Add files using upload-large-folder tool

ENCSR000ENR/cherimoya.fold_0.evaluate.json

@@ -0,0 +1,78 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_0.bed",
+        "valid_peaks.fold_0.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_0.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_0",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_0.bed",
+        "valid_nonpeaks.fold_0.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_0.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF301RSY.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "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"
+    ],
+    "verbose": true
+}

ENCSR000ENR/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": ["ENCFF301RSY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENR/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	2683	35.87672424316406	3.5704221725463867	231.81089782714844	1.0348589420318604	337.95904541015625	0.1904870569705963	0.34994316	3.7455365657806396	True
+1	5366	30.35912799835205	12.188981533050537	212.34439086914062	1.4020195007324219	300.83917236328125	0.3065672218799591	0.49131662	2.405163288116455	True
+2	8049	29.885828733444214	22.989011526107788	228.30517578125	0.8724849224090576	296.14764404296875	0.31723710894584656	0.49883842	1.627149224281311	True
+3	10732	30.546351194381714	0.5820469856262207	219.78567504882812	0.5556142330169678	293.5635070800781	0.3228112757205963	0.5241449	1.3251168727874756	True
+4	13415	29.865067958831787	27.195473194122314	223.26724243164062	0.8976618051528931	292.00970458984375	0.32762810587882996	0.53298604	1.1746951341629028	True
+5	16098	33.89431047439575	31.587092399597168	236.21974182128906	0.7456682920455933	290.7890930175781	0.3320986032485962	0.5452405	1.1463203430175781	True
+6	18781	34.33380174636841	24.058573246002197	245.73744201660156	0.6541839838027954	289.5464782714844	0.3362976312637329	0.55939424	1.1106175184249878	True
+7	21464	29.882193326950073	0.5876479148864746	188.44085693359375	0.5955337285995483	288.83612060546875	0.3383747935295105	0.5702607	1.0283514261245728	True
+8	24147	29.86298418045044	0.5767178535461426	198.40087890625	0.6791425943374634	288.0511169433594	0.34085020422935486	0.5785833	0.9707908034324646	True
+9	26830	29.93053960800171	0.5924770832061768	233.1223907470703	0.6416366100311279	287.1144714355469	0.344055712223053	0.5859171	0.9313520789146423	True
+10	29513	29.88433289527893	0.8626832962036133	203.33973693847656	0.5912595987319946	286.06414794921875	0.34602871537208557	0.6000404	0.8309391140937805	True
+11	32196	30.083770513534546	0.599506139755249	228.8909454345703	0.6188033223152161	285.253173828125	0.3486991822719574	0.60750306	0.7738471031188965	True
+12	34879	30.1723051071167	0.6059634685516357	211.25521850585938	0.5978245735168457	284.548095703125	0.35064417123794556	0.61960626	0.7095296382904053	True
+13	37562	30.155993223190308	0.5929341316223145	300.5572509765625	0.9590668678283691	283.9913635253906	0.35134369134902954	0.63321364	0.6342284679412842	True
+14	40245	30.088075637817383	35.72416806221008	293.8077392578125	0.6613070368766785	283.61431884765625	0.35184964537620544	0.6478295	0.5824973583221436	True
+15	42928	31.09560203552246	0.5780637264251709	222.00665283203125	0.5127372741699219	283.03472900390625	0.35373082756996155	0.65716887	0.5458201169967651	True
+16	45611	30.151302576065063	0.5753624439239502	262.0118408203125	0.4969853460788727	282.6499938964844	0.3553996980190277	0.66651475	0.507263720035553	True
+17	48294	30.019012689590454	0.5748748779296875	309.7059020996094	0.6362217664718628	282.68731689453125	0.3552553355693817	0.66843945	0.491824746131897	True
+18	50977	30.004778146743774	0.5747838020324707	197.8228759765625	0.454222708940506	282.5978088378906	0.3560830354690552	0.6653466	0.49211257696151733	False
+19	53660	32.10676836967468	13.78606653213501	183.96847534179688	0.3002427816390991	282.36767578125	0.3565908968448639	0.66561276	0.4949606657028198	False

ENCSR000ENR/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+282.68731689453125	0.45685645937919617	0.3552553057670593	0.09128955006599426	0.6684394478797913	0.6295320987701416	0.491824746131897

ENCSR000ENR/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,
+    "performance_filename": "cherimoya.fold_1.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF301RSY.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr10",
+        "chr11",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000ENR/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": ["ENCFF301RSY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENR/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	2703	33.742345333099365	3.8340792655944824	213.66110229492188	0.6503987312316895	368.72369384765625	0.192018523812294	0.38327283	3.966585636138916	True
+1	5406	30.017462015151978	11.71983289718628	265.136962890625	0.7099952101707458	328.9857482910156	0.3147927522659302	0.49241057	2.3132848739624023	True
+2	8109	29.253949642181396	0.7252945899963379	224.26885986328125	0.7419847249984741	321.39703369140625	0.33088254928588867	0.5187824	1.6018198728561401	True
+3	10812	29.24500823020935	0.7036113739013672	247.142333984375	0.8263672590255737	318.5325927734375	0.3344704806804657	0.5510477	1.2407310009002686	True
+4	13515	29.31106209754944	0.7179305553436279	225.29031372070312	0.6597805023193359	316.6301574707031	0.33834943175315857	0.5652248	1.0280410051345825	True
+5	16218	29.2051100730896	0.6888318061828613	254.563720703125	0.635513961315155	315.1585693359375	0.34209978580474854	0.579034	0.9521908164024353	True
+6	18921	29.235312938690186	0.6835896968841553	207.56765747070312	0.6754316091537476	313.2167663574219	0.34899958968162537	0.5874313	0.9500905275344849	True
+7	21624	29.175732612609863	1.3492155075073242	224.92852783203125	0.7175895571708679	312.2987060546875	0.35149744153022766	0.5907356	0.8798553943634033	True
+8	24327	29.252511024475098	0.6897237300872803	208.4119415283203	0.6468014121055603	312.07012939453125	0.35128340125083923	0.60207826	0.8126583695411682	True
+9	27030	29.18019461631775	0.681499719619751	185.92074584960938	0.7645083069801331	311.1493225097656	0.353890597820282	0.61661255	0.7674474716186523	True
+10	29733	29.16776728630066	0.707352876663208	196.841552734375	0.6716262102127075	310.09759521484375	0.3568790555000305	0.62910336	0.7453514337539673	True
+11	32436	29.153464555740356	0.8866837024688721	218.94528198242188	0.5144503116607666	308.9451599121094	0.3614083230495453	0.63717914	0.6831514835357666	True
+12	35139	29.21226716041565	0.6880924701690674	223.5855712890625	0.4051459729671478	308.32464599609375	0.36208316683769226	0.6499702	0.6781948208808899	True
+13	37842	29.16431760787964	1.4563767910003662	176.61471557617188	0.6967370510101318	308.006103515625	0.361299991607666	0.6628863	0.6223872900009155	True
+14	40545	29.27998447418213	3.6318438053131104	207.03720092773438	0.4240555167198181	307.3372802734375	0.36362606287002563	0.6719726	0.5825995802879333	True
+15	43248	29.258713245391846	0.6888425350189209	234.59352111816406	0.4861701428890228	306.46185302734375	0.36613866686820984	0.67948735	0.5553580522537231	True
+16	45951	29.210845232009888	0.7153847217559814	199.84104919433594	0.38552993535995483	306.0098876953125	0.3670486807823181	0.6856326	0.529951274394989	True
+17	48654	29.24815607070923	0.6829137802124023	212.32394409179688	0.5263775587081909	306.3221740722656	0.3654298782348633	0.68942845	0.5183570981025696	True
+18	51357	29.20939826965332	0.6782927513122559	223.1678466796875	0.45338860154151917	306.31976318359375	0.36558282375335693	0.6883731	0.5118093490600586	False
+19	54060	29.146774768829346	0.681654691696167	180.75901794433594	0.31128227710723877	306.19866943359375	0.36589595675468445	0.6888752	0.516739010810852	False

