jmschr commited on Jul 23

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ENCSR000EOO/cherimoya.fold_0.evaluate.json +78 -0
ENCSR000EOO/cherimoya.fold_0.fit.json +1 -0
ENCSR000EOO/cherimoya.fold_0.log +21 -0
ENCSR000EOO/cherimoya.fold_0.performance.tsv +2 -0
ENCSR000EOO/cherimoya.fold_1.evaluate.json +77 -0
ENCSR000EOO/cherimoya.fold_1.fit.json +1 -0
ENCSR000EOO/cherimoya.fold_1.log +21 -0
ENCSR000EOO/cherimoya.fold_1.performance.tsv +2 -0
ENCSR000EOO/cherimoya.fold_2.evaluate.json +76 -0
ENCSR000EOO/cherimoya.fold_2.fit.json +1 -0
ENCSR000EOO/cherimoya.fold_2.log +21 -0
ENCSR000EOO/cherimoya.fold_2.performance.tsv +2 -0
ENCSR000EOO/cherimoya.fold_3.evaluate.json +75 -0
ENCSR000EOO/cherimoya.fold_3.fit.json +1 -0
ENCSR000EOO/cherimoya.fold_3.log +21 -0
ENCSR000EOO/cherimoya.fold_3.performance.tsv +2 -0
ENCSR000EOO/cherimoya.fold_4.evaluate.json +75 -0
ENCSR000EOO/cherimoya.fold_4.fit.json +1 -0
ENCSR000EOO/cherimoya.fold_4.log +21 -0
ENCSR000EOO/cherimoya.fold_4.performance.tsv +2 -0
ENCSR000EPK/cherimoya.fold_0.evaluate.json +78 -0
ENCSR000EPK/cherimoya.fold_0.fit.json +1 -0
ENCSR000EPK/cherimoya.fold_0.log +21 -0
ENCSR000EPK/cherimoya.fold_0.performance.tsv +2 -0
ENCSR000EPK/cherimoya.fold_1.evaluate.json +77 -0
ENCSR000EPK/cherimoya.fold_1.fit.json +1 -0
ENCSR000EPK/cherimoya.fold_1.log +21 -0
ENCSR000EPK/cherimoya.fold_1.performance.tsv +2 -0
ENCSR000EPK/cherimoya.fold_2.evaluate.json +76 -0
ENCSR000EPK/cherimoya.fold_2.fit.json +1 -0
ENCSR000EPK/cherimoya.fold_2.log +21 -0
ENCSR000EPK/cherimoya.fold_2.performance.tsv +2 -0
ENCSR000EPK/cherimoya.fold_3.evaluate.json +75 -0
ENCSR000EPK/cherimoya.fold_3.fit.json +1 -0
ENCSR000EPK/cherimoya.fold_3.log +21 -0
ENCSR000EPK/cherimoya.fold_3.performance.tsv +2 -0
ENCSR000EPK/cherimoya.fold_4.evaluate.json +75 -0
ENCSR000EPK/cherimoya.fold_4.fit.json +1 -0
ENCSR000EPK/cherimoya.fold_4.log +21 -0
ENCSR000EPK/cherimoya.fold_4.performance.tsv +2 -0
ENCSR025BWH/cherimoya.fold_0.evaluate.json +78 -0
ENCSR025BWH/cherimoya.fold_0.log +21 -0
ENCSR025BWH/cherimoya.fold_1.evaluate.json +77 -0
ENCSR025BWH/cherimoya.fold_1.log +21 -0
ENCSR025BWH/cherimoya.fold_2.evaluate.json +76 -0
ENCSR025BWH/cherimoya.fold_2.fit.json +1 -0
ENCSR025BWH/cherimoya.fold_2.performance.tsv +2 -0
ENCSR025BWH/cherimoya.fold_3.fit.json +1 -0
ENCSR025BWH/cherimoya.fold_3.performance.tsv +2 -0
ENCSR025BWH/cherimoya.fold_4.fit.json +1 -0

