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ENCSR000EMZ/cherimoya.fold_0.evaluate.json

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+{
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+    "performance_filename": "cherimoya.fold_0.performance.tsv",
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+        "chrX",
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+    "validation_chroms": [
+        "chr8",
+        "chr20"
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+    "verbose": true
+}

ENCSR000EMZ/cherimoya.fold_0.fit.json

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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": ["ENCFF166ONC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EMZ/cherimoya.fold_0.log

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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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ENCSR000EMZ/cherimoya.fold_0.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000EMZ/cherimoya.fold_1.evaluate.json

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+{
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+    "performance_filename": "cherimoya.fold_1.performance.tsv",
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+    "summits": false,
+    "training_chroms": [
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+        "chr22",
+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000EMZ/cherimoya.fold_1.fit.json

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+{"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": ["ENCFF166ONC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EMZ/cherimoya.fold_1.log

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ENCSR000EMZ/cherimoya.fold_1.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+985.1939697265625	0.24742476642131805	0.5958569049835205	0.2946644425392151	0.7117655277252197	0.7068294286727905	0.402782142162323

ENCSR000EMZ/cherimoya.fold_2.evaluate.json

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+{
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+        "chr20",
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+}

ENCSR000EMZ/cherimoya.fold_2.fit.json

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+{"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": ["ENCFF166ONC.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EMZ/cherimoya.fold_2.log

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ENCSR000EMZ/cherimoya.fold_2.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000EMZ/cherimoya.fold_3.evaluate.json

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+}

ENCSR000EMZ/cherimoya.fold_3.fit.json

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ENCSR000EMZ/cherimoya.fold_3.log

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ENCSR000EMZ/cherimoya.fold_3.performance.tsv

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ENCSR000EMZ/cherimoya.fold_4.evaluate.json

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+}

ENCSR000EMZ/cherimoya.fold_4.fit.json

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ENCSR000EMZ/cherimoya.fold_4.log

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ENCSR000EMZ/cherimoya.fold_4.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000EQF/cherimoya.fold_0.evaluate.json

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+}

ENCSR000EQF/cherimoya.fold_0.fit.json

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ENCSR000EQF/cherimoya.fold_0.log

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ENCSR000EQF/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+606.1427612304688	0.47364598512649536	0.2701512575149536	0.0842326432466507	0.7488968372344971	0.7009241580963135	0.3768375813961029

ENCSR000EQF/cherimoya.fold_1.evaluate.json

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+{
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+    "performance_filename": "cherimoya.fold_1.performance.tsv",
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+    "training_chroms": [
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+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000EQF/cherimoya.fold_1.fit.json

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ENCSR000EQF/cherimoya.fold_1.log

@@ -0,0 +1,21 @@
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ENCSR000EQF/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000EQF/cherimoya.fold_2.evaluate.json

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+{
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+}

ENCSR000EQF/cherimoya.fold_2.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF056NMG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EQF/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
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ENCSR000EQF/cherimoya.fold_2.performance.tsv

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ENCSR000EQF/cherimoya.fold_3.evaluate.json

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+}

ENCSR000EQF/cherimoya.fold_3.fit.json

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ENCSR000EQF/cherimoya.fold_3.log

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ENCSR000EQF/cherimoya.fold_3.performance.tsv

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ENCSR000EQF/cherimoya.fold_4.evaluate.json

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+{
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+}

ENCSR000EQF/cherimoya.fold_4.fit.json

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ENCSR000EQF/cherimoya.fold_4.log

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ENCSR000EQF/cherimoya.fold_4.performance.tsv

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ENCSR053ZKP/cherimoya.fold_0.evaluate.json

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+{
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+}

ENCSR053ZKP/cherimoya.fold_0.fit.json

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ENCSR053ZKP/cherimoya.fold_0.log

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ENCSR053ZKP/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+875.6776733398438	0.3120982348918915	0.49136272072792053	0.2352205067873001	0.8213813304901123	0.777488648891449	0.3920044004917145

ENCSR053ZKP/cherimoya.fold_1.evaluate.json

@@ -0,0 +1,77 @@
+{
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+    "lw_wd": 0.0,
+    "max_epochs": 20,
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+    "model": "cherimoya.fold_1.torch",
+    "muon_lr": 0.025,
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+    "n_filters": 128,
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+    "negative_ratio": 0.25,
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+    "performance_filename": "cherimoya.fold_1.performance.tsv",
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+    "summits": false,
+    "training_chroms": [
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+        "chr3",
+        "chr4",
+        "chr5",
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+        "chr10",
+        "chr11",
+        "chr13",
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+        "chr15",
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+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR053ZKP/cherimoya.fold_1.fit.json

@@ -0,0 +1 @@
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ENCSR053ZKP/cherimoya.fold_1.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR053ZKP/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+986.6102905273438	0.2973428964614868	0.5043617486953735	0.2567906975746155	0.83887779712677	0.8127169609069824	0.398651659488678

ENCSR053ZKP/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
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+    "name": "cherimoya.fold_2",
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+    "sequences": "hg38.fa",
+    "signals": [
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+    "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
+}

ENCSR053ZKP/cherimoya.fold_2.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_2", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr5", "chr6", "chr8", "chr9", "chr10", "chr13", "chr14", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chrX"], "validation_chroms": ["chr22", "chr7"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_2.bed", "valid_peaks.fold_2.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_2.bed", "valid_nonpeaks.fold_2.bed"], "signals": ["ENCFF732RFP.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}