ENCSR000ENR/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+306.3221740722656	0.4464711546897888	0.36542990803718567	0.09722325205802917	0.689428448677063	0.6609253287315369	0.5183570981025696

ENCSR000ENR/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_2.bed",
+        "valid_peaks.fold_2.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_2.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_2",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_2.bed",
+        "valid_nonpeaks.fold_2.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_2.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF301RSY.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr10",
+        "chr13",
+        "chr14",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chrX"
+    ],
+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR000ENR/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": ["ENCFF301RSY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENR/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	2886	37.08751940727234	4.022672176361084	277.4508056640625	0.9209482073783875	341.6883850097656	0.19196628034114838	0.3491368	3.2109344005584717	True
+1	5772	31.777408123016357	0.5163013935089111	253.67832946777344	0.961327314376831	303.25994873046875	0.31319624185562134	0.47710255	2.6754837036132812	True
+2	8658	31.278521299362183	0.5015366077423096	173.74290466308594	0.7071061730384827	299.23004150390625	0.3207681179046631	0.49058387	1.4451483488082886	True
+3	11544	31.09076237678528	0.4958043098449707	267.8490905761719	0.8409023284912109	295.7858581542969	0.32855361700057983	0.5289751	1.1698040962219238	True
+4	14430	31.098041772842407	1.3078248500823975	258.7386474609375	0.8502821922302246	294.34808349609375	0.33253398537635803	0.53891057	1.076215386390686	True
+5	17316	31.175076007843018	0.505171537399292	205.85780334472656	0.5647721290588379	292.58447265625	0.3387924134731293	0.5483469	1.032808542251587	True
+6	20202	31.315122604370117	0.5066056251525879	222.46456909179688	0.6236469745635986	291.6018981933594	0.3417246639728546	0.5603539	1.0365804433822632	True
+7	23088	31.136927843093872	0.5017085075378418	212.82431030273438	0.9630367755889893	290.6396179199219	0.3446163833141327	0.56992114	0.9217387437820435	True
+8	25974	31.346759557724	27.861027240753174	222.39244079589844	0.6180703639984131	289.9885559082031	0.34718623757362366	0.57546246	0.9357782602310181	True
+9	28860	31.132904529571533	8.432681798934937	244.7154541015625	0.6954934597015381	288.8699951171875	0.35018086433410645	0.5881324	0.8175247311592102	True
+10	31746	31.13149857521057	1.7425100803375244	192.94232177734375	0.4836273789405823	288.6225280761719	0.34970664978027344	0.59452367	0.7809624075889587	True
+11	34632	31.2137393951416	8.813173770904541	170.26119995117188	0.49642273783683777	287.5307922363281	0.3533443808555603	0.60266244	0.7273221015930176	True
+12	37518	31.164634704589844	1.7127857208251953	197.06338500976562	0.5853899717330933	286.8450927734375	0.354422926902771	0.61351514	0.6793676614761353	True
+13	40404	31.097848653793335	1.290273666381836	227.68521118164062	0.5961387157440186	285.8397521972656	0.3582404553890228	0.6263308	0.6254265308380127	True
+14	43290	31.095531940460205	0.9002621173858643	254.46292114257812	0.5384172201156616	285.71795654296875	0.35794195532798767	0.63514	0.605079710483551	True
+15	46176	31.09093403816223	1.3694005012512207	248.8413543701172	0.4456508457660675	284.9027404785156	0.3604947328567505	0.6458745	0.5636093020439148	True
+16	49062	31.71883273124695	0.5076236724853516	230.70225524902344	0.42184627056121826	284.6847839355469	0.3605421781539917	0.65271187	0.5434838533401489	True
+17	51948	31.202033519744873	0.4874415397644043	202.85433959960938	0.4182186722755432	284.3936767578125	0.3619670569896698	0.6585162	0.5250712037086487	True
+18	54834	31.194443225860596	0.5039687156677246	215.36941528320312	0.40949228405952454	285.020263671875	0.3593844175338745	0.6601866	0.517615795135498	True
+19	57720	31.194924116134644	0.494248628616333	249.4766845703125	0.42191123962402344	284.5609130859375	0.36071568727493286	0.6603617	0.5192922949790955	True

ENCSR000ENR/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+284.5609130859375	0.45433586835861206	0.36071568727493286	0.09538287669420242	0.6603617072105408	0.6215336322784424	0.5192922949790955

