Remove per-fold metadata (restructure to checkpoints + aggregated tables)

ENCSR467LJT/cherimoya.fold_1.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2157	29.004281997680664	4.345808029174805	218.90696716308594	0.6240341067314148	449.0096435546875	0.16295403242111206	0.69403654	8.438509941101074	True
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-3	8628	24.009345769882202	0.6795654296875	245.93350219726562	0.4412629008293152	378.0001220703125	0.25167781114578247	0.8323945	1.2293639183044434	True
-4	10785	24.097275733947754	0.635286808013916	206.729736328125	0.6342784762382507	374.59051513671875	0.2575288712978363	0.83706415	1.0509233474731445	True
-5	12942	24.044113159179688	0.6407620906829834	302.634521484375	0.42338836193084717	372.49212646484375	0.2616983652114868	0.83978444	0.9428375959396362	True
-6	15099	24.053487539291382	0.6465814113616943	212.68629455566406	0.47745615243911743	371.84735107421875	0.2621639668941498	0.8438901	0.8561076521873474	True
-7	17256	24.05965828895569	0.6467432975769043	282.2359924316406	0.5857601165771484	370.897216796875	0.2624569833278656	0.85293925	0.796745777130127	True
-8	19413	24.0460262298584	25.18232035636902	275.90167236328125	0.38854432106018066	369.091064453125	0.2652784287929535	0.86341935	0.7094709873199463	True
-9	21570	24.83612370491028	0.6560506820678711	267.37786865234375	0.4230048656463623	368.2701416015625	0.2666720449924469	0.87039924	0.6258006691932678	True
-10	23727	24.090052127838135	1.178523302078247	277.1533203125	0.4519943594932556	366.1001281738281	0.27013644576072693	0.87567234	0.5658227205276489	True
-11	25884	24.02673649787903	0.6588599681854248	249.92576599121094	0.490795373916626	364.00750732421875	0.2733776569366455	0.8798358	0.52211594581604	True
-12	28041	23.95829486846924	0.6287455558776855	251.02841186523438	0.40349718928337097	363.8341369628906	0.273017942905426	0.885031	0.4878336489200592	True
-13	30198	23.987942218780518	1.4508624076843262	206.88294982910156	0.3934142589569092	363.106689453125	0.27327683568000793	0.8893095	0.46259286999702454	True
-14	32355	24.025190114974976	0.6436264514923096	261.58477783203125	0.3364369571208954	362.2783203125	0.2753002941608429	0.8920312	0.4404471218585968	True
-15	34512	23.9960196018219	0.6206316947937012	224.39749145507812	0.3925866484642029	361.7306823730469	0.2750157415866852	0.8936193	0.42792418599128723	True
-16	36669	24.014865398406982	0.627155065536499	190.0569610595703	0.4033634662628174	361.76873779296875	0.275055468082428	0.89398026	0.4234595000743866	True
-17	38826	23.524739503860474	0.6261730194091797	258.2326354980469	0.3021607995033264	361.8433532714844	0.275272399187088	0.89234036	0.4288408160209656	False
-18	40983	23.551204919815063	0.629690408706665	266.8482971191406	0.31008678674697876	361.94122314453125	0.27511587738990784	0.89148706	0.43459853529930115	False
-19	43140	23.482784032821655	0.6055786609649658	212.9467010498047	0.31127557158470154	362.484619140625	0.27419614791870117	0.89009255	0.4396456182003021	False

ENCSR467LJT/cherimoya.fold_1.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-361.76873779296875	0.4903869032859802	0.27505549788475037	0.09896761924028397	0.8939802646636963	0.8504928350448608	0.4234595000743866

ENCSR467LJT/cherimoya.fold_2.evaluate.json

@@ -1,76 +0,0 @@
-{
-    "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": [
-        "ENCFF020DFW.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
-}

ENCSR467LJT/cherimoya.fold_2.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR467LJT/cherimoya.fold_2.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2328	30.957398891448975	4.369951009750366	298.36669921875	0.5723681449890137	383.8170471191406	0.15430963039398193	0.67602044	6.674931526184082	True
-1	4656	25.834409475326538	0.5553956031799316	321.53924560546875	0.8425177931785583	336.7909851074219	0.21749556064605713	0.7919923	2.389535427093506	True
-2	6984	25.872389793395996	0.47730278968811035	332.1898193359375	0.7479868531227112	325.02471923828125	0.22616839408874512	0.81105506	1.261574387550354	True
-3	9312	25.82416534423828	1.5137896537780762	368.2694091796875	0.7534233331680298	321.6292419433594	0.23056969046592712	0.8158381	0.8802744746208191	True
-4	11640	25.884589433670044	0.46796464920043945	256.4305419921875	0.7111275792121887	319.89154052734375	0.2332727462053299	0.8203136	0.790863573551178	True
-5	13968	25.866905689239502	0.47620630264282227	254.88096618652344	0.5054042935371399	317.840087890625	0.23679856956005096	0.82807255	0.7704029679298401	True
-6	16296	25.863130807876587	0.4734492301940918	250.1759033203125	0.6042872071266174	317.11376953125	0.23828363418579102	0.8370407	0.7167477011680603	True
-7	18624	25.90097689628601	0.4758446216583252	231.944091796875	0.48279452323913574	315.8995666503906	0.24002127349376678	0.8434878	0.6686790585517883	True
-8	20952	25.824932098388672	0.4680445194244385	247.0543212890625	0.4901338815689087	314.7852478027344	0.24228082597255707	0.8480986	0.5795819163322449	True
-9	23280	25.81705665588379	0.7755386829376221	193.10928344726562	0.484529972076416	314.0762023925781	0.24341243505477905	0.8530997	0.5499141216278076	True
-10	25608	25.84494185447693	0.4955921173095703	174.24502563476562	0.5419780611991882	313.95819091796875	0.24390625953674316	0.85722286	0.5268793106079102	True
-11	27936	25.887707471847534	0.4758918285369873	257.103271484375	0.5516232252120972	312.4013671875	0.2462950497865677	0.8635692	0.494274377822876	True
-12	30264	25.87763261795044	0.4803178310394287	269.21533203125	0.6370142102241516	311.0347900390625	0.24867717921733856	0.8659347	0.46909022331237793	True
-13	32592	25.54821538925171	0.48775601387023926	279.34906005859375	0.3036620616912842	310.5636291503906	0.24851831793785095	0.8694566	0.4483329653739929	True
-14	34920	25.359986782073975	0.4672698974609375	181.44052124023438	0.27858126163482666	309.88104248046875	0.24877971410751343	0.87297434	0.4305245876312256	True
-15	37248	25.400776863098145	0.49015164375305176	296.0634460449219	0.36968332529067993	310.0763244628906	0.24829678237438202	0.874711	0.4207945764064789	True
-16	39576	25.3391854763031	0.473949670791626	213.7939453125	0.35844072699546814	309.3413391113281	0.249907985329628	0.8751178	0.4135192036628723	True
-17	41904	25.35158395767212	0.4724152088165283	222.5930938720703	0.3652615249156952	309.5668640136719	0.24967442452907562	0.8735285	0.41705322265625	False
-18	44232	25.36330008506775	0.4767277240753174	299.79937744140625	0.28422659635543823	310.13916015625	0.24813199043273926	0.87254775	0.4232114851474762	False
-19	46560	25.338587999343872	0.46153950691223145	258.6544189453125	0.42853662371635437	310.2540283203125	0.2481793314218521	0.8713608	0.4284152686595917	False

