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0.1325272023677826 387.9071350097656 0.30013471841812134 0.8655153 0.158929705619812 True +13 38864 30.939802169799805 0.5979928970336914 308.2626037597656 0.1484520137310028 387.36627197265625 0.3016381561756134 0.86879563 0.14836916327476501 True +14 41640 30.92797040939331 0.6026186943054199 308.5541076660156 0.13379797339439392 386.8047180175781 0.30299144983291626 0.8732214 0.14127452671527863 True +15 44416 31.055216789245605 0.6130921840667725 290.7611083984375 0.14211180806159973 386.18603515625 0.3042859733104706 0.8776562 0.1353878378868103 True +16 47192 31.007190227508545 0.613271951675415 323.1834716796875 0.19265282154083252 385.87335205078125 0.3042254149913788 0.88042593 0.1305857002735138 True +17 49968 31.01289391517639 1.0465359687805176 277.1199951171875 0.11801496148109436 385.9820861816406 0.3033049404621124 0.8827036 0.12795211374759674 True +18 52744 31.03574800491333 1.0148396492004395 300.4635009765625 0.10002162307500839 386.20831298828125 0.3038608133792877 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index 0000000000000000000000000000000000000000..751af3f5289f815f660e47d674983731a096df19 --- /dev/null +++ b/ENCSR176KYD/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": ["ENCFF058WTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at 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--git a/ENCSR346GIP/cherimoya.fold_4.log b/ENCSR346GIP/cherimoya.fold_4.log new file mode 100644 index 0000000000000000000000000000000000000000..4654b5f35bded79cd74ce23525c99b406ae74c88 --- /dev/null +++ b/ENCSR346GIP/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 2120 27.296398639678955 3.300591230392456 358.1856384277344 0.7845193147659302 523.1726684570312 0.16980333626270294 0.6238395 7.700412273406982 True +1 4240 23.54513955116272 0.47868824005126953 336.8015441894531 0.7646865844726562 476.72540283203125 0.22748228907585144 0.7280102 2.776913642883301 True +2 6360 23.375366926193237 0.4074110984802246 388.8848876953125 0.7209232449531555 460.28704833984375 0.2383398860692978 0.7599435 1.2637970447540283 True +3 8480 23.386436939239502 1.0866715908050537 449.6316833496094 0.471462607383728 452.2972412109375 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index 0000000000000000000000000000000000000000..a645066e036cc46a9663685d23070bfc79e8a75f --- /dev/null +++ b/ENCSR442OAV/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +395.9572448730469 0.2807275056838989 0.6537520885467529 0.26003730297088623 0.6608769297599792 0.6315458416938782 0.4790003299713135 \ No newline at end of file diff --git a/ENCSR442OAV/cherimoya.fold_1.evaluate.json b/ENCSR442OAV/cherimoya.fold_1.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..f7a1e9fbfe49bd9412c833a7e153a06129cbfd4e --- /dev/null +++ b/ENCSR442OAV/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": [ + 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506.2968444824219 0.47467389702796936 0.4751911 10.220202445983887 True +1 4302 23.97202157974243 0.4802517890930176 312.2154235839844 0.6520284414291382 431.8947448730469 0.5955117344856262 0.5668444 3.449821949005127 True +2 6453 24.031245470046997 0.48767828941345215 341.1151123046875 0.4130737781524658 419.5785827636719 0.6184806823730469 0.56291986 1.150190830230713 False +3 8604 24.026993989944458 0.4752655029296875 288.56427001953125 0.523338794708252 414.78662109375 0.626225471496582 0.5859555 0.9045798182487488 True +4 10755 24.033923625946045 0.47873735427856445 335.4771728515625 0.4611891508102417 412.3920593261719 0.6303102374076843 0.59001356 0.7983361482620239 True +5 12906 24.036436080932617 25.379624605178833 359.38336181640625 0.6528720855712891 411.0697326660156 0.6330468058586121 0.58656466 0.728727400302887 False +6 