ENCSR000ENR/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": [
+        "ENCFF301RSY.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
+}

ENCSR000ENR/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": ["ENCFF301RSY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENR/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	2761	34.308178424835205	3.541431188583374	233.843505859375	0.923799455165863	354.0873718261719	0.1958104819059372	0.36850506	3.6245296001434326	True
+1	5522	30.13351845741272	0.5970273017883301	232.70407104492188	0.9294846653938293	316.1968078613281	0.31191498041152954	0.50030386	2.3403520584106445	True
+2	8283	30.420990705490112	0.5892400741577148	239.90353393554688	0.7273653745651245	311.329345703125	0.3242180347442627	0.50502944	1.4112082719802856	True
+3	11044	30.333210229873657	0.5693581104278564	247.12490844726562	0.7533837556838989	309.15228271484375	0.32974928617477417	0.5195701	1.213912844657898	True
+4	13805	29.846307277679443	0.5634653568267822	217.9493865966797	0.7915856242179871	308.44293212890625	0.33114850521087646	0.52709925	1.228248119354248	True
+5	16566	29.844799995422363	0.5770103931427002	211.16455078125	0.7790812849998474	306.4981994628906	0.3375350534915924	0.5394989	1.1449646949768066	True
+6	19327	29.75601625442505	0.5756168365478516	217.6361083984375	0.7236143350601196	305.2210388183594	0.34241291880607605	0.5532663	1.112621784210205	True
+7	22088	29.785577058792114	0.5645027160644531	215.20150756835938	0.6328674554824829	304.69610595703125	0.3433375954627991	0.5593285	1.0672173500061035	True
+8	24849	30.03095841407776	0.5718526840209961	293.42950439453125	0.6346083283424377	303.8703308105469	0.345578670501709	0.5711974	1.0551246404647827	True
+9	27610	29.80507731437683	0.5821056365966797	320.37353515625	0.7408772706985474	303.04364013671875	0.34698691964149475	0.58078974	0.9331235885620117	True
+10	30371	29.76930856704712	0.5789623260498047	232.67149353027344	0.6272004842758179	302.0252990722656	0.35049793124198914	0.58625054	0.8988683819770813	True
+11	33132	29.88939905166626	0.578005313873291	230.4815673828125	0.697494626045227	301.2093505859375	0.35184019804000854	0.597786	0.8092371821403503	True
+12	35893	29.960935592651367	2.3813982009887695	244.12481689453125	0.46342185139656067	299.9916687011719	0.3559456467628479	0.6098302	0.7478569149971008	True
+13	38654	29.991307497024536	0.5784096717834473	187.3021697998047	0.49890854954719543	299.5975646972656	0.35609546303749084	0.6218526	0.688782811164856	True
+14	41415	30.00028657913208	0.595001220703125	222.07254028320312	0.46244049072265625	298.8475646972656	0.35788336396217346	0.63898957	0.6537326574325562	True
+15	44176	30.026244640350342	0.5751936435699463	215.1691131591797	0.469441294670105	298.02215576171875	0.3608437180519104	0.65172505	0.6037404537200928	True
+16	46937	29.954384565353394	0.5796575546264648	196.85507202148438	0.5567508935928345	297.6426086425781	0.3610830008983612	0.65731215	0.5692298412322998	True
+17	49698	29.959677696228027	0.5814614295959473	226.63424682617188	0.4132523536682129	297.758544921875	0.3603115677833557	0.66188526	0.5553171634674072	True
+18	52459	29.977272748947144	0.5834321975708008	209.61685180664062	0.3847728967666626	298.0604248046875	0.35917600989341736	0.6629235	0.5498114228248596	True
+19	55220	29.986448049545288	0.5819032192230225	238.12161254882812	0.44831979274749756	297.72705078125	0.36083459854125977	0.6611839	0.5501923561096191	False

ENCSR000ENR/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+298.0604248046875	0.45224258303642273	0.35917600989341736	0.09771819412708282	0.6629235148429871	0.6360957026481628	0.5498114228248596

ENCSR000ENR/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,
+    "performance_filename": "cherimoya.fold_4.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF301RSY.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr11",
+        "chr12",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr20",
+        "chr22",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr10",
+        "chr18"
+    ],
+    "verbose": true
+}

ENCSR000ENR/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": ["ENCFF301RSY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENR/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	2884	35.96135139465332	4.092160701751709	201.11337280273438	0.6641717553138733	340.369873046875	0.19350986182689667	0.34416097	3.61820650100708	True
+1	5768	31.550018548965454	0.5765047073364258	278.0926513671875	0.7887901067733765	301.175537109375	0.3167247474193573	0.47295806	1.9922024011611938	True
+2	8652	31.774850130081177	1.298738956451416	221.58670043945312	0.9113283753395081	298.6192321777344	0.32280245423316956	0.48436195	1.2628657817840576	True
+3	11536	31.619239807128906	0.5621852874755859	255.2421875	0.653771162033081	295.6233825683594	0.33002060651779175	0.4982608	1.0191186666488647	True
+4	14420	31.702385902404785	2.2072677612304688	241.61932373046875	0.6435945630073547	293.97845458984375	0.3332081139087677	0.5159356	0.9705982208251953	True
+5	17304	31.109487533569336	10.819525957107544	210.69927978515625	0.6571829319000244	293.3883972167969	0.33564653992652893	0.5232348	0.9278461337089539	True
+6	20188	31.1389901638031	17.764245986938477	233.16757202148438	0.4986213147640228	292.19866943359375	0.3394133746623993	0.5368911	0.8801859021186829	True
+7	23072	31.11890721321106	0.5534672737121582	228.14291381835938	0.7607458829879761	290.6194152832031	0.34452831745147705	0.54432136	0.7836006879806519	True
+8	25956	31.04460120201111	0.5364377498626709	271.83441162109375	1.0158555507659912	290.2750244140625	0.3445095121860504	0.55890614	0.7525089979171753	True
+9	28840	31.034976482391357	0.5505197048187256	257.0621337890625	0.7357786893844604	289.3911437988281	0.34727808833122253	0.57268417	0.7167145609855652	True
+10	31724	31.031221389770508	1.1338670253753662	221.41650390625	0.5513192415237427	288.90185546875	0.34819450974464417	0.58766955	0.6613775491714478	True
+11	34608	31.11376667022705	0.5490059852600098	191.16090393066406	0.7287821769714355	287.81884765625	0.3516690731048584	0.59853166	0.6202363967895508	True
+12	37492	31.08756113052368	0.5504238605499268	213.24560546875	0.571038007736206	286.82696533203125	0.3551284670829773	0.61278	0.5816622972488403	True
+13	40376	31.04531955718994	0.5583336353302002	236.638427734375	0.6077041625976562	286.60211181640625	0.35482463240623474	0.6254023	0.5500555038452148	True
+14	43260	31.047570943832397	0.5433261394500732	224.07095336914062	0.5785960555076599	286.04937744140625	0.3563137352466583	0.6395113	0.5299115777015686	True
+15	46144	31.072348594665527	0.5496621131896973	207.632568359375	0.4457934498786926	285.3481140136719	0.35879871249198914	0.6503516	0.5104297399520874	True
+16	49028	31.07137417793274	0.5476598739624023	226.23980712890625	0.48542520403862	284.60479736328125	0.3609674572944641	0.6576462	0.5004262328147888	True
+17	51912	31.059365034103394	0.552889347076416	235.01962280273438	0.39278534054756165	285.0400085449219	0.3590998649597168	0.659836	0.496656209230423	True
+18	54796	31.101794719696045	1.6204204559326172	208.82786560058594	0.22562110424041748	285.6606750488281	0.35622161626815796	0.66036654	0.4983183741569519	True
+19	57680	31.069571495056152	0.5442721843719482	253.298828125	0.4365638494491577	285.3761291503906	0.35764047503471375	0.65806067	0.5042034387588501	False