ENCSR000EOO/cherimoya.fold_0.evaluate.json ADDED Viewed

	@@ -0,0 +1,78 @@

+{
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+    "performance_filename": "cherimoya.fold_0.performance.tsv",
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+    "sequences": "hg38.fa",
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+    "validation_chroms": [
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+        "chr20"
+    ],
+    "verbose": true
+}

ENCSR000EOO/cherimoya.fold_0.fit.json ADDED Viewed

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+ {"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": ["ENCFF322TMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOO/cherimoya.fold_0.log ADDED Viewed

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+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR000EOO/cherimoya.fold_0.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 1859.6278076171875 0.20371606945991516 0.6365532875061035 0.38808968663215637 0.6558574438095093 0.6364486217498779 0.6452819108963013

ENCSR000EOO/cherimoya.fold_1.evaluate.json ADDED Viewed

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+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
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+    "device": "cuda",
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+    "lw_wd": 0.0,
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+    "model": "cherimoya.fold_1.torch",
+    "muon_lr": 0.025,
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+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_1",
+    "negative_ratio": 0.25,
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+    "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": [
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+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000EOO/cherimoya.fold_1.fit.json ADDED Viewed

	@@ -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": ["ENCFF322TMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOO/cherimoya.fold_1.log ADDED Viewed

	@@ -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?
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ENCSR000EOO/cherimoya.fold_1.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 1969.9122314453125 0.2006392627954483 0.6376428604125977 0.3972513973712921 0.6743011474609375 0.6513688564300537 0.6650609970092773

ENCSR000EOO/cherimoya.fold_2.evaluate.json ADDED Viewed

	@@ -0,0 +1,76 @@

+{
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+    "lw_wd": 0.0,
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+    "model": "cherimoya.fold_2.torch",
+    "muon_lr": 0.025,
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+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_2",
+    "negative_ratio": 0.25,
+    "negatives": [
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+        "valid_nonpeaks.fold_2.bed"
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
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+    "training_chroms": [
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+        "chr22",
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+    ],
+    "verbose": true
+}

ENCSR000EOO/cherimoya.fold_2.fit.json ADDED Viewed

	@@ -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": ["ENCFF322TMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOO/cherimoya.fold_2.log ADDED Viewed

	@@ -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?
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ENCSR000EOO/cherimoya.fold_2.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 1844.211669921875 0.20457325875759125 0.6342589855194092 0.38908863067626953 0.6590831279754639 0.6362557411193848 0.6537434458732605

ENCSR000EOO/cherimoya.fold_3.evaluate.json ADDED Viewed

	@@ -0,0 +1,75 @@

+{
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+        "chr6",
+        "chr21"
+    ],
+    "verbose": true
+}

ENCSR000EOO/cherimoya.fold_3.fit.json ADDED Viewed

	@@ -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": ["ENCFF322TMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOO/cherimoya.fold_3.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EOO/cherimoya.fold_3.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 1900.3106689453125 0.2017546445131302 0.641476571559906 0.3920963704586029 0.6639324426651001 0.6482459306716919 0.6733878254890442

ENCSR000EOO/cherimoya.fold_4.evaluate.json ADDED Viewed

	@@ -0,0 +1,75 @@

+{
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+}

ENCSR000EOO/cherimoya.fold_4.fit.json ADDED Viewed

	@@ -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": ["ENCFF322TMZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOO/cherimoya.fold_4.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EOO/cherimoya.fold_4.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 1824.2822265625 0.20344674587249756 0.6385800838470459 0.386581689119339 0.6572939157485962 0.6318334937095642 0.6195075511932373

ENCSR000EPK/cherimoya.fold_0.evaluate.json ADDED Viewed

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+{
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+}

ENCSR000EPK/cherimoya.fold_0.fit.json ADDED Viewed

	@@ -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": ["ENCFF034BGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPK/cherimoya.fold_0.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EPK/cherimoya.fold_0.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 468.0161437988281 0.4026676416397095 0.4136717617511749 0.14512810111045837 0.7175626754760742 0.6581080555915833 0.7428904175758362