ENCSR467LJT/cherimoya.fold_2.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-309.3413391113281	0.5117379426956177	0.249907985329628	0.08273471146821976	0.8751177787780762	0.8132820129394531	0.4135192036628723

ENCSR467LJT/cherimoya.fold_3.evaluate.json

@@ -1,75 +0,0 @@
-{
-    "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": [
-        "ENCFF020DFW.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
-}

ENCSR467LJT/cherimoya.fold_3.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR467LJT/cherimoya.fold_3.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2220	29.373500108718872	4.014675855636597	237.9110107421875	0.7583791017532349	377.0010681152344	0.1640334129333496	0.65754473	7.050030708312988	True
-1	4440	24.672168254852295	0.585848331451416	223.41761779785156	0.5494495630264282	339.81207275390625	0.22099129855632782	0.7603483	2.7817165851593018	True
-2	6660	24.69326400756836	0.44088292121887207	274.42578125	0.6891855597496033	330.27203369140625	0.22791382670402527	0.7777716	2.0235610008239746	True
-3	8880	24.679396152496338	0.4665224552154541	307.3570861816406	0.8959121704101562	323.72265625	0.2367897480726242	0.7927507	1.2830734252929688	True
-4	11100	24.719976663589478	0.47878551483154297	288.76641845703125	0.4867706298828125	320.9180603027344	0.24076971411705017	0.8042237	1.064479112625122	True
-5	13320	24.656165838241577	0.4409949779510498	267.31512451171875	0.705441415309906	319.04827880859375	0.24500979483127594	0.813288	0.9328219294548035	True
-6	15540	24.680514812469482	0.44230222702026367	211.9906005859375	0.4786945581436157	318.4001159667969	0.2458130568265915	0.82122916	0.8856309652328491	True
-7	17760	24.670480012893677	2.8332014083862305	238.42501831054688	0.4362431466579437	317.1965637207031	0.24773447215557098	0.8250792	0.8061318397521973	True
-8	19980	24.79328179359436	0.6447129249572754	235.80941772460938	0.6067725419998169	316.7680358886719	0.24835945665836334	0.82991713	0.7505665421485901	True
-9	22200	24.6892511844635	1.1776378154754639	218.4635772705078	0.7052568197250366	315.6273193359375	0.2504734694957733	0.8414965	0.6552781462669373	True
-10	24420	24.72346806526184	0.45548224449157715	282.8542175292969	0.4025379419326782	313.932861328125	0.25383973121643066	0.8482022	0.6227776408195496	True
-11	26640	24.81953763961792	0.4810347557067871	254.3394012451172	0.4130623936653137	313.1915283203125	0.2548346519470215	0.8537328	0.5601872801780701	True
-12	28860	25.251795291900635	8.261584997177124	212.186279296875	0.42780470848083496	312.1534423828125	0.25590330362319946	0.8615689	0.5023173093795776	True
-13	31080	24.707439184188843	0.4438023567199707	249.89932250976562	0.4790124297142029	311.10601806640625	0.25762274861335754	0.8664647	0.4797164797782898	True
-14	33300	24.762505531311035	0.4501333236694336	261.9554138183594	0.3606957197189331	310.6464538574219	0.25831636786460876	0.8709837	0.4647753834724426	True
-15	35520	24.71336317062378	0.45760655403137207	248.986572265625	0.4202633500099182	309.98138427734375	0.2592966854572296	0.8715249	0.4531456232070923	True
-16	37740	24.739706993103027	0.4594602584838867	268.5704650878906	0.24075326323509216	309.70355224609375	0.2592305839061737	0.8760969	0.4386473298072815	True
-17	39960	24.68956208229065	0.43525242805480957	251.80593872070312	0.5225629806518555	309.90411376953125	0.25825008749961853	0.873098	0.43833616375923157	False
-18	42180	24.711355924606323	0.7237522602081299	269.1609191894531	0.2779829502105713	310.0084533691406	0.2581581175327301	0.873092	0.4434809684753418	False
-19	44400	24.700833797454834	1.02180814743042	222.86453247070312	0.25582826137542725	310.0467529296875	0.2582261264324188	0.8711389	0.44543492794036865	False

ENCSR467LJT/cherimoya.fold_3.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-309.70355224609375	0.5064390301704407	0.2592305839061737	0.08393268287181854	0.8760969042778015	0.8067934513092041	0.4386473298072815

ENCSR467LJT/cherimoya.fold_4.evaluate.json

@@ -1,75 +0,0 @@
-{
-    "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": [
-        "ENCFF020DFW.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
-}

