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0.23520463705062866 0.87172264 0.5002942681312561 True +11 25176 22.91729187965393 0.5733804702758789 143.22201538085938 0.3863227069377899 258.92327880859375 0.23778192698955536 0.87517697 0.4739212989807129 True +12 27274 22.86007308959961 0.5888671875 188.18202209472656 0.3502543568611145 258.62078857421875 0.2382030189037323 0.8813225 0.4468468129634857 True +13 29372 22.835214376449585 0.5640926361083984 192.00428771972656 0.6138690114021301 258.4800720214844 0.23798254132270813 0.88499343 0.42601972818374634 True +14 31470 22.842479705810547 0.5642805099487305 181.046630859375 0.29106515645980835 257.9698486328125 0.23961269855499268 0.8860832 0.41451147198677063 True +15 33568 22.909121990203857 0.5656487941741943 121.6654281616211 0.32271894812583923 257.19091796875 0.2420228272676468 0.8882128 0.4012293815612793 True +16 35666 22.844815731048584 0.5768282413482666 203.84458923339844 0.5182878375053406 257.44586181640625 0.24100430309772491 0.891033 0.40116119384765625 True +17 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Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2140 28.209643125534058 3.19708514213562 178.64474487304688 0.6783522367477417 223.74270629882812 0.12828078866004944 0.67108196 4.599627494812012 True +1 4280 23.740848541259766 0.6751580238342285 185.71026611328125 0.5975450277328491 209.77403259277344 0.1703045517206192 0.76339585 2.0975804328918457 True +2 6420 23.754472970962524 0.4524106979370117 185.73805236816406 0.5887863636016846 203.5992431640625 0.18597735464572906 0.7961129 1.0893796682357788 True +3 8560 23.753247499465942 0.42823004722595215 223.8371124267578 0.7997250556945801 202.50982666015625 0.18749888241291046 0.80721635 0.6938106417655945 True +4 10700 23.743354082107544 0.42439723014831543 176.40684509277344 0.5184512734413147 201.5244903564453 0.18999509513378143 0.8112091 0.6259483098983765 True +5 12840 23.782743453979492 0.43009161949157715 184.5853271484375 0.5220659971237183 200.83935546875 0.19120332598686218 0.8147859 0.6050620079040527 True +6 14980 23.756234884262085 0.4310414791107178 210.76211547851562 0.6022825241088867 200.3290557861328 0.19283001124858856 0.82684404 0.5429130792617798 True +7 17120 23.763286113739014 0.4303305149078369 165.649658203125 0.38220566511154175 199.5950469970703 0.19517363607883453 0.8344431 0.49049052596092224 True +8 19260 23.755343437194824 0.42905473709106445 175.2768096923828 0.5436208248138428 199.3131866455078 0.19572453200817108 0.84163487 0.454157292842865 True +9 21400 23.798083305358887 0.4289724826812744 157.8489990234375 0.6096331477165222 198.54824829101562 0.19828282296657562 0.84536177 0.4326540529727936 True +10 23540 23.802470207214355 0.42455005645751953 208.50048828125 0.6353285312652588 198.20230102539062 0.199934720993042 0.85003984 0.419565349817276 True +11 25680 23.813732862472534 0.42071962356567383 174.26036071777344 0.7012243270874023 197.8148956298828 0.20108766853809357 0.8534972 0.40069594979286194 True +12 27820 23.80635356903076 0.4208409786224365 173.48468017578125 0.4481232762336731 197.5706024169922 0.20179438591003418 0.858123 0.3892839252948761 True +13 29960 23.758625984191895 0.41674208641052246 144.13563537597656 0.30497628450393677 197.11676025390625 0.20313356816768646 0.86241883 0.3793714940547943 True +14 32100 23.75424313545227 0.42108845710754395 173.2952880859375 0.499674916267395 197.15652465820312 0.2031189650297165 0.867065 0.3675179183483124 True +15 34240 23.51583766937256 0.42672133445739746 179.746826171875 0.5077275633811951 196.95877075195312 0.2034958451986313 0.86897165 0.3602883815765381 True +16 36380 23.352973461151123 0.41539764404296875 142.63775634765625 0.4646371603012085 196.87301635742188 0.2036428600549698 0.8694774 0.35666990280151367 True +17 38520 23.341723442077637 0.42455148696899414 125.1187744140625 0.26425525546073914 197.06591796875 0.20303846895694733 0.8698295 0.3582655191421509 True +18 40660 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8880 16.04714798927307 0.2857811450958252 457.7776184082031 0.9089651703834534 489.2621765136719 0.3553619980812073 0.7700233 1.2670230865478516 True +6 