15057 25.339192390441895 0.47408223152160645 299.0365905761719 0.5409646034240723 410.0072937011719 0.6355038285255432 0.59588706 0.7068663239479065 True +7 17208 23.987671375274658 12.96223783493042 305.8072509765625 0.5488235354423523 409.34063720703125 0.6370757222175598 0.59911245 0.7062209248542786 True +8 19359 24.238370895385742 0.48210859298706055 304.332275390625 0.37940725684165955 408.15484619140625 0.6392066478729248 0.60800433 0.6768532395362854 True +9 21510 24.02801775932312 0.8855953216552734 304.74725341796875 0.5349057912826538 407.0189208984375 0.6415835022926331 0.6177521 0.6399180889129639 True +10 23661 24.01776647567749 0.4728717803955078 318.59869384765625 0.45945194363594055 405.8155822753906 0.6435237526893616 0.62901986 0.6055241227149963 True +11 25812 23.99024224281311 0.4608428478240967 340.2777404785156 0.5532823204994202 404.7464294433594 0.645912766456604 0.64126796 0.5754910111427307 True +12 27963 24.044901132583618 0.4683806896209717 282.6907958984375 0.4055655896663666 403.8415832519531 0.6475821733474731 0.6502253 0.5472550392150879 True +13 30114 23.99872064590454 0.4654510021209717 318.8760681152344 0.4750610291957855 402.9551696777344 0.6486719846725464 0.6574655 0.5248818397521973 True +14 32265 23.989665269851685 0.8346428871154785 344.34967041015625 0.35567256808280945 401.8818664550781 0.6500070095062256 0.6643798 0.5110681653022766 True +15 34416 24.075923681259155 0.4680321216583252 312.2441101074219 0.34514889121055603 401.8023681640625 0.650202751159668 0.668642 0.5023838877677917 True +16 36567 24.021390199661255 22.142444610595703 299.9000244140625 0.3200755715370178 401.62615966796875 0.6500107645988464 0.67283607 0.49366995692253113 True +17 38718 26.471712350845337 0.47896409034729004 317.1075134277344 0.21594631671905518 402.41925048828125 0.649583101272583 0.67103535 0.49625787138938904 False +18 40869 24.05687713623047 0.46949172019958496 324.5234375 0.32327207922935486 401.82421875 0.6491056680679321 0.6681539 0.5025378465652466 False +19 43020 24.017593383789062 0.4707159996032715 263.31610107421875 0.32703906297683716 402.81549072265625 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31.134459972381592 0.528733491897583 386.56842041015625 0.5412770509719849 489.553955078125 0.6831682324409485 0.7210675 0.5133607387542725 True +11 34260 31.09549379348755 0.5282080173492432 319.39215087890625 0.33990833163261414 487.7546081542969 0.6854467988014221 0.72695243 0.49626532196998596 True +12 37115 31.068472385406494 0.5275595188140869 368.12310791015625 0.5937920808792114 486.058837890625 0.6872274875640869 0.7325032 0.4705239534378052 True +13 39970 31.0992271900177 0.5286352634429932 396.8740539550781 0.37260812520980835 484.51007080078125 0.6889027953147888 0.73916817 0.45695796608924866 True +14 42825 31.13136911392212 0.5561151504516602 374.1646423339844 0.3663952052593231 483.2288513183594 0.6904016137123108 0.74636555 0.43506699800491333 True +15 45680 31.102328062057495 0.538243293762207 438.26275634765625 0.36796173453330994 482.59454345703125 0.691164493560791 0.752676 0.42874401807785034 True +16 48535 31.095066785812378 0.5148677825927734 417.0908508300781 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23.57097601890564 186.99923706054688 1.2732746601104736 242.014404296875 0.24394455552101135 0.6896415 0.6202159523963928 True +5 16524 30.420710802078247 0.5417225360870361 147.28173828125 0.9048760533332825 241.28936767578125 0.24664057791233063 0.69953173 0.6269798278808594 True +6 19278 30.112316370010376 0.5114536285400391 160.27334594726562 0.6378939151763916 241.18240356445312 0.2466522455215454 0.7047124 0.6057996153831482 True +7 22032 30.08169460296631 0.504727840423584 182.00994873046875 0.566114604473114 240.5496368408203 0.24966485798358917 