ENCSR000EPK/cherimoya.fold_1.evaluate.json ADDED Viewed

	@@ -0,0 +1,77 @@

+{
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+}

ENCSR000EPK/cherimoya.fold_1.fit.json ADDED Viewed

	@@ -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": ["ENCFF034BGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPK/cherimoya.fold_1.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EPK/cherimoya.fold_1.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 515.2417602539062 0.38769203424453735 0.4283296465873718 0.15836484730243683 0.7452667355537415 0.6995428800582886 0.7309103608131409

ENCSR000EPK/cherimoya.fold_2.evaluate.json ADDED Viewed

	@@ -0,0 +1,76 @@

+{
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+}

ENCSR000EPK/cherimoya.fold_2.fit.json ADDED Viewed

	@@ -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": ["ENCFF034BGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPK/cherimoya.fold_2.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EPK/cherimoya.fold_2.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 475.55078125 0.4020173251628876 0.41308820247650146 0.1470090001821518 0.7248914837837219 0.6676404476165771 0.7508555054664612

ENCSR000EPK/cherimoya.fold_3.evaluate.json ADDED Viewed

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+}

ENCSR000EPK/cherimoya.fold_3.fit.json ADDED Viewed

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ENCSR000EPK/cherimoya.fold_3.log ADDED Viewed

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ENCSR000EPK/cherimoya.fold_3.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
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ENCSR000EPK/cherimoya.fold_4.evaluate.json ADDED Viewed

	@@ -0,0 +1,75 @@

+{
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+}

ENCSR000EPK/cherimoya.fold_4.fit.json ADDED Viewed

	@@ -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": ["ENCFF034BGQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EPK/cherimoya.fold_4.log ADDED Viewed

	@@ -0,0 +1,21 @@

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ENCSR000EPK/cherimoya.fold_4.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 455.4148864746094 0.405560702085495 0.4104014039039612 0.1408417671918869 0.7099996209144592 0.6491436958312988 0.739497184753418

ENCSR025BWH/cherimoya.fold_0.evaluate.json ADDED Viewed

	@@ -0,0 +1,78 @@

+{
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+    "validation_chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "verbose": true
+}

ENCSR025BWH/cherimoya.fold_0.log ADDED Viewed

	@@ -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?
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ENCSR025BWH/cherimoya.fold_1.evaluate.json ADDED Viewed

	@@ -0,0 +1,77 @@

+{
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+    "batch_size": 64,
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+    "name": "cherimoya.fold_1",
+    "negative_ratio": 0.25,
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+        "valid_nonpeaks.fold_1.bed"
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+    "performance_filename": "cherimoya.fold_1.performance.tsv",
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+    "sequences": "hg38.fa",
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+    "training_chroms": [
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+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR025BWH/cherimoya.fold_1.log ADDED Viewed

	@@ -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	2202	28.325729608535767	4.049350023269653	401.3150939941406	1.0542045831680298	886.3676147460938	0.1784089058637619	0.5882844	10.609041213989258	True
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ENCSR025BWH/cherimoya.fold_2.evaluate.json ADDED Viewed

	@@ -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": [
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+    ],
+    "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": [
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+        "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": [
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+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr2",
+        "chr3",
+        "chr5",
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+        "chr9",
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+        "chr13",
+        "chr14",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chrX"
+    ],
+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR025BWH/cherimoya.fold_2.fit.json ADDED Viewed

	@@ -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": ["ENCFF879TYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR025BWH/cherimoya.fold_2.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 505.4980163574219 0.48487570881843567 0.2604771554470062 0.10693153738975525 0.8645233511924744 0.78652024269104 0.4441353380680084

ENCSR025BWH/cherimoya.fold_3.fit.json ADDED Viewed

	@@ -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": ["ENCFF879TYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR025BWH/cherimoya.fold_3.performance.tsv ADDED Viewed

	@@ -0,0 +1,2 @@


1	+ profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
2	+ 546.028564453125 0.47150683403015137 0.280464231967926 0.12062320113182068 0.8503134846687317 0.7853981256484985 0.5646487474441528

ENCSR025BWH/cherimoya.fold_4.fit.json ADDED Viewed

	@@ -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": ["ENCFF879TYP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}