10360 16.01554846763611 0.2884101867675781 326.23309326171875 0.9965660572052002 488.3100280761719 0.3563932776451111 0.77203053 1.1688297986984253 True +7 11840 16.160768032073975 12.83010721206665 326.9969482421875 0.7469766139984131 483.687255859375 0.36125999689102173 0.7803295 0.9842800498008728 True +8 13320 16.076719760894775 0.2892453670501709 538.7282104492188 0.8733199238777161 478.9344482421875 0.3671637177467346 0.7892099 0.8777105212211609 True +9 14800 16.045017957687378 10.202729225158691 346.05035400390625 0.6150356531143188 475.5373840332031 0.3713475465774536 0.7897537 0.8394827842712402 True +10 16280 16.25434708595276 0.28525495529174805 425.0972900390625 0.5857104659080505 474.67315673828125 0.3698986768722534 0.7952573 0.8090081810951233 True +11 17760 16.006118059158325 1.4441864490509033 499.3184814453125 1.3246545791625977 471.0175476074219 0.374233603477478 0.79993814 0.7690516710281372 True +12 19240 16.4674232006073 4.1925950050354 362.59814453125 0.7863478660583496 467.3709716796875 0.3777850866317749 0.80691415 0.7321757674217224 True +13 20720 16.052754640579224 0.29575443267822266 387.254150390625 0.9534441828727722 466.03363037109375 0.3777623772621155 0.81172186 0.7059205174446106 True +14 22200 16.08341121673584 1.3439750671386719 425.22100830078125 0.5576654672622681 464.6474914550781 0.37893956899642944 0.8178477 0.6837015151977539 True +15 23680 16.053871393203735 0.2883622646331787 388.4483642578125 0.5774897933006287 463.631103515625 0.37995582818984985 0.82253796 0.666962742805481 True +16 25160 16.03874945640564 0.28896045684814453 309.66204833984375 0.44525808095932007 464.0650329589844 0.37861087918281555 0.8253028 0.6574240922927856 True +17 26640 16.062554836273193 0.2897927761077881 278.6663513183594 0.5328904390335083 464.9292907714844 0.37737783789634705 0.82662255 0.6548267006874084 True +18 28120 16.038007497787476 0.2816324234008789 328.2018737792969 0.39107856154441833 465.3965759277344 0.37730786204338074 0.82681644 0.6611619591712952 True +19 29600 16.042723178863525 0.2849445343017578 408.3111572265625 0.39460331201553345 466.62164306640625 0.3751673698425293 0.82536876 0.6656313538551331 False diff --git a/ENCSR180KMR/cherimoya.fold_1.evaluate.json b/ENCSR180KMR/cherimoya.fold_1.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..767617d81d09c24a0f524b92e96098975c04a249 --- /dev/null +++ b/ENCSR180KMR/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": [ + 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null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR180KMR/cherimoya.fold_3.evaluate.json b/ENCSR180KMR/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..b6eb58d573ed2947bd56cd25f914c88b63ee86c2 --- /dev/null +++ b/ENCSR180KMR/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, + 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mode 100644 index 0000000000000000000000000000000000000000..b8866caa96454576cd642e04f1092884b20a9af3 --- /dev/null +++ b/ENCSR180KMR/cherimoya.fold_3.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +492.53759765625 0.4069686532020569 0.39495572447776794 0.14963692426681519 0.8251532912254333 0.7811030745506287 0.7132996320724487 \ No newline at end of file diff --git a/ENCSR180KMR/cherimoya.fold_4.fit.json b/ENCSR180KMR/cherimoya.fold_4.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..6d447f54ed461b0b5be8acd71bfe4eac0dda4e0c --- /dev/null +++ b/ENCSR180KMR/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", 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19.599518299102783 2.6388120651245117 456.09716796875 1.3950175046920776 654.82421875 0.17005327343940735 0.49417192 15.435911178588867 True +1 2928 16.146837949752808 0.25367307662963867 398.1778869628906 1.1379053592681885 582.9396362304688 0.2506643533706665 0.66011494 8.62031078338623 True +2 4392 16.163812160491943 0.25783276557922363 425.36480712890625 1.3270845413208008 507.88031005859375 0.3173326849937439 0.714884 3.773958206176758 True +3 5856 16.150761365890503 0.24890422821044922 313.49334716796875 0.4867727756500244 482.7286682128906 0.33481335639953613 0.74088186 1.8849903345108032 True +4 7320 16.16420888900757 0.25688815116882324 