ENCSR467LJT/cherimoya.fold_4.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF020DFW.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR467LJT/cherimoya.fold_4.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2242	29.40229821205139	4.798060417175293	243.32864379882812	0.8159230947494507	329.9683837890625	0.1522715836763382	0.6785965	5.749883651733398	True
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-3	8968	25.01275134086609	0.4708080291748047	197.98829650878906	0.5497087836265564	285.3414611816406	0.2158796191215515	0.8066834	0.9143130779266357	True
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-6	15694	24.958878993988037	0.4538722038269043	198.30810546875	0.7167954444885254	279.59881591796875	0.2257377654314041	0.8278702	0.6221991777420044	True
-7	17936	24.950188636779785	0.4512791633605957	232.228515625	0.5131058692932129	279.0624084472656	0.22618955373764038	0.8352064	0.568234384059906	True
-8	20178	25.019976139068604	0.45183444023132324	232.2249755859375	0.43961232900619507	278.0964050292969	0.22751228511333466	0.8421569	0.5267385244369507	True
-9	22420	24.993887186050415	0.4636268615722656	253.37081909179688	0.4464433491230011	277.7956848144531	0.22725602984428406	0.84883064	0.49012118577957153	True
-10	24662	24.962198972702026	0.4574863910675049	227.00833129882812	0.5691692233085632	276.6934509277344	0.23010119795799255	0.8533354	0.45726674795150757	True
-11	26904	24.92859196662903	0.460446834564209	263.83538818359375	0.4608685374259949	275.7777099609375	0.2318161278963089	0.85756135	0.43294140696525574	True
-12	29146	25.019882678985596	0.6262338161468506	301.388671875	0.49216729402542114	275.59600830078125	0.23111554980278015	0.8629033	0.40099719166755676	True
-13	31388	25.040348291397095	0.4608278274536133	175.54190063476562	0.5945791602134705	274.8765869140625	0.23280684649944305	0.86674607	0.3906096816062927	True
-14	33630	25.001235246658325	1.3581666946411133	223.85963439941406	0.2824428379535675	274.3114318847656	0.23390182852745056	0.8691913	0.38023456931114197	True
-15	35872	25.01939582824707	0.4562251567840576	176.67539978027344	0.33403903245925903	274.68658447265625	0.2329588085412979	0.8731895	0.37201666831970215	True
-16	38114	25.077432870864868	9.207828998565674	200.94464111328125	0.291690468788147	274.506103515625	0.23341098427772522	0.8732759	0.36817067861557007	True
-17	40356	25.05478286743164	0.46390295028686523	234.20565795898438	0.3048962652683258	274.3995056152344	0.23402093350887299	0.87385345	0.37039610743522644	True
-18	42598	25.05311346054077	0.45523595809936523	299.55242919921875	0.355121910572052	274.883544921875	0.23348468542099	0.8717356	0.37505394220352173	False
-19	44840	25.078444719314575	0.4569435119628906	246.9058837890625	0.28614816069602966	275.0286560058594	0.2333877980709076	0.8716158	0.3795240521430969	False

ENCSR467LJT/cherimoya.fold_4.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-274.3995056152344	0.5255016684532166	0.23402093350887299	0.07348351925611496	0.8738534450531006	0.7927107214927673	0.37039610743522644

ENCSR468AKF/cherimoya.fold_0.evaluate.json

@@ -1,78 +0,0 @@
-{
-    "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": [
-        "ENCFF802PTA.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
-}

ENCSR468AKF/cherimoya.fold_0.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR468AKF/cherimoya.fold_0.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2700	34.53184628486633	4.246556758880615	540.1788330078125	0.5354247093200684	870.1289672851562	0.1465969681739807	0.7047552	5.779707908630371	True
-1	5400	30.084356546401978	0.6116464138031006	586.654541015625	0.4267949163913727	805.9110717773438	0.18598568439483643	0.7465209	2.123725652694702	True
-2	8100	30.071836709976196	4.891034364700317	789.7887573242188	0.4573359787464142	790.0303344726562	0.1915401965379715	0.7574442	1.9253629446029663	True
-3	10800	30.136012077331543	1.200418472290039	562.2957763671875	0.3892439901828766	777.0252075195312	0.19608677923679352	0.7673519	1.37836754322052	True
-4	13500	30.0900616645813	1.30403470993042	598.7669677734375	0.4435843229293823	773.0532836914062	0.19925262033939362	0.76985687	1.6410889625549316	True
-5	16200	30.086731672286987	1.41023588180542	565.0001220703125	0.44866424798965454	768.3670043945312	0.20251795649528503	0.7716579	1.0203944444656372	True
-6	18900	30.07952094078064	0.8307838439941406	699.30517578125	0.46853065490722656	763.350341796875	0.20508119463920593	0.7791775	0.9040338397026062	True
-7	21600	30.08034324645996	0.7563855648040771	610.825439453125	0.4682616591453552	759.7859497070312	0.20704729855060577	0.7781309	0.8864566087722778	False
-8	24300	30.17010259628296	1.0950257778167725	655.1136474609375	0.30057525634765625	755.616943359375	0.20940124988555908	0.79048896	0.791576087474823	True
-9	27000	30.10038161277771	0.609473466873169	677.555419921875	0.4422271251678467	751.7435302734375	0.21175315976142883	0.7893171	0.6735851168632507	False
-10	29700	30.106525182724	0.6115241050720215	588.8417358398438	0.3262351155281067	748.2215576171875	0.21421748399734497	0.80182695	0.5938320159912109	True
-11	32400	30.082067728042603	0.5892620086669922	604.8009033203125	0.41578638553619385	745.0718383789062	0.21677570044994354	0.8057326	0.5276010036468506	True
-12	35100	30.117863655090332	0.6165018081665039	597.7386474609375	0.2968935966491699	741.156982421875	0.21876615285873413	0.8216236	0.452260822057724	True
-13	37800	30.03753972053528	0.6158668994903564	650.5154418945312	0.42246735095977783	738.3958740234375	0.22018657624721527	0.8292709	0.38825592398643494	True
-14	40500	29.635724544525146	0.619408130645752	527.0230712890625	0.3252446949481964	736.2117309570312	0.22139514982700348	0.8380458	0.3401283919811249	True
-15	43200	29.61504888534546	0.5852797031402588	648.791259765625	0.37145453691482544	734.0404663085938	0.22253572940826416	0.84548116	0.30396586656570435	True
-16	45900	29.492364168167114	0.9941599369049072	560.885009765625	0.304751455783844	732.7819213867188	0.22319556772708893	0.85011566	0.28326183557510376	True
-17	48600	29.56808590888977	4.765033483505249	581.6475830078125	0.26267024874687195	732.7562255859375	0.2233169823884964	0.85282695	0.27046090364456177	True
-18	51300	29.5568265914917	1.3330333232879639	717.1151123046875	0.4670168161392212	732.7011108398438	0.22328726947307587	0.8518253	0.2657153308391571	False
-19	54000	29.53577160835266	1.837637186050415	742.416748046875	0.22048808634281158	733.718505859375	0.2222825288772583	0.8511464	0.2678168714046478	False