0.7090817 0.5791229009628296 True +8 24786 30.051851511001587 0.5023679733276367 187.575927734375 0.5674617290496826 240.09312438964844 0.251992791891098 0.71430624 0.5793658494949341 True +9 27540 30.04210114479065 1.6920835971832275 209.7938995361328 0.47581928968429565 239.2635955810547 0.25613126158714294 0.7167358 0.536038339138031 True +10 30294 30.017030715942383 0.5057122707366943 182.67547607421875 0.8178693056106567 239.0281982421875 0.25677815079689026 0.7239349 0.5287650227546692 True +11 33048 29.983569622039795 0.505413293838501 195.64105224609375 0.5350764393806458 238.6025390625 0.25759971141815186 0.7296523 0.4871482253074646 True +12 35802 29.98676872253418 0.5145769119262695 206.3621368408203 0.5175803899765015 237.84364318847656 0.2613344192504883 0.7323622 0.4715854525566101 True +13 38556 29.986944913864136 0.761681318283081 207.3685302734375 0.441989541053772 237.77392578125 0.26160767674446106 0.7405607 0.44393667578697205 True +14 41310 30.091496467590332 0.5059716701507568 216.90789794921875 0.457075834274292 237.45184326171875 0.262747585773468 0.74617577 0.4389095604419708 True +15 44064 30.030388355255127 0.506939172744751 209.72930908203125 0.3664144277572632 236.87852478027344 0.2655772268772125 0.75176144 0.4254257082939148 True +16 46818 30.031992197036743 0.5080399513244629 185.22801208496094 0.442975789308548 237.14002990722656 0.2636188864707947 0.75490224 0.4217430055141449 True +17 49572 31.08613395690918 30.77992296218872 210.6273193359375 0.5157719850540161 237.2787628173828 0.2625661790370941 0.75599116 0.4213891625404358 True +18 52326 31.96098041534424 0.511737585067749 191.47525024414062 0.36846408247947693 237.1212921142578 0.26366275548934937 0.75431305 0.4264204502105713 False +19 55080 30.070292234420776 0.5049419403076172 170.04566955566406 0.42641156911849976 237.27435302734375 0.26276957988739014 0.75381565 0.43116098642349243 False diff --git a/ENCSR531HPD/cherimoya.fold_3.evaluate.json b/ENCSR531HPD/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..e590f5f67a3ede78ce3acc8ca93c9a0b7f4e7e4b --- /dev/null +++ b/ENCSR531HPD/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": 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No newline at end of file diff --git a/ENCSR531HPD/cherimoya.fold_4.fit.json b/ENCSR531HPD/cherimoya.fold_4.fit.json new file mode 100644 index 0000000000000000000000000000000000000000..bca4d8d367576524b1e1a5f7ae889ee23e2568c8 --- /dev/null +++ b/ENCSR531HPD/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": ["ENCFF551PIV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR542RNG/cherimoya.fold_0.evaluate.json b/ENCSR542RNG/cherimoya.fold_0.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..4acc130c90cfe438a26ccb97581323d19b52b136 --- /dev/null +++ b/ENCSR542RNG/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, 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0000000000000000000000000000000000000000..1872a676a5fad61092eed25fd69a82a9d892aa53 --- /dev/null +++ b/ENCSR542RNG/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": ["ENCFF848SUE.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline 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30.701733350753784 0.5611281394958496 455.61187744140625 0.24977725744247437 524.4010009765625 0.39345458149909973 0.80185026 0.2570478022098541 True +7 22848 30.768512725830078 0.5761778354644775 452.0369873046875 0.22728709876537323 522.2319946289062 0.3965857923030853 0.80837125 0.242413729429245 True +8 25704 30.65452551841736 0.5783154964447021 453.72613525390625 0.21808567643165588 520.394775390625 0.3999972939491272 0.8126364 0.23608586192131042 True +9 28560 30.732102394104004 3.10434889793396 450.259521484375 0.2633497416973114 520.1895141601562 0.39945557713508606 0.8181721 