "train_nonpeaks.fold_3.bed", + "valid_nonpeaks.fold_3.bed" + ], + "num_workers": 1, + "out_window": 1000, + "performance_filename": "cherimoya.fold_3.performance.tsv", + "random_state": null, + "residual_scale": 0.15, + "reverse_complement": false, + "reverse_complement_average": false, + "sequences": "hg38.fa", + "signals": [ + "ENCFF055MUP.bigWig" + ], + "skip": false, + "summits": false, + "training_chroms": [ + "chr1", + "chr2", + "chr3", + "chr4", + "chr7", + "chr8", + "chr9", + "chr11", + "chr12", + "chr13", + "chr15", + "chr16", + "chr17", + "chr19", + "chrX", + "chrY" + ], + "validation_chroms": [ + "chr6", + "chr21" + ], + "verbose": true +} \ No newline at end of file diff --git a/ENCSR420HOT/cherimoya.fold_3.fit.json b/ENCSR420HOT/cherimoya.fold_3.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..6a1a02a5f51a5c077217f90940b4b902d5a797be --- /dev/null +++ b/ENCSR420HOT/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": ["ENCFF055MUP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR420HOT/cherimoya.fold_3.log b/ENCSR420HOT/cherimoya.fold_3.log new file mode 100644 index 0000000000000000000000000000000000000000..88c0aa73c844e7ab892a5b93cd0d8c3d45d6c568 --- /dev/null +++ b/ENCSR420HOT/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 2743 34.90530323982239 4.314447402954102 374.71173095703125 0.6665381193161011 430.3049011230469 0.2013782262802124 0.7171363 4.091394424438477 True +1 5486 30.564793586730957 3.4222047328948975 329.47760009765625 0.5191907286643982 403.22125244140625 0.24224738776683807 0.78622043 1.1617828607559204 True +2 8229 30.921090602874756 0.5578098297119141 301.2330322265625 0.3477006256580353 399.6253662109375 0.24496957659721375 0.80236596 0.9186520576477051 True +3 10972 29.88364267349243 0.6112043857574463 360.85760498046875 0.3627682030200958 398.85028076171875 0.24545499682426453 0.8035783 0.6940605044364929 True +4 13715 29.844374895095825 0.5661146640777588 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0.3189413547515869 194.49569702148438 0.9020490646362305 239.7227020263672 0.4922108054161072 0.56712717 0.9121798872947693 True +4 8800 19.340359926223755 0.34369754791259766 188.405029296875 0.5095949172973633 237.8854522705078 0.4984253942966461 0.59021443 0.6330967545509338 True +5 10560 19.371790647506714 0.32491159439086914 175.46728515625 0.6207015514373779 237.02105712890625 0.5016237497329712 0.6051875 0.5613240599632263 True +6 12320 19.415868997573853 0.6521134376525879 158.18051147460938 0.5494529604911804 236.42398071289062 0.5041361451148987 0.6131161 0.5363305807113647 True +7 14080 19.10709309577942 0.3116779327392578 184.54537963867188 0.527801513671875 235.771240234375 0.5064620971679688 0.619513 0.5175617337226868 True +8 15840 19.018378257751465 0.6135175228118896 160.9329376220703 0.5143511295318604 235.2942657470703 0.5084043741226196 0.6255018 0.511538565158844 True +9 17600 19.023593187332153 0.3167304992675781 191.54757690429688 0.4618135690689087 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Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 3612 44.55624461174011 5.099907159805298 391.4053649902344 1.34855318069458 661.089111328125 0.6320779919624329 0.5453474 8.400590896606445 True +1 7224 39.902159214019775 2.520231008529663 349.27069091796875 1.5117971897125244 566.8307495117188 0.7367782592773438 0.556081 2.05904483795166 True +2 10836 39.944772243499756 0.8624975681304932 349.9497985839844 1.0059375762939453 556.4861450195312 0.745617151260376 0.5609119 1.6304305791854858 True +3 14448 39.85367703437805 0.9089066982269287 403.93353271484375 1.2834932804107666 548.7535400390625 0.7528512477874756 0.5657007 1.5334367752075195 True +4 18060 39.86280632019043 0.8638596534729004 361.5985412597656 1.034301996231079 547.115234375 0.7562452554702759 0.5655503 1.7131556272506714 False +5 21672 39.93527841567993 0.8344686031341553 372.564208984375 1.2146130800247192 545.9085693359375 0.7585045099258423 0.5768213 1.70404851436615 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a/ENCSR512YXO/cherimoya.fold_1.fit.json b/ENCSR512YXO/cherimoya.fold_1.