ENCSR468AKF/cherimoya.fold_0.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-732.7562255859375	0.5181871652603149	0.2233169823884964	0.07858559489250183	0.8528269529342651	0.775798499584198	0.27046090364456177

ENCSR468AKF/cherimoya.fold_1.evaluate.json

@@ -1,77 +0,0 @@
-{
-    "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": [
-        "ENCFF802PTA.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
-}

ENCSR468AKF/cherimoya.fold_1.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR468AKF/cherimoya.fold_1.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2700	35.110148429870605	5.31849217414856	740.217529296875	0.6163145303726196	1067.446044921875	0.16267447173595428	0.70454526	6.341463088989258	True
-1	5400	30.078912258148193	1.159745216369629	670.8892211914062	0.30731716752052307	981.2007446289062	0.2119743674993515	0.7543692	2.5257065296173096	True
-2	8100	30.215314865112305	0.6675901412963867	862.816650390625	0.6436439752578735	968.0450439453125	0.21466664969921112	0.7584295	1.5596991777420044	True
-3	10800	30.02474808692932	0.6845800876617432	583.52978515625	0.3188720941543579	944.7877807617188	0.22015444934368134	0.77422255	1.2356407642364502	True
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-5	16200	30.049926280975342	0.6717357635498047	684.2567138671875	0.4007314443588257	922.8765258789062	0.23060087859630585	0.789666	1.2157261371612549	True
-6	18900	30.03618359565735	0.682044506072998	629.4078369140625	0.38477009534835815	912.6483764648438	0.23569422960281372	0.8004368	0.9315680265426636	True
-7	21600	30.00295925140381	0.6860721111297607	680.3038330078125	0.6521528959274292	904.23486328125	0.23975525796413422	0.8099597	0.7661095261573792	True
-8	24300	30.059695720672607	0.6828789710998535	638.947998046875	0.45898112654685974	898.083251953125	0.24376904964447021	0.81484216	0.7529616355895996	True
-9	27000	30.012684106826782	0.6907365322113037	544.0966186523438	0.3254051208496094	892.6824951171875	0.2463182955980301	0.8188436	0.6664518713951111	True
-10	29700	29.862866163253784	0.9076955318450928	803.6492309570312	0.3582063615322113	888.966552734375	0.2486461102962494	0.8258992	0.612616240978241	True
-11	32400	29.481706619262695	0.6901493072509766	512.0106201171875	0.2903206944465637	882.3929443359375	0.2517603039741516	0.83429813	0.5307910442352295	True
-12	35100	29.58592915534973	0.6830568313598633	628.1718139648438	0.42885246872901917	879.8851318359375	0.2532693147659302	0.8367135	0.49500030279159546	True
-13	37800	29.493680715560913	0.6839761734008789	507.939208984375	0.4495972692966461	875.9747924804688	0.25507116317749023	0.8429923	0.44097089767456055	True
-14	40500	29.53846526145935	0.6784670352935791	660.6773681640625	0.5520167350769043	873.6510009765625	0.25596195459365845	0.8479814	0.4074352979660034	True
-15	43200	29.538565635681152	0.6865084171295166	596.874755859375	0.29975640773773193	871.2749633789062	0.2570219039916992	0.8548362	0.3738476634025574	True
-16	45900	29.515236377716064	0.6895921230316162	616.0631103515625	0.2620546519756317	870.9697265625	0.2570396363735199	0.85755116	0.34989216923713684	True
-17	48600	29.561330318450928	0.6885027885437012	628.6565551757812	0.23962578177452087	871.8929443359375	0.2559640109539032	0.861487	0.33034488558769226	True
-18	51300	29.432849407196045	0.6692924499511719	574.808837890625	0.22924895584583282	871.0437622070312	0.2567293345928192	0.8615629	0.32718008756637573	True
-19	54000	29.55951237678528	0.678765058517456	703.466796875	0.37332046031951904	869.5344848632812	0.25778526067733765	0.8633624	0.3236086368560791	True

ENCSR468AKF/cherimoya.fold_1.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-869.5344848632812	0.489761620759964	0.25778526067733765	0.0970606878399849	0.8633623719215393	0.8231304883956909	0.3236086368560791

ENCSR468AKF/cherimoya.fold_2.evaluate.json

@@ -1,76 +0,0 @@
-{
-    "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": [
-        "ENCFF802PTA.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
-}

ENCSR468AKF/cherimoya.fold_2.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR468AKF/cherimoya.fold_2.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2872	36.76777362823486	4.987877368927002	689.917236328125	0.5091899633407593	913.473876953125	0.15265026688575745	0.6967678	5.281152248382568	True
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-5	17232	31.870599508285522	0.5670163631439209	905.6663818359375	0.680645227432251	796.51513671875	0.21320652961730957	0.78820366	0.9948855638504028	True
-6	20104	31.827136516571045	0.5654220581054688	610.865966796875	0.4374069273471832	793.2418823242188	0.2143774777650833	0.79278624	0.9387199878692627	True
-7	22976	31.83517098426819	1.1641442775726318	627.3095703125	0.6587705612182617	786.8984375	0.21905767917633057	0.79595166	0.9054584503173828	True
-8	25848	31.836780309677124	0.6620094776153564	720.759033203125	0.4709663987159729	781.7841796875	0.22210292518138885	0.8023588	0.8195104598999023	True
-9	28720	31.163194179534912	0.5567798614501953	699.9115600585938	0.7167593240737915	779.7433471679688	0.22295255959033966	0.8079195	0.6882292628288269	True
-10	31592	31.18947958946228	0.5566184520721436	643.1558837890625	0.36031895875930786	775.9397583007812	0.22571402788162231	0.81731576	0.6246585249900818	True
-11	34464	31.27164077758789	0.5602819919586182	545.8026733398438	0.34331485629081726	773.0084228515625	0.22735662758350372	0.8207879	0.5310454368591309	True
-12	37336	31.27588129043579	0.5489239692687988	557.034423828125	0.20138156414031982	768.7924194335938	0.22975000739097595	0.8284372	0.45092517137527466	True
-13	40208	31.267271757125854	0.5399675369262695	732.2521362304688	0.3669765889644623	765.95849609375	0.23144292831420898	0.8320073	0.4013162851333618	True
-14	43080	31.245118379592896	0.546663761138916	624.47412109375	0.1507047414779663	762.9948120117188	0.23300574719905853	0.8382265	0.35457611083984375	True
-15	45952	31.23732352256775	0.5604374408721924	614.6566162109375	0.2915021777153015	761.7932739257812	0.23285050690174103	0.84535235	0.322864294052124	True
-16	48824	31.27571177482605	0.55084228515625	617.7450561523438	0.22292816638946533	758.5901489257812	0.2346441149711609	0.8504	0.300458163022995	True
-17	51696	31.23516535758972	0.5594170093536377	662.895263671875	0.2876027822494507	758.879150390625	0.2340567260980606	0.8532072	0.2880484163761139	True
-18	54568	31.30744242668152	0.5471920967102051	712.5159912109375	0.3463767170906067	759.0877075195312	0.23384816944599152	0.8530109	0.28372350335121155	False
-19	57440	31.281824350357056	0.5416803359985352	690.4034423828125	0.28306230902671814	761.1979370117188	0.23238971829414368	0.85256577	0.2842600345611572	False