ENCSR000ENR/cherimoya.fold_4.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+285.6606750488281	0.45581597089767456	0.35622161626815796	0.09498211741447449	0.6603665351867676	0.6230810284614563	0.4983183741569519

ENCSR000EPE/cherimoya.fold_0.evaluate.json

@@ -0,0 +1,78 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_0.bed",
+        "valid_peaks.fold_0.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_0.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_0",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_0.bed",
+        "valid_nonpeaks.fold_0.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_0.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF886GIK.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "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"
+    ],
+    "verbose": true
+}

ENCSR000EPE/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": ["ENCFF886GIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPE/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	2742	39.457128286361694	4.3827314376831055	743.8118896484375	1.8905144929885864	1360.9515380859375	0.29549330472946167	0.34517467	7.759799003601074	True
+1	5484	30.64297890663147	0.5821082592010498	900.208251953125	1.620566964149475	1054.370849609375	0.48720359802246094	0.46400258	5.744274616241455	True
+2	8226	30.672199964523315	0.5573873519897461	682.8338012695312	1.9013797044754028	1026.6136474609375	0.5044870376586914	0.4544129	2.737123489379883	False
+3	10968	30.67493438720703	0.5658910274505615	665.1024169921875	1.5641660690307617	1003.6644287109375	0.5168028473854065	0.49645337	2.399862051010132	True
+4	13710	30.640730619430542	0.6202936172485352	791.11865234375	1.151921272277832	994.1766967773438	0.5223021507263184	0.5117579	1.9784599542617798	True
+5	16452	30.596606492996216	0.5610747337341309	872.183349609375	1.2176333665847778	984.3543701171875	0.5291743278503418	0.51727456	1.5598804950714111	True
+6	19194	30.61560821533203	0.5935029983520508	830.7156372070312	1.0691449642181396	978.287841796875	0.532913088798523	0.52620345	1.595988392829895	True
+7	21936	30.595120191574097	0.5646426677703857	751.666015625	1.2095333337783813	969.046875	0.5399726629257202	0.5378901	1.3648459911346436	True
+8	24678	32.805994749069214	0.5512895584106445	799.4314575195312	1.0871071815490723	962.1593017578125	0.5447551012039185	0.53978276	1.3313266038894653	True
+9	27420	30.79980754852295	0.5527431964874268	810.8829956054688	1.2129731178283691	954.182861328125	0.5489981174468994	0.55401826	1.2035385370254517	True
+10	30162	30.77415657043457	0.5485894680023193	832.3341064453125	1.1435412168502808	948.4569091796875	0.5540049076080322	0.5644001	1.2087641954421997	True
+11	32904	30.797839879989624	24.302977323532104	803.5817260742188	0.9471536874771118	943.2835083007812	0.5561445355415344	0.5835645	1.0938334465026855	True
+12	35646	31.24456214904785	0.6079764366149902	804.0167846679688	0.8877308368682861	936.8389282226562	0.5595266222953796	0.60026765	1.0176498889923096	True
+13	38388	30.321988344192505	0.542809009552002	669.0584106445312	0.8274429440498352	930.2277221679688	0.564010500907898	0.6104185	1.0117186307907104	True
+14	41130	30.0930278301239	0.7864642143249512	789.0499267578125	0.8051576614379883	924.8782348632812	0.5669478178024292	0.6287901	0.9137803912162781	True
+15	43872	30.06586265563965	0.5526690483093262	636.9500732421875	0.6099447011947632	924.4169311523438	0.5665673017501831	0.6440339	0.8573645949363708	True
+16	46614	29.995049238204956	0.5391557216644287	735.5460205078125	0.8243582844734192	922.0097045898438	0.5667331218719482	0.65216404	0.8230382204055786	True
+17	49356	30.99628496170044	26.216195344924927	857.8589477539062	0.5557984113693237	918.0490112304688	0.5701450109481812	0.65792954	0.8033034801483154	True
+18	52098	30.058032989501953	0.570880651473999	600.8111572265625	0.4578520357608795	917.158203125	0.5707445740699768	0.66018945	0.7944747805595398	True
+19	54840	30.197919607162476	1.6188318729400635	754.9034423828125	0.6713298559188843	918.5931396484375	0.5690954923629761	0.6602937	0.7935234904289246	True

ENCSR000EPE/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+918.5931396484375	0.2680555582046509	0.5690954923629761	0.2799272835254669	0.660293698310852	0.6349843144416809	0.7935234904289246