0.22613932192325592 True +10 31416 30.859294891357422 0.5712428092956543 414.84893798828125 0.2352132499217987 519.1546020507812 0.40091243386268616 0.8229395 0.22025316953659058 True +11 34272 30.707707405090332 0.5688607692718506 454.3201904296875 0.21361210942268372 517.2809448242188 0.40458205342292786 0.8297745 0.20655614137649536 True +12 37128 30.765129327774048 0.5755531787872314 565.2269287109375 0.21494752168655396 516.7099609375 0.40453144907951355 0.8329697 0.19795691967010498 True +13 39984 30.736608028411865 0.5692992210388184 501.0755920410156 0.17819300293922424 516.3839111328125 0.40465596318244934 0.8403886 0.19094668328762054 True +14 42840 30.662782907485962 0.5816450119018555 442.4173889160156 0.15787772834300995 514.4912109375 0.4074437618255615 0.84546244 0.18538756668567657 True +15 45696 30.710795402526855 0.569512128829956 454.7334289550781 0.22551590204238892 514.515380859375 0.40746578574180603 0.85009956 0.18085360527038574 True +16 48552 30.652783155441284 0.5628607273101807 477.2606201171875 0.23364034295082092 513.3643798828125 0.4105992913246155 0.8537272 0.17660057544708252 True +17 51408 30.75308108329773 0.5826880931854248 448.41107177734375 0.14124508202075958 513.5717163085938 0.4101790189743042 0.8557317 0.17535367608070374 True +18 54264 30.72647213935852 0.5671563148498535 479.13092041015625 0.1480039805173874 513.4669799804688 0.41038334369659424 0.856466 0.17457245290279388 True +19 57120 30.738869428634644 0.5745456218719482 391.2527160644531 0.16862444579601288 513.4591064453125 0.41011714935302734 0.8554784 0.1745016723871231 False diff --git a/ENCSR645HET/cherimoya.fold_4.performance.tsv b/ENCSR645HET/cherimoya.fold_4.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..b8347805b098acf59ee22803b6ade2417bc1d92a --- /dev/null +++ b/ENCSR645HET/cherimoya.fold_4.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +513.4669799804688 0.3786781132221222 0.41038331389427185 0.1605885773897171 0.8564659953117371 0.823611855506897 0.17457245290279388 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_0.evaluate.json b/ENCSR649XRC/cherimoya.fold_0.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..2dffe9aecce7c4cb66430803bc799d596e6d395c --- /dev/null +++ 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Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved? +0 2350 29.78504204750061 3.3883156776428223 125.34986877441406 0.6789788603782654 174.19119262695312 0.09451694786548615 0.68268657 3.336925506591797 True +1 4700 26.19731330871582 0.50498366355896 162.0029296875 0.9406115412712097 162.61444091796875 0.13684244453907013 0.7514804 1.7291346788406372 True +2 7050 26.134682178497314 0.4787015914916992 112.19715881347656 0.5393877029418945 158.61521911621094 0.14340634644031525 0.757299 0.9075345993041992 True +3 9400 26.135130643844604 2.766035795211792 126.39279174804688 0.37356334924697876 156.78135681152344 0.14798246324062347 0.7781561 0.7319774627685547 True +4 11750 26.11405873298645 0.48542094230651855 135.698974609375 0.6089112758636475 155.43568420410156 0.15227927267551422 0.7939929 0.573427140712738 True +5 14100 26.10621976852417 0.4873485565185547 99.22958374023438 0.2361818552017212 154.7822723388672 0.15387742221355438 0.8081557 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0.4882659912109375 115.36210632324219 0.2750728726387024 152.1120147705078 0.16269880533218384 0.8536651 0.3202267289161682 True +13 32900 25.759755849838257 0.49062252044677734 111.4822006225586 0.367791086435318 151.79803466796875 0.16384157538414001 0.8587394 0.3083750605583191 True +14 35250 25.743313550949097 0.4755442142486572 157.80224609375 0.4401826858520508 151.5306854248047 0.16497914493083954 0.860269 0.3002079725265503 True +15 37600 25.697233200073242 0.47458696365356445 