ENCSR468AKF/cherimoya.fold_2.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-758.879150390625	0.5100278854370117	0.2340567260980606	0.0877637267112732	0.8532071709632874	0.7905654311180115	0.2880484163761139

ENCSR468AKF/cherimoya.fold_3.evaluate.json

@@ -1,75 +0,0 @@
-{
-    "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": [
-        "ENCFF802PTA.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
-}

ENCSR468AKF/cherimoya.fold_3.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR468AKF/cherimoya.fold_3.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2738	35.29062032699585	4.35115122795105	603.5126953125	0.7188969850540161	901.2633056640625	0.15860867500305176	0.6998956	5.545566558837891	True
-1	5476	30.432868003845215	0.5868375301361084	599.5777587890625	0.5643138289451599	839.5177612304688	0.19653011858463287	0.7399232	2.207456111907959	True
-2	8214	30.471753120422363	0.6059463024139404	704.18017578125	0.5630444884300232	828.5056762695312	0.20165158808231354	0.7423678	1.6849555969238281	True
-3	10952	30.408527374267578	0.5795340538024902	555.9869995117188	0.33595389127731323	815.5125732421875	0.20610445737838745	0.76435745	1.277631163597107	True
-4	13690	30.35874915122986	0.5655333995819092	958.282470703125	0.4684061110019684	806.5045166015625	0.20946063101291656	0.77313787	1.2439420223236084	True
-5	16428	30.38255763053894	0.5681741237640381	773.9354248046875	0.6919560432434082	801.8505859375	0.21203695237636566	0.7781277	1.0485373735427856	True
-6	19166	30.398789167404175	0.5745680332183838	702.3316650390625	0.5524909496307373	794.78466796875	0.21673108637332916	0.7801492	0.9654102325439453	True
-7	21904	30.41829013824463	0.5764923095703125	685.5820922851562	0.4896143078804016	792.14892578125	0.21822884678840637	0.7867088	0.8436633348464966	True
-8	24642	30.430070877075195	0.5759172439575195	613.918701171875	0.4496604800224304	786.9740600585938	0.2223445326089859	0.7873469	0.8034684658050537	True
-9	27380	30.42865562438965	0.9279663562774658	566.2606811523438	0.44430065155029297	783.099365234375	0.22452259063720703	0.79378814	0.7336609363555908	True
-10	30118	29.893153190612793	2.1205666065216064	573.4056396484375	0.3278481364250183	778.9863891601562	0.227333664894104	0.80329376	0.6252869963645935	True
-11	32856	29.796116828918457	0.6189441680908203	710.1932373046875	0.4782615602016449	775.8483276367188	0.22911794483661652	0.8116937	0.554884672164917	True
-12	35594	29.820044994354248	0.5765419006347656	644.9088134765625	0.5450025796890259	772.0517578125	0.23119065165519714	0.8199762	0.4998316764831543	True
-13	38332	29.798156261444092	0.5573503971099854	535.409912109375	0.42434054613113403	770.5150756835938	0.23197709023952484	0.82693785	0.44355249404907227	True
-14	41070	29.784976959228516	0.5763895511627197	630.215576171875	0.30756083130836487	766.5259399414062	0.23389585316181183	0.8403965	0.38449299335479736	True
-15	43808	29.77325415611267	2.4492952823638916	560.9559326171875	0.42113107442855835	763.4361572265625	0.23546752333641052	0.84714806	0.3484429121017456	True
-16	46546	29.814138174057007	0.5666983127593994	611.4329223632812	0.30768951773643494	762.184326171875	0.23559902608394623	0.8542012	0.31467512249946594	True
-17	49284	29.95028519630432	0.5745346546173096	598.6697998046875	0.3409164547920227	760.93896484375	0.23633714020252228	0.8571265	0.30144113302230835	True
-18	52022	29.983092546463013	0.601459264755249	743.9840087890625	0.41827213764190674	761.7097778320312	0.23573586344718933	0.85775894	0.2920428216457367	True
-19	54760	29.94750738143921	0.5822932720184326	594.3375244140625	0.19299045205116272	761.0687255859375	0.23606762290000916	0.8574681	0.2921421229839325	False

ENCSR468AKF/cherimoya.fold_3.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-761.7097778320312	0.5096011757850647	0.23573584854602814	0.08410030603408813	0.8577589392662048	0.7952336072921753	0.2920428216457367

ENCSR468AKF/cherimoya.fold_4.evaluate.json

@@ -1,75 +0,0 @@
-{
-    "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": [
-        "ENCFF802PTA.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
-}

ENCSR468AKF/cherimoya.fold_4.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF802PTA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR468AKF/cherimoya.fold_4.log