356.3587341308594 0.7211668491363525 472.3955078125 0.3423384726047516 0.7553261 1.3778076171875 True +5 8784 16.141799926757812 0.25208544731140137 356.000732421875 0.8416826128959656 467.7400207519531 0.3462873101234436 0.7604539 1.0901055335998535 True +6 10248 16.16011929512024 0.24828481674194336 286.06097412109375 0.9183319807052612 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"performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR747RGR/cherimoya.fold_1.log b/ENCSR747RGR/cherimoya.fold_1.log new file mode 100644 index 0000000000000000000000000000000000000000..5ddaa2dc03e784b0e67f3b3782e54e11bfee026c --- /dev/null +++ b/ENCSR747RGR/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 2717 35.01084613800049 2.505786180496216 419.4571838378906 0.40885087847709656 722.4265747070312 0.22126278281211853 0.71710783 7.922393798828125 True +1 5434 30.372204780578613 0.6913650035858154 466.24664306640625 0.4650742709636688 632.4429931640625 0.27142876386642456 0.8022693 2.7370903491973877 True +2 8151 30.378371477127075 0.6691164970397949 344.1087646484375 0.689667820930481 614.4017333984375 0.2778962254524231 0.8183328 1.5737055540084839 True +3 10868 30.306914806365967 0.6875002384185791 378.5399169921875 0.42359572649002075 608.9174194335938 0.28042110800743103 0.8176176 1.4510204792022705 False +4 13585 30.258970975875854 0.6670739650726318 415.32049560546875 0.3767865002155304 598.0584106445312 0.2842933237552643 0.8331355 0.8917017579078674 True +5 16302 30.482768297195435 2.423630475997925 435.660400390625 0.3245187997817993 588.9469604492188 0.2901897430419922 0.8474813 0.7366788983345032 True +6 19019 30.23741888999939 0.6682116985321045 360.5040283203125 0.3704913854598999 584.4962158203125 0.29210200905799866 0.8603262 0.6412231922149658 True +7 21736 30.25845694541931 0.6491928100585938 380.02392578125 0.4327728748321533 580.0733032226562 0.29505327343940735 0.86433256 0.6319342851638794 True +8 24453 33.32713484764099 36.136298179626465 328.2033386230469 0.3567560315132141 573.7916870117188 0.30006536841392517 0.8732021 0.535147488117218 True +9 27170 30.339963912963867 2.219536304473877 362.7996826171875 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185.6721649169922 0.7459886074066162 241.16912841796875 0.21501560509204865 0.80428666 0.39784497022628784 True +10 24068 24.35119867324829 0.4196169376373291 191.33995056152344 0.39700520038604736 240.8576202392578 0.21625304222106934 0.80897826 0.39311346411705017 True +11 26256 24.296713829040527 0.5790340900421143 187.0106201171875 0.2861059904098511 240.79885864257812 0.21643783152103424 0.8134161 0.38469424843788147 True +12 28444 24.44100260734558 0.41410160064697266 179.53231811523438 0.5238603353500366 240.4757843017578 0.2180289626121521 0.8162771 0.3813647925853729 True +13 30632 24.283814907073975 0.4162132740020752 203.1557159423828 0.42489853501319885 240.05653381347656 0.21950021386146545 0.8197982 0.3772892653942108 True +14 32820 24.214078187942505 19.931146144866943 143.38816833496094 0.423305481672287 240.17364501953125 0.2189866155385971 0.8231756 0.37332379817962646 True +15 35008 26.44630217552185 19.774919748306274 204.82867431640625 0.3945622444152832 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Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2747 34.7888970375061 4.444772243499756 210.510009765625 1.2781741619110107 338.9031066894531 0.15371401607990265 0.5852901 3.9044902324676514 True +1 5494 30.412184238433838 0.608684778213501 314.8554382324219 0.9462108612060547 318.2874755859375 0.234641432762146 0.6658136 1.9751871824264526 True +2 8241 30.30717635154724 1.1209611892700195 236.79196166992188 1.0281894207000732 313.267822265625 0.24661099910736084 0.6773841 0.7907913327217102 True +3 10988 30.304301738739014 0.562222957611084 229.43896484375 0.6903596520423889 311.4431457519531 0.25236910581588745 0.68719584 0.7487043738365173 True +4 13735 30.23159384727478 0.5590944290161133 245.3246307373047 0.7121100425720215 310.33819580078125 0.2568298876285553 0.69102603 0.7604236602783203 True +5 16482 30.266533374786377 0.5705001354217529 250.39837646484375 0.7427124977111816 310.1117858886719 0.256979376077652 