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..fc18b6e2311730cd9411b778b9229b4dc5de851a --- /dev/null +++ b/ENCSR512YXO/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": ["ENCFF582MTA.bigWig"], "controls": null, 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b/ENCSR619BNL/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 2750 34.62619495391846 4.19049596786499 208.37464904785156 0.716486930847168 264.10906982421875 0.13920031487941742 0.5159646 3.1997289657592773 True +1 5500 30.157975673675537 0.754927396774292 198.38943481445312 0.8539397716522217 255.09512329101562 0.19269968569278717 0.630289 0.7558860182762146 True +2 8250 30.217965126037598 0.6775579452514648 174.91268920898438 0.5613753795623779 252.9119110107422 0.20250098407268524 0.64541835 0.45051416754722595 True +3 11000 29.63488006591797 0.8436434268951416 226.50308227539062 0.5539715886116028 251.97036743164062 0.20528392493724823 0.65055805 0.45370176434516907 True +4 13750 29.60932230949402 0.5744104385375977 221.82791137695312 0.4533163607120514 251.21994018554688 0.20873333513736725 0.6585641 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0.5810017585754395 180.64743041992188 0.3176652193069458 248.7880401611328 0.22172313928604126 0.6966988 0.39999064803123474 True +12 35750 29.683418035507202 0.5754745006561279 199.0654296875 0.3958144783973694 248.6326904296875 0.2227199673652649 0.70195675 0.38138872385025024 True +13 38500 29.683549880981445 0.6142702102661133 196.00863647460938 0.3780047595500946 248.2713623046875 0.22445420920848846 0.70824087 0.3514256477355957 True +14 41250 29.58569836616516 0.5748610496520996 179.92034912109375 0.25566619634628296 248.13302612304688 0.22500628232955933 0.7162268 0.33469393849372864 True +15 44000 29.62336826324463 0.6156413555145264 213.79934692382812 0.45709261298179626 248.00485229492188 0.22644968330860138 0.72411704 0.3213721215724945 True +16 46750 29.565429210662842 1.8408594131469727 195.79757690429688 0.3893584907054901 247.92454528808594 0.22665224969387054 0.7284645 0.314871221780777 True +17 49500 29.679746866226196 0.5948657989501953 204.4417266845703 0.3667554259300232 247.8052215576172 0.22710172832012177 0.7306685 0.3116055727005005 True +18 52250 29.645416975021362 1.6163339614868164 224.80935668945312 0.26071321964263916 247.79049682617188 0.22751444578170776 0.73181504 0.3133850395679474 True +19 55000 29.604654550552368 0.5725188255310059 188.20697021484375 0.24129846692085266 247.87823486328125 0.2265760600566864 0.72991914 0.31741172075271606 False diff --git a/ENCSR619BNL/cherimoya.fold_0.performance.tsv b/ENCSR619BNL/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..2feaf00d434459ee4651249639487d5d7a80b4ed --- /dev/null +++ b/ENCSR619BNL/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +247.79049682617188 0.5243867039680481 0.22751444578170776 0.06273748725652695 0.7318150401115417 0.7007058262825012 0.3133850395679474 \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_1.evaluate.json b/ENCSR619BNL/cherimoya.fold_1.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..5633820d1cd1dfcb4d788bff7ba634609f95a711 --- /dev/null +++ b/ENCSR619BNL/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": [ + 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0000000000000000000000000000000000000000..bc48c10c907f767dbc8a87163bb27be4265da79a --- /dev/null +++ b/ENCSR619BNL/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 2748 34.68035054206848 3.4380862712860107 189.75006103515625 0.6552748680114746 295.7373962402344 0.1477222442626953 0.5743673 3.7287399768829346 True +1 5496 30.125550031661987 1.0117170810699463 188.2562255859375 0.7836867570877075 284.6708068847656 0.20760875940322876 0.67042834 0.8671219944953918 True +2 8244 30.138237953186035 0.707866907119751 233.67874145507812 0.6129734516143799 281.985595703125 0.2157704085111618 0.6859783 0.5030566453933716 True +3 10992 30.112127780914307 0.9284746646881104 210.1786346435547 0.5600247383117676 280.6681213378906 0.22049130499362946 0.69619757 0.48878586292266846 True +4 13740 29.595842599868774 0.8829238414764404 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\ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_2.evaluate.json b/ENCSR619BNL/cherimoya.fold_2.