@@ -1,21 +0,0 @@
-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	36.65672969818115	3.925086736679077	602.6295166015625	0.5058010816574097	810.3133544921875	0.14498166739940643	0.6950701	3.916970729827881	True
-1	5740	31.894332885742188	1.054889440536499	729.62890625	0.5241798758506775	760.6547241210938	0.179341122508049	0.73461705	1.6287617683410645	True
-2	8610	31.848507165908813	20.881136894226074	541.7992553710938	0.33130964636802673	755.543701171875	0.1808495968580246	0.73900306	1.4010721445083618	True
-3	11480	31.90997815132141	0.5816571712493896	617.76416015625	0.3557058870792389	742.29296875	0.18653526902198792	0.7538743	1.084520936012268	True
-4	14350	31.838807344436646	0.5883963108062744	551.9675903320312	0.2973549962043762	733.8203735351562	0.19097307324409485	0.76629573	0.9259946942329407	True
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-6	20090	31.903775930404663	0.5692753791809082	595.8902587890625	0.39909130334854126	724.6183471679688	0.19692185521125793	0.7713115	0.7485531568527222	False
-7	22960	31.78365731239319	0.5699787139892578	710.30908203125	0.45688962936401367	720.8743286132812	0.19934846460819244	0.7771055	0.6922053694725037	True
-8	25830	31.884737253189087	0.5825695991516113	567.7037963867188	0.3415842056274414	716.7478637695312	0.2019454538822174	0.78281265	0.6008278727531433	True
-9	28700	31.824278354644775	0.5813689231872559	569.2457275390625	0.25725728273391724	712.331298828125	0.2053108811378479	0.78747606	0.5867178440093994	True
-10	31570	31.871450185775757	0.5839660167694092	702.747314453125	0.4379296600818634	710.2244873046875	0.20647604763507843	0.7919077	0.508714497089386	True
-11	34440	31.55432391166687	0.5637094974517822	566.9411010742188	0.26667559146881104	708.686279296875	0.20691105723381042	0.80169004	0.44186821579933167	True
-12	37310	31.282638788223267	0.5647127628326416	643.962646484375	0.28493988513946533	705.6832275390625	0.209548220038414	0.80618775	0.4076055884361267	True
-13	40180	31.295836448669434	0.574429988861084	646.8902587890625	0.29192012548446655	702.8076782226562	0.21101818978786469	0.81175226	0.3574290871620178	True
-14	43050	31.27675151824951	0.575340986251831	672.7355346679688	0.42766064405441284	701.1837768554688	0.21189025044441223	0.8204361	0.3196117579936981	True
-15	45920	31.332534313201904	0.5624172687530518	663.3055419921875	0.21120920777320862	699.9169311523438	0.21236979961395264	0.82734144	0.2917844355106354	True
-16	48790	31.22429370880127	1.313843011856079	652.0831298828125	0.1936098039150238	697.4733276367188	0.2139783799648285	0.8308928	0.2753196656703949	True
-17	51660	31.258325576782227	0.5787553787231445	601.952880859375	0.2675396203994751	698.6926879882812	0.21330271661281586	0.83333695	0.2662739157676697	True
-18	54530	31.371049880981445	2.1235411167144775	593.5293579101562	0.41808873414993286	698.3933715820312	0.21341992914676666	0.834366	0.2649255692958832	True
-19	57400	31.30956482887268	0.5842127799987793	656.4630126953125	0.22137300670146942	699.45068359375	0.21269509196281433	0.83483785	0.2649456858634949	True

ENCSR468AKF/cherimoya.fold_4.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-699.45068359375	0.524977445602417	0.21269510686397552	0.07152768224477768	0.8348378539085388	0.7562339305877686	0.2649456858634949

ENCSR470QCE/cherimoya.fold_0.evaluate.json

@@ -1,78 +0,0 @@
-{
-    "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": [
-        "ENCFF724DCZ.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
-}

ENCSR470QCE/cherimoya.fold_0.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR470QCE/cherimoya.fold_0.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2189	28.053953409194946	3.484429121017456	185.67962646484375	0.48218926787376404	266.221923828125	0.1358102411031723	0.6755686	5.203961372375488	True
-1	4378	24.4992253780365	0.5101828575134277	214.12203979492188	0.5292813777923584	249.59510803222656	0.17847689986228943	0.77221173	1.6616380214691162	True
-2	6567	24.59465789794922	0.47454261779785156	235.46212768554688	0.6517711877822876	241.79356384277344	0.19502274692058563	0.795548	1.0399924516677856	True
-3	8756	24.539169311523438	0.473466157913208	229.3111114501953	0.48582449555397034	240.32235717773438	0.19622208178043365	0.8042369	0.6416451930999756	True
-4	10945	24.540164470672607	0.4790670871734619	259.4090270996094	0.6754955053329468	239.4961395263672	0.19765885174274445	0.8124515	0.6226841807365417	True
-5	13134	24.54255962371826	0.47919607162475586	200.816162109375	0.5221608877182007	238.45257568359375	0.2009766548871994	0.8180308	0.5478722453117371	True
-6	15323	24.556038856506348	0.473330020904541	212.64923095703125	0.3964870572090149	237.940673828125	0.20172040164470673	0.8271933	0.4933921992778778	True
-7	17512	24.5770161151886	0.4681425094604492	239.22796630859375	0.465505987405777	237.3773956298828	0.20378968119621277	0.83443785	0.45561015605926514	True
-8	19701	24.596145391464233	0.4692401885986328	195.85157775878906	0.5970571041107178	236.7889404296875	0.2060587853193283	0.8391307	0.43025410175323486	True
-9	21890	24.612333059310913	0.4791452884674072	205.19903564453125	0.44339269399642944	236.15065002441406	0.20744745433330536	0.8470647	0.4037206768989563	True
-10	24079	24.60275387763977	0.47583699226379395	213.37481689453125	0.5588750839233398	235.56089782714844	0.20920100808143616	0.84968245	0.3747442662715912	True
-11	26268	24.555014610290527	0.4752652645111084	190.6841583251953	0.29460474848747253	235.18589782714844	0.2097613662481308	0.85399055	0.3426697254180908	True
-12	28457	24.550138235092163	0.4801621437072754	242.9832305908203	0.45178988575935364	234.53330993652344	0.2116590291261673	0.85779786	0.3291322588920593	True
-13	30646	24.55565595626831	0.48270273208618164	241.68157958984375	0.30507951974868774	234.30084228515625	0.2119046151638031	0.86407626	0.3119838833808899	True
-14	32835	24.54386568069458	0.4854271411895752	211.8201446533203	0.35724809765815735	234.5738525390625	0.21059618890285492	0.86516136	0.3038789629936218	True
-15	35024	24.569430351257324	0.48129749298095703	227.66598510742188	0.294256329536438	233.848388671875	0.21269425749778748	0.8673439	0.29746100306510925	True
-16	37213	24.542653799057007	0.4831833839416504	219.66795349121094	0.23689240217208862	233.8106231689453	0.21297475695610046	0.86844707	0.2941966950893402	True
-17	39402	24.527894258499146	0.4826836585998535	183.1907958984375	0.24651119112968445	234.12001037597656	0.2122344672679901	0.86850137	0.2970339357852936	True
-18	41591	25.051077365875244	0.4832437038421631	264.0255432128906	0.19670169055461884	234.197021484375	0.21161732077598572	0.8666403	0.29872408509254456	False
-19	43780	24.59147596359253	17.7651686668396	223.74771118164062	0.22705848515033722	234.3199005126953	0.211395263671875	0.8657973	0.3008439242839813	False