0.69659585 0.7558907270431519 True +6 19229 30.335694074630737 0.5696258544921875 243.4718475341797 0.7384241819381714 309.1563415527344 0.2604226768016815 0.702393 0.7211097478866577 True +7 21976 30.16698908805847 0.5623188018798828 258.83050537109375 0.5328176021575928 308.8236083984375 0.26118120551109314 0.7060201 0.69102543592453 True +8 24723 29.7389874458313 3.0831456184387207 207.92242431640625 0.771872878074646 307.6175842285156 0.2656244933605194 0.7085801 0.692704439163208 True +9 27470 29.819729804992676 16.68657159805298 265.514892578125 0.869337260723114 306.8922119140625 0.26882749795913696 0.7115436 0.6886141300201416 True +10 30217 29.76349639892578 1.7682580947875977 207.34249877929688 0.572848379611969 306.1170654296875 0.2721467912197113 0.71936864 0.6542918682098389 True +11 32964 29.727411031723022 1.7865486145019531 249.9835205078125 0.610893726348877 305.20831298828125 0.27527865767478943 0.7237385 0.6246566772460938 True +12 35711 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Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2921 36.89322304725647 20.39488458633423 256.957275390625 1.087675929069519 349.42669677734375 0.16540788114070892 0.5931676 4.3083062171936035 True +1 5842 32.51234245300293 0.6627035140991211 237.99642944335938 0.8658308982849121 327.5174255371094 0.24139127135276794 0.6817207 1.5885365009307861 True +2 8763 32.25926852226257 0.5467736721038818 255.43209838867188 1.4266021251678467 322.4077453613281 0.2519051134586334 0.69242066 0.8406282663345337 True +3 11684 32.072953939437866 0.5129358768463135 229.9404754638672 0.6309524774551392 320.5736389160156 0.2571480870246887 0.7031408 0.7200356125831604 True +4 14605 31.59380340576172 0.5139114856719971 260.92138671875 0.6834222078323364 319.6697998046875 0.26040783524513245 0.70930696 0.6784012317657471 True +5 17526 31.521310091018677 0.5196175575256348 231.69400024414062 0.6478939056396484 319.0975341796875 0.2625606954097748 0.7098309 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242.70494079589844 0.5608189105987549 313.6644592285156 0.279806524515152 0.73713523 0.6274656653404236 True +13 40894 31.596837520599365 0.5197052955627441 262.1839904785156 0.5838391780853271 313.3916015625 0.280227392911911 0.74367803 0.5921972393989563 True +14 43815 31.5455322265625 0.545548677444458 196.36309814453125 0.7773479223251343 312.1548767089844 0.28425106406211853 0.7491808 0.5747938752174377 True +15 46736 31.58045196533203 0.5148065090179443 219.26824951171875 0.516693115234375 311.45123291015625 0.2860548794269562 0.7557558 0.5511950254440308 True +16 49657 31.537678003311157 0.5226345062255859 270.5450439453125 0.737933337688446 311.30181884765625 0.28587305545806885 0.7601748 0.5450558066368103 True +17 52578 31.55405879020691 0.5258193016052246 227.3634490966797 0.3618212938308716 311.9735107421875 0.28373050689697266 0.76242363 0.5320158004760742 True +18 55499 31.552327632904053 0.5196084976196289 243.35618591308594 0.42963361740112305 311.9973449707031 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index 0000000000000000000000000000000000000000..f9c14233a95d3eb4828eec51b3752c83e06ed71c --- /dev/null +++ b/ENCSR859KGQ/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": ["ENCFF836TQP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR859KGQ/cherimoya.fold_4.log b/ENCSR859KGQ/cherimoya.fold_4.log new file mode 100644 index 0000000000000000000000000000000000000000..3a0ae0de763a1b7d7811244f60220f37f2441095 --- /dev/null +++ b/ENCSR859KGQ/cherimoya.fold_4.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 2866 36.41678190231323 3.9033520221710205 312.10736083984375 1.7068326473236084 338.8717956542969 0.1594129353761673 0.5804243 3.851992130279541 True +1 5732 31.607226848602295 1.3409423828125 222.60462951660156 0.9534720778465271 319.9460754394531 0.23343713581562042 0.650222 1.8503625392913818 True +2 8598 31.172186374664307 0.6595878601074219 220.6105194091797 0.8243741393089294 316.004638671875 0.2421182543039322 0.6637934 0.9554376006126404 True +3 11464 31.005390167236328 1.1637420654296875 254.31192016601562 0.8238002061843872 313.7659606933594 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