ENCSR000EPE/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,
+    "performance_filename": "cherimoya.fold_1.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF886GIK.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr10",
+        "chr11",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000EPE/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": ["ENCFF886GIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPE/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	2752	36.87750434875488	4.108018636703491	945.5022583007812	1.756040334701538	1486.27783203125	0.30209895968437195	0.40500286	10.34707260131836	True
+1	5504	30.6926007270813	0.6891191005706787	1108.0380859375	1.7336384057998657	1172.668212890625	0.49382928013801575	0.47339684	5.516873836517334	True
+2	8256	30.665461778640747	40.42298746109009	747.2845458984375	1.6591721773147583	1144.30078125	0.5057443976402283	0.47911996	2.7470693588256836	True
+3	11008	30.983369827270508	0.7516815662384033	824.3382568359375	1.1434382200241089	1117.0877685546875	0.51799476146698	0.5142499	2.0671210289001465	True
+4	13760	33.792465925216675	0.6872947216033936	893.5116577148438	1.3412787914276123	1105.174560546875	0.5226713418960571	0.52053195	1.6895359754562378	True
+5	16512	30.70180320739746	2.478851318359375	748.4896240234375	2.1422834396362305	1094.1422119140625	0.5282285213470459	0.53268707	1.6732871532440186	True
+6	19264	30.726118803024292	0.6775784492492676	671.320068359375	1.2002822160720825	1084.0418701171875	0.5331755876541138	0.5383196	1.5429742336273193	True
+7	22016	30.674723148345947	0.6647276878356934	775.4976806640625	1.2797458171844482	1073.2672119140625	0.5403428077697754	0.55393875	1.3606950044631958	True
+8	24768	30.714258909225464	0.6800134181976318	801.7338256835938	1.5879532098770142	1062.9405517578125	0.5464352369308472	0.56430066	1.2739546298980713	True
+9	27520	30.85387372970581	32.57810688018799	710.1611938476562	1.4795126914978027	1054.69921875	0.5518369078636169	0.5713561	1.2600306272506714	True
+10	30272	30.72087860107422	2.01194429397583	766.5366821289062	1.4081194400787354	1052.446533203125	0.5523772239685059	0.5858461	1.2963649034500122	True
+11	33024	30.75458526611328	0.9213700294494629	664.00439453125	0.927808940410614	1042.6630859375	0.5589404106140137	0.6009387	1.192838191986084	True
+12	35776	30.786773443222046	0.6774508953094482	639.4361572265625	1.1135339736938477	1035.0152587890625	0.5607662796974182	0.6204939	1.0892887115478516	True
+13	38528	30.504095315933228	32.79808068275452	808.59423828125	1.2458548545837402	1022.7063598632812	0.5689274668693542	0.6365724	1.0109977722167969	True
+14	41280	30.211282968521118	0.742405891418457	679.6019287109375	0.7798165678977966	1020.7762451171875	0.5685762166976929	0.65337044	0.9354321360588074	True
+15	44032	30.295127391815186	0.8610877990722656	644.065185546875	0.8589656352996826	1014.3031616210938	0.5726882815361023	0.6672401	0.8739889860153198	True
+16	46784	30.358635663986206	0.6918368339538574	888.638427734375	0.8998309969902039	1011.1793212890625	0.5741958618164062	0.67684454	0.8425577878952026	True
+17	49536	30.225776195526123	2.2835171222686768	613.8629150390625	0.6617981195449829	1011.8900146484375	0.5725444555282593	0.67972684	0.818058967590332	True
+18	52288	31.44782853126526	32.09016704559326	565.3028564453125	0.4165216088294983	1012.1405639648438	0.5721092820167542	0.68231195	0.8060736060142517	True
+19	55040	30.33749771118164	8.566814661026001	598.3876342773438	0.6634373664855957	1010.279296875	0.5744016766548157	0.68540686	0.7977477312088013	True

ENCSR000EPE/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+1010.279296875	0.2599550485610962	0.5744016170501709	0.2915697991847992	0.6854068636894226	0.658420205116272	0.7977477312088013

ENCSR000EPE/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_2.bed",
+        "valid_peaks.fold_2.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_2.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_2",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_2.bed",
+        "valid_nonpeaks.fold_2.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_2.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF886GIK.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr10",
+        "chr13",
+        "chr14",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chrX"
+    ],
+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR000EPE/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": ["ENCFF886GIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPE/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	2870	36.3016996383667	3.573741912841797	773.5966186523438	1.5644609928131104	1529.116455078125	0.2909344732761383	0.34371778	10.406034469604492	True
+1	5740	31.987508535385132	0.591278076171875	901.16455078125	1.3515013456344604	1175.3204345703125	0.4870940148830414	0.48201266	5.730994701385498	True
+2	8610	31.96562361717224	0.576531171798706	650.9892578125	1.5516600608825684	1142.7525634765625	0.5053225755691528	0.47519752	3.0063130855560303	False
+3	11480	32.04001545906067	0.578300952911377	771.700927734375	1.2152771949768066	1121.802001953125	0.5141338109970093	0.48460287	2.4592936038970947	True
+4	14350	32.04742908477783	0.5859208106994629	827.8876953125	1.4370841979980469	1106.3319091796875	0.5252417325973511	0.5010042	2.453947067260742	True
+5	17220	38.580060720443726	24.540173530578613	602.7957763671875	1.4062340259552002	1091.6785888671875	0.5327261090278625	0.5106311	2.1078550815582275	True
+6	20090	35.37982749938965	18.919846296310425	812.6472778320312	1.7023231983184814	1086.826416015625	0.5347272753715515	0.5198012	1.9158886671066284	True
+7	22960	32.39515161514282	0.6188030242919922	919.1793212890625	1.1592819690704346	1075.99951171875	0.5405493974685669	0.5358813	1.6738307476043701	True
+8	25830	32.10229015350342	0.6051385402679443	694.689697265625	1.1981847286224365	1066.615966796875	0.5438141226768494	0.5414031	1.6444895267486572	True
+9	28700	32.17344784736633	0.6021778583526611	709.93701171875	1.0557968616485596	1056.6209716796875	0.5491202473640442	0.5498518	1.5578229427337646	True
+10	31570	32.78214979171753	3.343174695968628	602.578369140625	1.2171820402145386	1049.9769287109375	0.5534657835960388	0.5597431	1.4341785907745361	True
+11	34440	32.14570450782776	0.6154909133911133	827.978759765625	1.0125243663787842	1039.9775390625	0.558107316493988	0.57805145	1.4386324882507324	True
+12	37310	32.13430833816528	1.3044016361236572	650.062255859375	0.8178694248199463	1035.0390625	0.5595945119857788	0.58881986	1.383777141571045	True
+13	40180	31.53299617767334	1.4720797538757324	703.6908569335938	1.2008275985717773	1028.00732421875	0.5617138743400574	0.6072443	1.2686346769332886	True
+14	43050	31.66144061088562	0.6048905849456787	671.4093017578125	1.023082971572876	1018.9625244140625	0.5660822987556458	0.62397647	1.1812089681625366	True
+15	45920	31.455259561538696	0.5847382545471191	742.28564453125	0.5348973274230957	1013.4844970703125	0.5685392618179321	0.6359547	1.1298266649246216	True
+16	48790	31.38888144493103	0.5747301578521729	606.8780517578125	1.1116256713867188	1016.592529296875	0.5638679265975952	0.64562166	1.0710383653640747	True
+17	51660	31.38589906692505	0.5972263813018799	727.6346435546875	0.9717101454734802	1010.3394165039062	0.5695608258247375	0.6521264	1.0152356624603271	True
+18	54530	31.516268253326416	2.5625758171081543	779.1122436523438	0.8622342944145203	1009.1614990234375	0.5697469711303711	0.6531436	0.9992761611938477	True
+19	57400	31.365362882614136	0.5918254852294922	771.2922973632812	0.7296419143676758	1009.0079956054688	0.5705890655517578	0.6535513	0.9893749356269836	True