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..ad4f77fc8b6e49fe9320303c731a40bf4f5964fb --- /dev/null +++ b/ENCSR619BNL/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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b/ENCSR619BNL/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": ["ENCFF453LUU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR619BNL/cherimoya.fold_3.log b/ENCSR619BNL/cherimoya.fold_3.log new file mode 100644 index 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263.704833984375 0.148782417178154 340.3306884765625 0.6566712260246277 0.8095456 0.18885308504104614 True +13 23996 18.517661333084106 0.49372172355651855 261.760986328125 0.19379708170890808 339.84527587890625 0.6576730012893677 0.8149169 0.18640612065792084 True +14 25710 18.51526427268982 0.42218899726867676 273.21295166015625 0.13087403774261475 339.537353515625 0.6580585241317749 0.81704926 0.18453852832317352 True +15 27424 18.49865984916687 0.41986536979675293 263.45751953125 0.11102885007858276 339.4105224609375 0.6580989360809326 0.8183005 0.18214665353298187 True +16 29138 18.490280866622925 0.42166590690612793 258.96917724609375 0.12700264155864716 339.4895935058594 0.6576374769210815 0.8186075 0.1826574206352234 True +17 30852 18.50725483894348 0.7891438007354736 261.2132568359375 0.09954681247472763 339.81170654296875 0.6566362380981445 0.8164151 0.18513965606689453 False +18 32566 18.451798677444458 0.42395520210266113 276.80548095703125 0.11500106751918793 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251.20782470703125 0.20150189101696014 325.0605773925781 0.6438966989517212 0.80452967 0.20443940162658691 True +13 25256 20.95896315574646 10.132777452468872 272.39788818359375 0.2930441200733185 324.6966247558594 0.6445719003677368 0.8073976 0.19702765345573425 True +14 27060 19.9514377117157 0.9381237030029297 258.1615295410156 0.18592259287834167 324.4820556640625 0.6452167630195618 0.81037194 0.2001308798789978 True +15 28864 19.85825276374817 1.2272615432739258 249.72195434570312 0.13279294967651367 324.40985107421875 0.6452818512916565 0.81108904 0.19612213969230652 True +16 30668 19.86086630821228 0.334136962890625 284.4392395019531 0.09912601113319397 324.6051330566406 0.6446033120155334 0.813058 0.19655165076255798 True +17 32472 19.687377452850342 1.2538373470306396 246.30015563964844 0.1447008103132248 325.0231628417969 0.6433908343315125 0.8108635 0.19728338718414307 False +18 34276 19.48936891555786 0.33730292320251465 242.9971160888672 0.08213281631469727 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21.784790754318237 896.2545776367188 0.2601061463356018 1178.556640625 0.5265887379646301 0.8180028 0.2921118140220642 True +19 55140 29.751206874847412 0.5579686164855957 1107.3076171875 0.22281873226165771 1183.1065673828125 0.5225157737731934 0.8201749 0.29298579692840576 True diff --git a/ENCSR678PDD/cherimoya.fold_3.performance.tsv b/ENCSR678PDD/cherimoya.fold_3.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..6a74d6805dcb57915c0a680ff78381e15cea565b --- /dev/null +++ b/ENCSR678PDD/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +1183.1065673828125 0.25960618257522583 0.5225158333778381 0.2842444181442261 0.8201748728752136 0.7717374563217163 0.29298579692840576 \ No newline at end of file diff --git a/ENCSR678PDD/cherimoya.fold_4.evaluate.json b/ENCSR678PDD/cherimoya.fold_4.evaluate.json new file mode 100644 index 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True +12 37128 30.895315408706665 6.319931983947754 1062.30029296875 0.36820465326309204 