102.54762268066406 0.3184739649295807 151.34921264648438 0.16550317406654358 0.86334157 0.29351523518562317 True +16 39950 25.631633043289185 0.4772963523864746 122.65287780761719 0.2619941830635071 151.38641357421875 0.1650315225124359 0.8637638 0.29191672801971436 True +17 42300 25.679588079452515 0.4752037525177002 127.9485855102539 0.3904632031917572 151.473876953125 0.16416482627391815 0.86396736 0.29199227690696716 True +18 44650 25.65248131752014 0.47471094131469727 173.68289184570312 0.23553702235221863 151.26792907714844 0.16590429842472076 0.86406 0.29450657963752747 True +19 47000 25.601807355880737 0.4792768955230713 126.86991882324219 0.398062527179718 151.49168395996094 0.1647145301103592 0.8621251 0.2981337606906891 False diff --git a/ENCSR649XRC/cherimoya.fold_0.performance.tsv b/ENCSR649XRC/cherimoya.fold_0.performance.tsv new file mode 100644 index 0000000000000000000000000000000000000000..c82d53855a116ccd8912f0e990ebeca7a35e2b46 --- /dev/null +++ b/ENCSR649XRC/cherimoya.fold_0.performance.tsv @@ -0,0 +1,2 @@ +profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse +151.26792907714844 0.5830125212669373 0.16590429842472076 0.03919600695371628 0.8640599846839905 0.7517369389533997 0.29450657963752747 \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_1.evaluate.json b/ENCSR649XRC/cherimoya.fold_1.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..2af35ba0fed8a90be47997aaabb8c99fb7c271c9 --- /dev/null +++ b/ENCSR649XRC/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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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": ["ENCFF430ZZU.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false} \ No newline at end of file diff --git a/ENCSR649XRC/cherimoya.fold_1.log b/ENCSR649XRC/cherimoya.fold_1.log new file mode 100644 index 0000000000000000000000000000000000000000..cb6b0e09022cda0569ec12dc90183dc028565d22 --- /dev/null +++ b/ENCSR649XRC/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 2339 30.2563738822937 3.437596082687378 120.7616958618164 0.7211534976959229 225.39466857910156 0.11461389064788818 0.657867 4.6424336433410645 True +1 4678 25.78019881248474 0.6021103858947754 145.67098999023438 0.5199114084243774 208.25674438476562 0.17010542750358582 0.74160457 2.109802484512329 True +2 7017 25.69510531425476 0.5847516059875488 138.0126953125 0.5160822868347168 205.12124633789062 0.1750665009021759 0.74855113 1.406125783920288 True +3 9356 25.644216537475586 0.5807266235351562 129.37625122070312 0.5125036239624023 200.71286010742188 0.1848868429660797 0.7691105 1.041333794593811 True +4 11695 25.686097383499146 1.2723987102508545 133.21728515625 0.549042284488678 198.99484252929688 0.1877659559249878 0.785759 0.9123117923736572 True +5 14034 25.64818549156189 0.6082768440246582 155.6681365966797 0.4681892395019531 197.61752319335938 0.19161216914653778 0.8022634 0.8142621517181396 True +6 16373 25.657039403915405 0.5994551181793213 150.97906494140625 0.4819318354129791 196.3558807373047 0.19515183568000793 0.81616735 0.7024433612823486 True +7 18712 25.68966817855835 0.6007065773010254 110.4560546875 0.4232436418533325 196.0518035888672 0.19625376164913177 0.81340736 0.7259196639060974 False +8 21051 25.675628900527954 0.5927512645721436 178.5734405517578 0.6164196729660034 195.26708984375 0.19826073944568634 0.826451 0.6338158249855042 True +9 23390 25.711796760559082 3.7460989952087402 97.86626434326172 0.3473885655403137 194.7615509033203 0.20025040209293365 0.8335556 0.5956342220306396 True +10 25729 25.67039942741394 0.6008415222167969 162.85684204101562 0.5337804555892944 194.25619506835938 0.2015203982591629 0.844521 0.5278694033622742 True +11 28068 25.684767246246338 0.5935566425323486 133.77609252929688 0.45179039239883423 