ENCSR000EPE/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+1009.0079956054688	0.26316535472869873	0.5705890655517578	0.29208746552467346	0.6535512804985046	0.625415563583374	0.9893749356269836

ENCSR000EPE/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": [
+        "ENCFF886GIK.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
+}

ENCSR000EPE/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": ["ENCFF886GIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPE/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	2829	36.196839809417725	3.561812162399292	786.0010375976562	1.808267593383789	1373.3779296875	0.30210328102111816	0.38748595	10.70151138305664	True
+1	5658	31.54254651069641	0.5992035865783691	743.031982421875	1.3126299381256104	1091.113525390625	0.48950907588005066	0.42028236	5.351587772369385	True
+2	8487	31.605315446853638	0.5846593379974365	767.1435546875	1.3080837726593018	1066.8770751953125	0.498821884393692	0.45046782	2.768411159515381	True
+3	11316	31.52387523651123	0.5856096744537354	772.4772338867188	1.550978660583496	1039.4959716796875	0.5135593414306641	0.4992065	2.0628957748413086	True
+4	14145	31.585339307785034	0.5871553421020508	593.5505981445312	1.639371395111084	1024.73974609375	0.5225862264633179	0.5087516	1.8905969858169556	True
+5	16974	31.81173849105835	1.2612922191619873	759.2040405273438	1.3233743906021118	1014.8815307617188	0.5289197564125061	0.51165205	1.7930867671966553	True
+6	19803	31.53491473197937	0.593759298324585	710.6025390625	1.005468726158142	1007.6441650390625	0.5329245328903198	0.52040684	1.4227877855300903	True
+7	22632	31.96468424797058	12.42509388923645	864.9491577148438	1.555382490158081	1003.74462890625	0.536169171333313	0.52214247	1.4727814197540283	True
+8	25461	31.551380395889282	0.6132054328918457	837.092041015625	1.318481206893921	994.1277465820312	0.5432424545288086	0.5376835	1.4552090167999268	True
+9	28290	31.555625200271606	38.14978909492493	711.3448486328125	1.0409998893737793	987.5689086914062	0.5487779974937439	0.544664	1.4356448650360107	True
+10	31119	31.61244034767151	0.5994992256164551	774.5654296875	0.8756771683692932	983.3353271484375	0.550004780292511	0.5622802	1.3441294431686401	True
+11	33948	31.57304835319519	0.5955801010131836	700.3660888671875	1.119907259941101	976.9782104492188	0.5529881119728088	0.5776113	1.2813383340835571	True
+12	36777	31.731894493103027	0.5888020992279053	667.11376953125	1.2159823179244995	968.9330444335938	0.5593166947364807	0.5898931	1.1851227283477783	True
+13	39606	30.94544792175293	5.295007228851318	780.063720703125	1.0635830163955688	960.8021240234375	0.563381016254425	0.60262966	1.0954928398132324	True
+14	42435	31.029564142227173	0.6003584861755371	637.9947509765625	0.9604262113571167	956.934814453125	0.5635767579078674	0.62240475	1.0169378519058228	True
+15	45264	30.94725728034973	2.5497195720672607	735.1708984375	0.8056915998458862	951.215576171875	0.5666701793670654	0.63966906	0.9226089715957642	True
+16	48093	30.948598861694336	0.6473939418792725	642.9849243164062	0.7838848829269409	947.492919921875	0.5708398222923279	0.65019965	0.8749755620956421	True
+17	50922	30.977333784103394	0.8298401832580566	604.5135498046875	0.6182050704956055	950.9067993164062	0.5656908750534058	0.6581987	0.8255462050437927	True
+18	53751	30.95190119743347	0.5833165645599365	658.15625	1.0343493223190308	951.9754028320312	0.563966691493988	0.6625204	0.8026671409606934	True
+19	56580	30.92426061630249	22.239772081375122	682.0557861328125	0.8429092168807983	947.3702392578125	0.569054901599884	0.66178536	0.8009200692176819	False

ENCSR000EPE/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+951.9754028320312	0.26615673303604126	0.5639666318893433	0.28140753507614136	0.6625204086303711	0.6396550536155701	0.8026671409606934

ENCSR000EPE/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,
+    "performance_filename": "cherimoya.fold_4.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF886GIK.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr11",
+        "chr12",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr20",
+        "chr22",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr10",
+        "chr18"
+    ],
+    "verbose": true
+}