1120.2196044921875 0.5128911137580872 0.7591054 0.31795400381088257 True +13 39984 30.9679114818573 0.5833845138549805 1073.718994140625 0.3170420527458191 1115.2720947265625 0.5163818597793579 0.7693196 0.30771636962890625 True +14 42840 31.096911907196045 0.5696465969085693 1023.1621704101562 0.2824298143386841 1110.6890869140625 0.5206652283668518 0.779241 0.2965705394744873 True +15 45696 30.76975917816162 0.5652437210083008 843.5670776367188 0.24988187849521637 1109.9261474609375 0.5209957361221313 0.7879177 0.289342999458313 True +16 48552 30.909220933914185 0.5653200149536133 1080.7308349609375 0.2525918483734131 1110.397705078125 0.5195052623748779 0.79609823 0.27886441349983215 True +17 51408 30.910691022872925 0.5726978778839111 928.8348388671875 0.2701631188392639 1110.783203125 0.5192002654075623 0.8006211 0.27445581555366516 True +18 54264 32.4084632396698 34.005518436431885 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0.3742053210735321 894.7420043945312 0.46793484687805176 0.7953322 0.5842936038970947 True +12 35594 30.235119819641113 0.5608415603637695 759.6448974609375 0.4820295572280884 890.3158569335938 0.4713684022426605 0.80175257 0.5301700234413147 True +13 38332 30.334643363952637 8.444834232330322 820.9745483398438 0.3856913447380066 883.2216796875 0.4742685556411743 0.8108022 0.47309550642967224 True +14 41070 30.295626878738403 0.5738592147827148 791.4307861328125 0.32565370202064514 877.7041625976562 0.47845837473869324 0.81866586 0.4213108718395233 True +15 43808 31.391121864318848 15.913520812988281 741.8504638671875 0.309112548828125 877.4254760742188 0.47760075330734253 0.8264773 0.39530810713768005 True +16 46546 30.271507024765015 33.94357967376709 713.219482421875 0.3154633045196533 872.9735107421875 0.48125043511390686 0.83031213 0.37627559900283813 True +17 49284 33.40787672996521 0.56111741065979 826.79443359375 0.3352329730987549 876.6708374023438 0.47836121916770935 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0000000000000000000000000000000000000000..83b4ae5659ee828fa641cb4d325f8e238236e92e --- /dev/null +++ b/ENCSR819GAF/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": ["ENCFF203WKR.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file 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0.5671014785766602 445.1143798828125 0.41655948758125305 753.9140014648438 0.4387589991092682 0.85075676 0.4705601930618286 True +13 38458 30.577784299850464 0.7913558483123779 587.82470703125 0.32396769523620605 750.4714965820312 0.44244346022605896 0.85567296 0.42956918478012085 True +14 41205 30.54004716873169 0.890244722366333 555.7533569335938 0.41761767864227295 749.5882568359375 0.44263726472854614 0.86196244 0.39118123054504395 True +15 43952 30.650248050689697 0.9616503715515137 677.8099975585938 0.29438498616218567 749.3446044921875 0.4419369697570801 0.8676644 0.3621181845664978 True +16 46699 30.63081645965576 1.231205940246582 608.7305908203125 0.5257574319839478 748.0606689453125 0.4430620074272156 0.8697675 0.3450932204723358 True +17 49446 30.6909921169281 0.5764889717102051 643.3834838867188 0.2869768738746643 749.0 0.44117262959480286 0.8715638 0.3344494700431824 True +18 52193 30.705054998397827 0.5796310901641846 703.8544311523438 0.2642681896686554 749.9431762695312 0.4415628910064697 0.8720554 0.33054032921791077 True +19 54940 30.599902868270874 0.5763688087463379 502.30987548828125 0.20346224308013916 749.1577758789062 0.4422350227832794 0.86999255 0.33196255564689636 False diff --git a/ENCSR933GMM/cherimoya.fold_4.evaluate.json b/ENCSR933GMM/cherimoya.fold_4.