ENCSR470QCE/cherimoya.fold_0.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-234.12001037597656	0.540611743927002	0.2122344672679901	0.06027243658900261	0.8685013651847839	0.7890928387641907	0.2970339357852936

ENCSR470QCE/cherimoya.fold_1.evaluate.json

@@ -1,77 +0,0 @@
-{
-    "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": [
-        "ENCFF724DCZ.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
-}

ENCSR470QCE/cherimoya.fold_1.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR470QCE/cherimoya.fold_1.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2156	28.038177013397217	3.5459201335906982	178.22218322753906	0.806788444519043	325.5743713378906	0.14986765384674072	0.67217517	6.2728753089904785	True
-1	4312	24.09299111366272	0.63681960105896	144.5338592529297	0.471341073513031	303.78692626953125	0.19974404573440552	0.7784334	2.215684652328491	True
-2	6468	24.186156749725342	15.235931158065796	225.92416381835938	0.48742324113845825	295.11669921875	0.21523067355155945	0.8022683	1.2483755350112915	True
-3	8624	24.105112314224243	0.6286320686340332	212.00372314453125	0.6040753126144409	290.85028076171875	0.2228430211544037	0.8142588	0.7900233864784241	True
-4	10780	24.107173442840576	0.6320648193359375	214.6367950439453	0.5386284589767456	289.75360107421875	0.2249409258365631	0.8144423	0.7336066961288452	True
-5	12936	24.094627380371094	0.6336474418640137	202.50511169433594	0.3935820758342743	288.67828369140625	0.2277105301618576	0.8248313	0.67357337474823	True
-6	15092	24.117287635803223	0.630840539932251	202.79269409179688	0.41708433628082275	288.3797912597656	0.22831258177757263	0.8299284	0.6505731344223022	True
-7	17248	24.114730834960938	0.6206467151641846	221.83377075195312	0.44319218397140503	287.6688537597656	0.23081815242767334	0.8367577	0.6284686326980591	True
-8	19404	24.573179006576538	1.6967904567718506	175.0400848388672	0.29271259903907776	286.2613830566406	0.23362436890602112	0.84862274	0.5515958666801453	True
-9	21560	24.183651447296143	0.6577596664428711	183.85098266601562	0.41309410333633423	285.35357666015625	0.2357841581106186	0.85691667	0.4566918611526489	True
-10	23716	24.176458597183228	1.5152661800384521	237.71102905273438	0.43800264596939087	284.6572570800781	0.23722365498542786	0.8630643	0.42572021484375	True
-11	25872	24.238288402557373	0.6444151401519775	222.3145751953125	0.2892971336841583	284.1981506347656	0.23775742948055267	0.8701387	0.39416342973709106	True
-12	28028	24.29593253135681	0.6413891315460205	214.49331665039062	0.39600199460983276	283.3816833496094	0.239556223154068	0.8737369	0.37159159779548645	True
-13	30184	24.210697412490845	18.50656223297119	178.18748474121094	0.3249233365058899	283.0116271972656	0.24020123481750488	0.87837195	0.34944427013397217	True
-14	32340	24.619585275650024	0.6416423320770264	176.04464721679688	0.3423101305961609	282.6043701171875	0.2407577782869339	0.8814518	0.3386766314506531	True
-15	34496	24.253156185150146	11.282816886901855	185.15261840820312	0.28332948684692383	282.3055419921875	0.24181945621967316	0.88300985	0.33388277888298035	True
-16	36652	24.17428159713745	0.649101734161377	178.77169799804688	0.22996509075164795	282.06842041015625	0.24205128848552704	0.8819213	0.33199721574783325	False
-17	38808	24.60648012161255	12.559687376022339	206.04661560058594	0.17394694685935974	282.4331970214844	0.24122992157936096	0.88154334	0.3364088833332062	False
-18	40964	24.14548897743225	0.648576021194458	159.74717712402344	0.3264733552932739	282.71942138671875	0.24037431180477142	0.88014716	0.341279000043869	False
-19	43120	24.186800003051758	0.6518104076385498	182.0319366455078	0.40171176195144653	282.7771911621094	0.24017535150051117	0.8792935	0.3464365303516388	False

ENCSR470QCE/cherimoya.fold_1.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-282.3055419921875	0.5158541798591614	0.24181947112083435	0.07448366284370422	0.8830098509788513	0.8392500877380371	0.33388277888298035

ENCSR470QCE/cherimoya.fold_2.evaluate.json

@@ -1,76 +0,0 @@
-{
-    "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": [
-        "ENCFF724DCZ.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
-}