ENCSR000EPE/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": ["ENCFF886GIK.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPE/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	2882	38.49072980880737	3.5811727046966553	671.4371337890625	2.046534299850464	1337.7308349609375	0.29115569591522217	0.3766402	8.455634117126465	True
+1	5764	32.11007809638977	0.5505938529968262	771.4268188476562	0.9717340469360352	1040.6575927734375	0.4923251271247864	0.44007003	4.4284162521362305	True
+2	8646	32.31590294837952	5.855639696121216	752.8776245117188	1.4100676774978638	1018.1504516601562	0.5031341910362244	0.4710623	2.4373233318328857	True
+3	11528	32.14732098579407	0.5678160190582275	958.7266235351562	1.574876308441162	1000.5355834960938	0.5122812390327454	0.4809833	1.6203376054763794	True
+4	14410	33.02458214759827	35.002113580703735	715.6976318359375	1.6785225868225098	990.5133056640625	0.5208989977836609	0.48695666	1.5242979526519775	True
+5	17292	33.92116594314575	0.5451579093933105	813.6959228515625	1.0530171394348145	979.9285278320312	0.52712082862854	0.5035356	1.468191146850586	True
+6	20174	32.38927507400513	0.5374393463134766	710.4749145507812	1.3473588228225708	971.9949951171875	0.532116711139679	0.5125814	1.354824185371399	True
+7	23056	32.29766798019409	0.5434002876281738	659.5466918945312	1.137615442276001	963.8596801757812	0.5378735661506653	0.5260935	1.2859052419662476	True
+8	25938	32.15622544288635	0.5215866565704346	788.880859375	1.0647554397583008	959.1807861328125	0.5415272116661072	0.53272355	1.234862208366394	True
+9	28820	32.142016649246216	2.0054049491882324	683.005615234375	1.3993650674819946	949.4007568359375	0.5484315752983093	0.5416045	1.2226556539535522	True
+10	31702	32.16132402420044	0.5173535346984863	708.5606689453125	0.8523225784301758	946.2661743164062	0.5506596565246582	0.54997164	1.2231217622756958	True
+11	34584	32.05324459075928	0.5210185050964355	842.9051513671875	1.2103502750396729	939.28955078125	0.5546566843986511	0.56708896	1.169904351234436	True
+12	37466	31.498767375946045	0.5225965976715088	734.9228515625	1.0949019193649292	932.218017578125	0.5591692924499512	0.5800133	1.0596904754638672	True
+13	40348	31.51175808906555	1.4274630546569824	732.3779907226562	0.6838642358779907	923.6762084960938	0.5639086365699768	0.6041349	0.9554522037506104	True
+14	43230	31.477846384048462	0.5187172889709473	582.4046630859375	1.4824020862579346	919.2134399414062	0.5660370588302612	0.6171519	0.9160320162773132	True
+15	46112	31.48838210105896	0.5209178924560547	715.848876953125	0.9768468141555786	913.7877197265625	0.5674595236778259	0.6364825	0.8652138113975525	True
+16	48994	32.54548788070679	7.211302995681763	604.1171875	0.8569585680961609	912.8018798828125	0.5678938627243042	0.6481239	0.8223201632499695	True
+17	51876	31.48903512954712	0.5235402584075928	621.8331298828125	0.7500333786010742	916.6021728515625	0.5615342855453491	0.6544389	0.7944949865341187	True
+18	54758	31.523166179656982	0.5209853649139404	607.681396484375	0.609472930431366	912.5831909179688	0.5668344497680664	0.65663975	0.7870913743972778	True
+19	57640	31.56042790412903	0.5192019939422607	666.9752197265625	0.706562876701355	910.5613403320312	0.5691413879394531	0.6557805	0.7880565524101257	False

ENCSR000EPE/cherimoya.fold_4.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+912.5831909179688	0.2681536376476288	0.5668344497680664	0.277569442987442	0.6566397547721863	0.6285704970359802	0.7870913743972778

ENCSR000EPI/cherimoya.fold_0.evaluate.json

@@ -0,0 +1,78 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_0.bed",
+        "valid_peaks.fold_0.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_0.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_0",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_0.bed",
+        "valid_nonpeaks.fold_0.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_0.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF361WNT.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "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"
+    ],
+    "verbose": true
+}

ENCSR000EPI/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": ["ENCFF361WNT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPI/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	2701	33.72053527832031	3.6355063915252686	446.0698547363281	1.0283124446868896	784.7523803710938	0.2537452280521393	0.35208324	10.358881950378418	True
+1	5402	29.73631477355957	0.6702766418457031	532.3466796875	1.0206891298294067	651.39013671875	0.41547903418540955	0.34727493	5.9280571937561035	False
+2	8103	29.784652709960938	0.6271979808807373	404.7937316894531	1.2623482942581177	635.1253662109375	0.43121299147605896	0.35129425	4.7182230949401855	False
+3	10804	29.839165449142456	0.6349520683288574	442.28680419921875	0.6648707389831543	623.9937133789062	0.4438357949256897	0.37110707	4.2998576164245605	True
+4	13505	29.80050539970398	0.6299481391906738	576.351806640625	0.9913849234580994	618.7778930664062	0.4511839747428894	0.3911216	3.4212558269500732	True
+5	16206	29.816713333129883	1.2248857021331787	383.5601806640625	0.8250505924224854	616.7493896484375	0.4550663232803345	0.39943424	2.8954126834869385	True
+6	18907	29.80165195465088	2.179473400115967	499.6912536621094	0.8513134717941284	612.6251831054688	0.45926234126091003	0.40268	2.7108891010284424	True
+7	21608	29.884414434432983	0.6473934650421143	491.42156982421875	0.8738479614257812	612.1724243164062	0.45898234844207764	0.40291572	2.347928285598755	True
+8	24309	29.823120832443237	1.3744871616363525	387.01190185546875	0.9362295866012573	606.0576782226562	0.46847832202911377	0.40089878	2.2338247299194336	False
+9	27010	29.9040629863739	0.6544132232666016	390.672607421875	0.7822617292404175	601.1358642578125	0.474587619304657	0.4095852	1.9327486753463745	True
+10	29711	29.894811153411865	0.6534533500671387	529.6018676757812	0.9800207018852234	598.4513549804688	0.4748231768608093	0.41550496	1.7135928869247437	True
+11	32412	29.85641312599182	1.258826732635498	510.07830810546875	0.6268941164016724	594.4310302734375	0.47933709621429443	0.4281301	1.589873194694519	True
+12	35113	29.343847036361694	17.509701251983643	511.38641357421875	0.9037981033325195	590.05322265625	0.48382967710494995	0.44420764	1.384640097618103	True
+13	37814	29.268084049224854	0.6348955631256104	375.46124267578125	0.539665699005127	585.1255493164062	0.4908427894115448	0.45924887	1.262079119682312	True
+14	40515	29.537575483322144	29.835891246795654	482.18603515625	0.7194722294807434	583.7503051757812	0.4913555085659027	0.47048175	1.2005480527877808	True
+15	43216	29.914562702178955	16.179364442825317	362.40997314453125	0.4372873306274414	581.412353515625	0.4916550815105438	0.48403147	1.1215183734893799	True
+16	45917	29.199795246124268	0.6511690616607666	475.70880126953125	0.6805984973907471	580.732177734375	0.49272799491882324	0.495435	1.0653460025787354	True
+17	48618	29.233484029769897	0.6470654010772705	388.55242919921875	0.46665430068969727	580.5968627929688	0.49242541193962097	0.5057831	1.0167614221572876	True
+18	51319	29.234070539474487	0.6396195888519287	327.80560302734375	0.6474743485450745	578.5520629882812	0.49739667773246765	0.5072197	0.9966776967048645	True
+19	54020	29.212243795394897	0.6259996891021729	374.1693115234375	0.6742918491363525	578.5504760742188	0.49659761786460876	0.50984854	0.9974396228790283	True