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..9c72dc69f93dbf0ddbca7fec7a47cfe66940653d --- /dev/null +++ b/ENCSR933GMM/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, + 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/dev/null +++ b/ENCSR948MQC/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": ["ENCFF360EKV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR948MQC/cherimoya.fold_0.log 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True +4 16985 38.76233673095703 0.6507914066314697 580.392822265625 0.5131766200065613 720.78759765625 0.7885275483131409 0.774212 0.5377893447875977 False +5 20382 37.400391817092896 0.6608984470367432 623.587158203125 0.23467886447906494 716.3255615234375 0.7908012866973877 0.7809548 0.48140424489974976 True +6 23779 36.647866010665894 0.6606347560882568 634.16015625 0.5154487490653992 713.6036987304688 0.7920520901679993 0.7768433 0.4234546422958374 False +7 27176 40.076844692230225 0.6564788818359375 628.060546875 0.41638240218162537 709.4862670898438 0.7945747375488281 0.78348696 0.4172627031803131 True +8 30573 38.76456260681152 21.923529863357544 573.6177978515625 0.45490920543670654 705.3997802734375 0.7966892719268799 0.79077685 0.39762404561042786 True +9 33970 36.67810583114624 0.6446983814239502 526.9161376953125 0.36240437626838684 702.9384155273438 0.7986815571784973 0.787078 0.40343573689460754 False +10 37367 37.7982223033905 39.70029830932617 627.1611328125 0.3588191866874695 699.6970825195312 0.8004502058029175 0.7962056 0.38894709944725037 True +11 40764 38.22093963623047 16.671048879623413 650.513916015625 0.46244293451309204 696.3250732421875 0.8024663925170898 0.8010671 0.3641328811645508 True +12 44161 36.99361252784729 10.503157377243042 528.4703369140625 0.3191364109516144 693.2938842773438 0.8043688535690308 0.80738497 0.35515454411506653 True +13 47558 36.7029504776001 0.6422898769378662 571.29833984375 0.32384753227233887 690.8658447265625 0.8063453435897827 0.81497526 0.33755871653556824 True +14 50955 36.63368630409241 0.6548416614532471 542.2724609375 0.3317449688911438 688.616455078125 0.8077146410942078 0.8204792 0.32523390650749207 True +15 54352 36.767646074295044 0.6546924114227295 633.835205078125 0.45266222953796387 687.2060546875 0.8088288307189941 0.82521105 0.3164605498313904 True +16 57749 36.82913064956665 0.6509814262390137 590.399658203125 0.34295937418937683 686.5005493164062 0.809190571308136 0.8267908 0.3095325231552124 True +17 61146 36.68569278717041 1.089677095413208 648.300048828125 0.2560611367225647 686.9852294921875 0.809174120426178 0.8279268 0.309978723526001 True +18 64543 36.67569136619568 0.6430454254150391 541.5556640625 0.1902984082698822 687.495361328125 0.8090037107467651 0.82734984 0.31138768792152405 False +19 67940 36.654420375823975 0.6414587497711182 520.24169921875 0.30751556158065796 687.958740234375 0.8087877631187439 0.8250958 0.3153515160083771 False diff --git a/ENCSR948MQC/cherimoya.fold_0.performance.tsv b/ENCSR948MQC/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..cd5acd50e20a5f9d32c6ebb9ab1830a63014f8fd --- /dev/null +++ b/ENCSR948MQC/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +686.9852294921875 0.15457968413829803 0.8091740608215332 0.4635126292705536 0.8279268145561218 0.7387924790382385 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1392.988037109375 0.4132465720176697 1702.6119384765625 0.4756948947906494 0.6928357 0.4393480122089386 True +15 45312 31.755647897720337 0.5701582431793213 1332.1737060546875 0.34607160091400146 1695.845703125 0.4788365364074707 0.7074819 0.39028695225715637 True +16 48144 31.58230185508728 0.5478436946868896 1338.83642578125 0.2628551125526428 1690.331787109375 0.4809238016605377 0.71432054 0.35909411311149597 True +17 50976 31.47793197631836 0.5330102443695068 1451.3582763671875 0.36749589443206787 1691.6544189453125 0.4791887700557709 0.7214006 0.3389054834842682 True +18 53808 31.48559546470642 0.5389163494110107 1341.0233154296875 0.2550252079963684 1689.207763671875 0.48097553849220276 0.72330654 0.33038485050201416 True +19 56640 31.438302040100098 0.5368258953094482 1159.10888671875 0.34347519278526306 1690.1785888671875 0.48060154914855957 0.72402674 0.32757285237312317 True diff --git a/ENCSR964MZQ/cherimoya.fold_4.performance.tsv 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