ENCSR470QCE/cherimoya.fold_2.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR470QCE/cherimoya.fold_2.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2309	29.851123094558716	3.436781406402588	212.67486572265625	0.42112523317337036	275.0636291503906	0.14157360792160034	0.66162443	4.543892860412598	True
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-2	6927	25.860061645507812	0.4790360927581787	196.686279296875	0.3778626322746277	249.60281372070312	0.19800737500190735	0.7941395	0.8871275782585144	True
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-4	11545	25.81328535079956	0.48174452781677246	207.35482788085938	0.32820451259613037	246.68765258789062	0.20283620059490204	0.8089092	0.542862057685852	True
-5	13854	25.801003217697144	0.48129725456237793	222.9080810546875	0.46573972702026367	245.7892303466797	0.20529070496559143	0.81466144	0.5484494566917419	True
-6	16163	25.820956468582153	1.3618991374969482	179.74923706054688	0.32330065965652466	244.4893341064453	0.20840127766132355	0.82240456	0.5089167356491089	True
-7	18472	26.169513702392578	11.171697854995728	204.58213806152344	0.3356475532054901	243.83680725097656	0.21007627248764038	0.8206701	0.5122888684272766	False
-8	20781	25.795836210250854	0.49501490592956543	193.6127471923828	0.3770497143268585	243.61602783203125	0.20972704887390137	0.8325225	0.4639626741409302	True
-9	23090	25.83263325691223	0.9605226516723633	187.31103515625	0.34504061937332153	243.29885864257812	0.21126671135425568	0.8380275	0.4180658459663391	True
-10	25399	25.855836153030396	0.4879014492034912	223.55963134765625	0.31802064180374146	242.21060180664062	0.21434302628040314	0.8430057	0.3937205374240875	True
-11	27708	25.87834858894348	0.4801979064941406	220.97955322265625	0.30064356327056885	241.8014678955078	0.215298593044281	0.84767807	0.3697737157344818	True
-12	30017	25.88324213027954	0.47528910636901855	224.330078125	0.4349142611026764	241.7872314453125	0.21497277915477753	0.85413706	0.3490155041217804	True
-13	32326	25.884735107421875	0.47981834411621094	189.90521240234375	0.3396272659301758	241.67303466796875	0.2146369069814682	0.8555057	0.3469763994216919	True
-14	34635	25.8657546043396	0.48636698722839355	186.6326904296875	0.3292151093482971	241.04054260253906	0.2165803164243698	0.85995364	0.3331391513347626	True
-15	36944	25.805696725845337	0.48168325424194336	152.33334350585938	0.2854883670806885	240.71530151367188	0.21763591468334198	0.8610988	0.3216928541660309	True
-16	39253	25.798842191696167	0.48087406158447266	190.0297393798828	0.37832319736480713	240.51272583007812	0.21823656558990479	0.8646128	0.3139536678791046	True
-17	41562	25.831438779830933	0.47998476028442383	179.8021240234375	0.2283797562122345	240.6157684326172	0.21799075603485107	0.86158806	0.31596627831459045	False
-18	43871	25.842880487442017	0.4835665225982666	169.78717041015625	0.27565932273864746	240.93983459472656	0.21666765213012695	0.8615417	0.3198091685771942	False
-19	46180	25.804728746414185	0.4797632694244385	195.81005859375	0.2793314456939697	241.19308471679688	0.21569208800792694	0.8595423	0.32246485352516174	False

ENCSR470QCE/cherimoya.fold_2.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-240.51272583007812	0.5362424850463867	0.21823656558990479	0.06323893368244171	0.8646128177642822	0.8042017817497253	0.3139536678791046

ENCSR470QCE/cherimoya.fold_3.evaluate.json

@@ -1,75 +0,0 @@
-{
-    "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": [
-        "ENCFF724DCZ.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
-}

ENCSR470QCE/cherimoya.fold_3.fit.json

@@ -1 +0,0 @@
-{"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": ["ENCFF724DCZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR470QCE/cherimoya.fold_3.log

@@ -1,21 +0,0 @@
-Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
-0	2204	30.13941502571106	3.4148406982421875	225.4474639892578	0.4329558312892914	284.5237731933594	0.14716963469982147	0.6360704	5.239624977111816	True
-1	4408	24.744174003601074	0.48598241806030273	179.6117401123047	0.3220161199569702	266.7174377441406	0.19176410138607025	0.7299808	2.143453598022461	True
-2	6612	24.69442129135132	0.4755096435546875	226.8425750732422	0.47178366780281067	260.11224365234375	0.20549042522907257	0.76497006	1.3120450973510742	True
-3	8816	24.720549821853638	0.4735689163208008	221.0323944091797	0.5211567878723145	258.20440673828125	0.20783047378063202	0.7754449	0.8327914476394653	True
-4	11020	24.6652615070343	0.4683840274810791	171.44961547851562	0.47971364855766296	256.5871887207031	0.21125008165836334	0.7904128	0.733562707901001	True
-5	13224	24.72859239578247	0.4730093479156494	181.62149047851562	0.204271599650383	255.51071166992188	0.21450601518154144	0.7962587	0.6931695342063904	True
-6	15428	24.6882004737854	0.47445011138916016	224.06784057617188	0.5110903978347778	255.2251434326172	0.21515095233917236	0.8020632	0.6767099499702454	True
-7	17632	24.66882586479187	0.473111629486084	212.47421264648438	0.45306798815727234	254.48948669433594	0.21687187254428864	0.8089562	0.6281410455703735	True
-8	19836	24.6590359210968	8.011810541152954	203.8548583984375	0.4876599907875061	253.94046020507812	0.21840207278728485	0.81988686	0.57257080078125	True
-9	22040	24.670385599136353	0.479736328125	162.86703491210938	0.35256537795066833	253.14984130859375	0.22070254385471344	0.82081324	0.5607231259346008	True
-10	24244	24.680001974105835	0.483734130859375	226.92208862304688	0.19497208297252655	252.91970825195312	0.22105920314788818	0.8250281	0.5343478322029114	True
-11	26448	24.673311710357666	0.48346519470214844	228.63070678710938	0.4169776737689972	251.974853515625	0.2241034358739853	0.83506715	0.49547523260116577	True
-12	28652	24.646111011505127	0.47350192070007324	242.4775390625	0.24283510446548462	251.76678466796875	0.22443512082099915	0.83934003	0.4589821398258209	True
-13	30856	24.69924235343933	0.46829795837402344	167.40896606445312	0.337030291557312	251.13946533203125	0.22582906484603882	0.8451096	0.4296600818634033	True
-14	33060	24.6878023147583	0.4746105670928955	165.08114624023438	0.33067354559898376	250.52391052246094	0.22738860547542572	0.8543183	0.39816609025001526	True
-15	35264	24.739877700805664	0.48000168800354004	220.90902709960938	0.49359777569770813	250.39942932128906	0.2268582135438919	0.8594015	0.3723891079425812	True
-16	37468	24.742933988571167	0.4791128635406494	193.92938232421875	0.3633904457092285	250.23361206054688	0.22708538174629211	0.8616842	0.35987451672554016	True
-17	39672	24.760738134384155	0.47344183921813965	202.12484741210938	0.2175549864768982	250.1761474609375	0.22691963613033295	0.8632059	0.35435765981674194	True
-18	41876	24.77829074859619	0.4777836799621582	205.337646484375	0.233820378780365	250.41265869140625	0.22617670893669128	0.86190915	0.35635849833488464	False
-19	44080	24.77170491218567	0.4991159439086914	192.58816528320312	0.22809302806854248	250.18408203125	0.2270749807357788	0.8599506	0.35918739438056946	False

ENCSR470QCE/cherimoya.fold_3.performance.tsv

@@ -1,2 +0,0 @@
-profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
-250.1761474609375	0.5294259190559387	0.22691960632801056	0.07032044976949692	0.8632059097290039	0.7981179356575012	0.35435765981674194