Add files using upload-large-folder tool

ENCSR134BSY/cherimoya.fold_0.evaluate.json

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+{
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+    "muon_lr": 0.025,
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+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_0",
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+        "valid_nonpeaks.fold_0.bed"
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+    "performance_filename": "cherimoya.fold_0.performance.tsv",
+    "random_state": null,
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+    "sequences": "hg38.fa",
+    "signals": [
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+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr4",
+        "chr5",
+        "chr7",
+        "chr9",
+        "chr10",
+        "chr11",
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+        "chr13",
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+        "chr15",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "verbose": true
+}

ENCSR134BSY/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": ["ENCFF517EIH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR134BSY/cherimoya.fold_1.evaluate.json

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+{
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+    "batch_size": 64,
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+    "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,
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+        "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,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF517EIH.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
+}

ENCSR134BSY/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": ["ENCFF517EIH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR134BSY/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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ENCSR134BSY/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": ["ENCFF517EIH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR134BSY/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?
+0	2909	36.050081968307495	3.9673056602478027	237.25497436523438	0.7834606766700745	297.7585144042969	0.13510677218437195	0.68463147	3.869513511657715	True
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ENCSR134BSY/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+250.34027099609375	0.5356976985931396	0.21949593722820282	0.06342422217130661	0.8646211624145508	0.7982994318008423	0.33523982763290405

ENCSR134BSY/cherimoya.fold_4.evaluate.json

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+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr10",
+        "chr18"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
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+    ],
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+    "loci": [
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+        "valid_peaks.fold_4.bed"
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+    "lw_lr": 0.001,
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+    "lw_wd": 0.0,
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+    "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"
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+    "performance_filename": "cherimoya.fold_4.performance.tsv",
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+        "chr12",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr20",
+        "chr22",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr10",
+        "chr18"
+    ],
+    "verbose": true
+}

ENCSR134BSY/cherimoya.fold_4.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+205.17318725585938	0.5584061741828918	0.1914346069097519	0.05349152535200119	0.8651641607284546	0.7797526717185974	0.23713399469852448

ENCSR139PLJ/cherimoya.fold_2.evaluate.json

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+{
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+    "name": "cherimoya.fold_2",
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+        "valid_nonpeaks.fold_2.bed"
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+    "performance_filename": "cherimoya.fold_2.performance.tsv",
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+    "training_chroms": [
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+        "chr3",
+        "chr5",
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+        "chr9",
+        "chr10",
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+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chrX"
+    ],
+    "validation_chroms": [
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+        "chr7"
+    ],
+    "verbose": true
+}

ENCSR139PLJ/cherimoya.fold_4.log

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ENCSR227FVE/cherimoya.fold_1.fit.json

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ENCSR227FVE/cherimoya.fold_3.log

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ENCSR459AYS/cherimoya.fold_0.log

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ENCSR459AYS/cherimoya.fold_3.evaluate.json

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+{
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+}

ENCSR459AYS/cherimoya.fold_4.evaluate.json

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+{
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+}

ENCSR565DSD/cherimoya.fold_0.evaluate.json

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

ENCSR565DSD/cherimoya.fold_0.log

@@ -0,0 +1,21 @@
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ENCSR565DSD/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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ENCSR565DSD/cherimoya.fold_1.evaluate.json

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+    "verbose": true
+}

ENCSR565DSD/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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ENCSR565DSD/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
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+        "chr21",
+        "chrX"
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+    "validation_chroms": [
+        "chr22",
+        "chr7"
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+    "verbose": true
+}

ENCSR565DSD/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": ["ENCFF539IPH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR565DSD/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
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ENCSR565DSD/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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ENCSR565DSD/cherimoya.fold_3.fit.json

@@ -0,0 +1 @@
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ENCSR565DSD/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR565DSD/cherimoya.fold_4.fit.json

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ENCSR565DSD/cherimoya.fold_4.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR590EFT/cherimoya.fold_0.evaluate.json

@@ -0,0 +1,78 @@
+{
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+    "batch_size": 64,
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+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "verbose": true
+}

ENCSR590EFT/cherimoya.fold_0.fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR590EFT/cherimoya.fold_0.log

@@ -0,0 +1,21 @@
+Epoch	Iteration	Training Time	Validation Time	Training MNLL	Training Count MSE	Validation MNLL	Validation Profile Pearson	Validation Count Pearson	Validation Count MSE	Saved?
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ENCSR590EFT/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+450.9592590332031	0.44494402408599854	0.30284690856933594	0.10715848952531815	0.918362557888031	0.9039835929870605	0.07730576395988464

ENCSR590EFT/cherimoya.fold_1.evaluate.json

@@ -0,0 +1,77 @@
+{
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+    "adam_wd": 0.0,
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+    "name": "cherimoya.fold_1",
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+        "valid_nonpeaks.fold_1.bed"
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+    "performance_filename": "cherimoya.fold_1.performance.tsv",
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+    "training_chroms": [
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+        "chrY"
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+    "validation_chroms": [
+        "chr12",
+        "chr17"
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+    "verbose": true
+}

ENCSR590EFT/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": ["ENCFF934GCV.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR590EFT/cherimoya.fold_1.log

@@ -0,0 +1,21 @@
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ENCSR590EFT/cherimoya.fold_1.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR590EFT/cherimoya.fold_2.evaluate.json

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+{
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+    "summits": false,
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+    "validation_chroms": [
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+    ],
+    "verbose": true
+}

ENCSR590EFT/cherimoya.fold_2.fit.json

@@ -0,0 +1 @@
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ENCSR590EFT/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
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ENCSR590EFT/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR590EFT/cherimoya.fold_3.evaluate.json

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+{
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+        "chrX",
+        "chrY"
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+    "validation_chroms": [
+        "chr6",
+        "chr21"
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+    "verbose": true
+}

ENCSR590EFT/cherimoya.fold_3.fit.json

@@ -0,0 +1 @@
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ENCSR590EFT/cherimoya.fold_3.log

@@ -0,0 +1,21 @@
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ENCSR590EFT/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR590EFT/cherimoya.fold_4.evaluate.json

@@ -0,0 +1,75 @@
+{
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+}

ENCSR590EFT/cherimoya.fold_4.fit.json

@@ -0,0 +1 @@
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ENCSR590EFT/cherimoya.fold_4.log

@@ -0,0 +1,21 @@
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+13	39522	30.75468158721924	15.764957189559937	365.57958984375	0.08193840086460114	428.7456970214844	0.2924038767814636	0.9065241	0.0810622125864029	True
+14	42345	31.01643991470337	0.6188304424285889	416.9805908203125	0.14592793583869934	428.09588623046875	0.29381611943244934	0.90932703	0.0779958963394165	True
+15	45168	31.20568585395813	0.6141517162322998	396.19805908203125	0.08928835391998291	427.806396484375	0.2944841682910919	0.91393536	0.07610055804252625	True
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+17	50814	31.120170831680298	0.6296288967132568	393.4285888671875	0.07639415562152863	427.5361633300781	0.29420310258865356	0.9144385	0.07249197363853455	True
+18	53637	30.7722749710083	0.6214520931243896	399.80841064453125	0.04709776118397713	427.7421875	0.2939910292625427	0.916222	0.07236605882644653	True
+19	56460	30.710046529769897	0.6139678955078125	368.6102294921875	0.06935294717550278	427.6287841796875	0.2944748103618622	0.91573334	0.07253710925579071	False

ENCSR590EFT/cherimoya.fold_4.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+427.7421875	0.4530104398727417	0.2939910292625427	0.09898067265748978	0.9162219762802124	0.8998091220855713	0.07236605882644653