Add files using upload-large-folder tool

ENCSR000ENC/cherimoya.fold_0.evaluate.json

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+{
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+        "chr22",
+        "chrX",
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+    "validation_chroms": [
+        "chr8",
+        "chr20"
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+    "verbose": true
+}

ENCSR000ENC/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": ["ENCFF110RWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENC/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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ENCSR000ENC/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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ENCSR000ENC/cherimoya.fold_1.evaluate.json

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+{
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+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr22",
+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000ENC/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": ["ENCFF110RWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENC/cherimoya.fold_1.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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ENCSR000ENC/cherimoya.fold_1.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+365.0158996582031	0.4115762710571289	0.4352041482925415	0.12046842277050018	0.7005035877227783	0.648590624332428	0.5547738075256348

ENCSR000ENC/cherimoya.fold_2.evaluate.json

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+{
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+        "chr19",
+        "chr20",
+        "chr21",
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+    "validation_chroms": [
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+        "chr7"
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+}

ENCSR000ENC/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": ["ENCFF110RWJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENC/cherimoya.fold_2.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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ENCSR000ENC/cherimoya.fold_2.performance.tsv

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ENCSR000ENC/cherimoya.fold_3.evaluate.json

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+}

ENCSR000ENC/cherimoya.fold_3.fit.json

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ENCSR000ENC/cherimoya.fold_3.log

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ENCSR000ENC/cherimoya.fold_3.performance.tsv

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ENCSR000ENC/cherimoya.fold_4.evaluate.json

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+}

ENCSR000ENC/cherimoya.fold_4.fit.json

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ENCSR000ENC/cherimoya.fold_4.log

@@ -0,0 +1,21 @@
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ENCSR000ENC/cherimoya.fold_4.performance.tsv

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ENCSR000ENZ/cherimoya.fold_0.evaluate.json

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+}

ENCSR000ENZ/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": ["ENCFF050TSV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENZ/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000ENZ/cherimoya.fold_1.evaluate.json

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+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
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+        "chr17"
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+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
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+    "loci": [
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+        "valid_peaks.fold_1.bed"
+    ],
+    "lw_lr": 0.001,
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+    "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"
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+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_1.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
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+    "sequences": "hg38.fa",
+    "signals": [
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+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr10",
+        "chr11",
+        "chr13",
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+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR000ENZ/cherimoya.fold_1.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF050TSV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENZ/cherimoya.fold_1.performance.tsv

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ENCSR000ENZ/cherimoya.fold_2.evaluate.json

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+{
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+    "n_filters": 128,
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+        "valid_nonpeaks.fold_2.bed"
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
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+    "signals": [
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+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR000ENZ/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": ["ENCFF050TSV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENZ/cherimoya.fold_2.log

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ENCSR000ENZ/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR000ENZ/cherimoya.fold_3.evaluate.json

@@ -0,0 +1,75 @@
+{
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+    "chroms": [
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+    "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_3.performance.tsv",
+    "random_state": null,
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+    "signals": [
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+    "summits": false,
+    "training_chroms": [
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+        "chr3",
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+        "chr12",
+        "chr13",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr19",
+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr6",
+        "chr21"
+    ],
+    "verbose": true
+}

ENCSR000ENZ/cherimoya.fold_3.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF050TSV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENZ/cherimoya.fold_3.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR000ENZ/cherimoya.fold_4.evaluate.json

@@ -0,0 +1,75 @@
+{
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+    "verbose": true
+}

ENCSR000ENZ/cherimoya.fold_4.log

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ENCSR038XTK/cherimoya.fold_0.evaluate.json

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+}

ENCSR038XTK/cherimoya.fold_0.fit.json

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ENCSR038XTK/cherimoya.fold_0.log

@@ -0,0 +1,21 @@
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ENCSR038XTK/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR038XTK/cherimoya.fold_1.evaluate.json

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+{
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+}

ENCSR038XTK/cherimoya.fold_1.fit.json

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ENCSR038XTK/cherimoya.fold_1.log

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ENCSR038XTK/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR038XTK/cherimoya.fold_2.evaluate.json

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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+    "summits": false,
+    "training_chroms": [
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+        "chrX"
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+    "validation_chroms": [
+        "chr22",
+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR038XTK/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": ["ENCFF635FWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR038XTK/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR038XTK/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+1633.5765380859375	0.2702721059322357	0.5492931604385376	0.28553861379623413	0.6658895015716553	0.6390413641929626	0.6157057285308838

ENCSR038XTK/cherimoya.fold_3.evaluate.json

@@ -0,0 +1,75 @@
+{
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+    "batch_size": 64,
+    "chroms": [
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+    "loci": [
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+    "muon_lr": 0.025,
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+    "n_filters": 128,
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+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_3",
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+        "valid_nonpeaks.fold_3.bed"
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+    "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": [
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+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr2",
+        "chr3",
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+        "chr9",
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+        "chr13",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr19",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr6",
+        "chr21"
+    ],
+    "verbose": true
+}

ENCSR038XTK/cherimoya.fold_3.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_3", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr2", "chr3", "chr4", "chr7", "chr8", "chr9", "chr11", "chr12", "chr13", "chr15", "chr16", "chr17", "chr19", "chrX", "chrY"], "validation_chroms": ["chr6", "chr21"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_3.bed", "valid_peaks.fold_3.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_3.bed", "valid_nonpeaks.fold_3.bed"], "signals": ["ENCFF635FWG.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR038XTK/cherimoya.fold_3.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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