193.83084106445312 0.20208172500133514 0.851052 0.4745836853981018 True +12 30407 25.69076180458069 0.5922071933746338 153.26719665527344 0.49785587191581726 193.1223907470703 0.20460359752178192 0.8581879 0.45509767532348633 True +13 32746 25.759449243545532 0.6154358386993408 124.92704010009766 0.43480491638183594 192.79379272460938 0.20487599074840546 0.86434627 0.421362966299057 True +14 35085 25.615883588790894 1.535430908203125 102.53887939453125 0.43991556763648987 192.61619567871094 0.20509833097457886 0.8677952 0.39784669876098633 True +15 37424 25.23749041557312 0.5975275039672852 105.23694610595703 0.4242854118347168 192.361083984375 0.20595742762088776 0.8705091 0.3854706585407257 True +16 39763 25.281128644943237 0.6069839000701904 93.21112060546875 0.4268479347229004 192.31541442871094 0.20587942004203796 0.8704498 0.37689223885536194 False +17 42102 25.165701150894165 0.5887608528137207 125.4584732055664 0.34571942687034607 192.42666625976562 0.20530645549297333 0.870951 0.3763268291950226 True +18 44441 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"validation_chroms": [ + "chr12", + "chr17" + ], + "verbose": true +} \ No newline at end of file diff --git a/ENCSR989YIV/cherimoya.fold_3.evaluate.json b/ENCSR989YIV/cherimoya.fold_3.evaluate.json new file mode 100644 index 0000000000000000000000000000000000000000..2214ed4db29acc69b6dd767990ed7fd3b06fffa8 --- /dev/null +++ b/ENCSR989YIV/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, + 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/dev/null +++ b/ENCSR989YIV/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 2806 40.43014717102051 3.82912540435791 227.75332641601562 0.9193063378334045 247.03138732910156 0.149123415350914 0.5775326 3.599280595779419 True +1 5612 31.023504972457886 0.620307445526123 162.21585083007812 0.6726515293121338 232.41310119628906 0.22367125749588013 0.6628942 1.9023224115371704 True +2 8418 31.03766942024231 0.5895471572875977 203.69468688964844 0.7371058464050293 229.6620635986328 0.23217898607254028 0.68086785 1.0544395446777344 True +3 11224 31.03950834274292 1.581418514251709 173.01129150390625 0.5639842748641968 227.7578887939453 0.24007096886634827 0.68968433 0.8768095970153809 True +4 14030 31.0664222240448 0.5877537727355957 121.40170288085938 0.9222900867462158 227.67356872558594 0.23913739621639252 0.6944664 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0.5896544456481934 164.56631469726562 0.4197850525379181 224.31919860839844 0.2554200291633606 0.7338145 0.4828082025051117 True +12 36478 31.082420825958252 20.246337890625 139.26535034179688 0.44772565364837646 223.88499450683594 0.25743386149406433 0.7376036 0.474195271730423 True +13 39284 31.004339933395386 1.6503372192382812 201.87448120117188 0.5824717283248901 223.50962829589844 0.2591542899608612 0.7446431 0.4425468146800995 True +14 42090 31.099766492843628 21.178971529006958 157.94143676757812 0.4512127935886383 223.37937927246094 0.2589869499206543 0.75199914 0.423437237739563 True +15 44896 31.94133496284485 0.5878002643585205 170.7144012451172 0.5503484606742859 223.3103790283203 0.25923144817352295 0.75705963 0.41410472989082336 True +16 47702 31.23698616027832 0.6028008460998535 208.66864013671875 0.5193883180618286 223.23410034179688 0.2597295939922333 0.7624295 0.40318453311920166 True +17 50508 31.086349964141846 0.5909111499786377 170.09768676757812 0.2783315181732178 223.3691864013672 0.25852450728416443 0.764379 0.40031442046165466 True +18 53314 35.76102900505066 23.43786907196045 180.94482421875 0.35305503010749817 223.1518096923828 0.2597448527812958 0.7630436 0.39866575598716736 False +19 56120 30.47586679458618 0.5800416469573975 198.59727478027344 0.2416015863418579 223.0371551513672 0.26069334149360657 0.7613304 0.4051746129989624 False