ENCSR000EPI/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+578.5504760742188	0.35265761613845825	0.49659761786460876	0.1616111695766449	0.5098485350608826	0.4925127625465393	0.9974396228790283

ENCSR000EPI/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,
+    "performance_filename": "cherimoya.fold_1.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF361WNT.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr10",
+        "chr11",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000EPI/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": ["ENCFF361WNT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPI/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	2705	33.652220010757446	4.350903272628784	502.2038879394531	1.2864981889724731	800.6216430664062	0.2598859369754791	0.39927748	8.152243614196777	True
+1	5410	29.847869873046875	0.7263627052307129	398.8472900390625	1.6376079320907593	672.0087890625	0.41396787762641907	0.43874642	6.209752559661865	True
+2	8115	29.817787647247314	7.905381679534912	501.379150390625	1.0475656986236572	646.91943359375	0.4387344419956207	0.43745497	5.181879997253418	False
+3	10820	29.878944873809814	0.7021071910858154	571.962158203125	1.0670894384384155	637.7833862304688	0.4447678029537201	0.45972264	3.8672900199890137	True
+4	13525	29.839561462402344	1.9502713680267334	404.711181640625	0.8195629119873047	629.0084838867188	0.4570932984352112	0.4691012	3.1482388973236084	True
+5	16230	29.880544424057007	0.7062387466430664	544.6640014648438	0.919963002204895	623.7394409179688	0.46453431248664856	0.4805619	2.82536244392395	True
+6	18935	29.878253698349	0.7220730781555176	417.14703369140625	0.8182042837142944	621.2433471679688	0.4662776589393616	0.48434454	2.455413579940796	True
+7	21640	29.860766649246216	0.694495677947998	427.13946533203125	0.8878934383392334	620.1968383789062	0.46855688095092773	0.4773662	2.2853634357452393	False
+8	24345	29.848095893859863	0.7007706165313721	440.12060546875	0.837647557258606	614.6098022460938	0.47506022453308105	0.49227202	2.135181427001953	True
+9	27050	29.854320526123047	0.6919431686401367	425.23333740234375	0.7752423286437988	612.0037231445312	0.47484177350997925	0.49251217	1.815971851348877	True
+10	29755	29.213339805603027	1.6275229454040527	310.96856689453125	0.9155052900314331	603.8772583007812	0.48366230726242065	0.50650847	1.59307062625885	True
+11	32460	29.30206871032715	0.6935675144195557	332.90020751953125	0.6574263572692871	599.0906982421875	0.4890819787979126	0.5208066	1.4068691730499268	True
+12	35165	29.329520225524902	0.7167942523956299	450.94036865234375	0.7617613077163696	594.8246459960938	0.49194982647895813	0.5353144	1.248846173286438	True
+13	37870	29.27392077445984	5.290344953536987	382.50823974609375	1.3586368560791016	589.78662109375	0.4961233139038086	0.5504275	1.085490345954895	True
+14	40575	29.432979106903076	0.7362678050994873	411.2650146484375	0.7839351892471313	588.117919921875	0.49832963943481445	0.56644917	1.0445996522903442	True
+15	43280	29.76820707321167	0.7075223922729492	498.9183044433594	0.9005905389785767	586.4996337890625	0.4964430630207062	0.5836305	0.928514301776886	True
+16	45985	29.37836718559265	0.6913423538208008	368.7276611328125	0.6072987914085388	583.83203125	0.49965065717697144	0.5978757	0.8657503724098206	True
+17	48690	29.371098518371582	0.695181131362915	458.7931213378906	0.5760496258735657	583.3997192382812	0.5006288886070251	0.604818	0.81740802526474	True
+18	51395	29.37100338935852	0.6931941509246826	440.05035400390625	0.4344760775566101	583.5562133789062	0.5005444288253784	0.6075169	0.7930137515068054	True
+19	54100	29.294178009033203	0.691727876663208	439.8524169921875	0.6774764657020569	580.740234375	0.5075662136077881	0.60746276	0.7849500179290771	False

ENCSR000EPI/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+583.5562133789062	0.3498181998729706	0.5005444288253784	0.1688748449087143	0.607516884803772	0.5889623761177063	0.7930137515068054

ENCSR000EPI/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_2.bed",
+        "valid_peaks.fold_2.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_2.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_2",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_2.bed",
+        "valid_nonpeaks.fold_2.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_2.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF361WNT.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr10",
+        "chr13",
+        "chr14",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chrX"
+    ],
+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR000EPI/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": ["ENCFF361WNT.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}