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ENCSR000ENI/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": ["ENCFF432NXL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENI/cherimoya.fold_1.evaluate.json

@@ -0,0 +1,77 @@
+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
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+        "chr17"
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+    "controls": null,
+    "device": "cuda",
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+    "early_stopping": 20,
+    "exclusion_lists": [
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+    "loci": [
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+        "valid_peaks.fold_1.bed"
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+    "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"
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+    "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": [
+        "ENCFF432NXL.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
+}

ENCSR000ENI/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": ["ENCFF432NXL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000ENI/cherimoya.fold_1.performance.tsv

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ENCSR000ENI/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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ENCSR000ENI/cherimoya.fold_3.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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ENCSR000ENI/cherimoya.fold_3.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+1379.79296875	0.23499266803264618	0.6082478165626526	0.3283499479293823	0.6889554858207703	0.6711482405662537	0.6518705487251282

ENCSR000ENI/cherimoya.fold_4.evaluate.json

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+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
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+    "loci": [
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+        "valid_peaks.fold_4.bed"
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+    "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"
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+    "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": [
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+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
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+        "chr2",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr8",
+        "chr9",
+        "chr11",
+        "chr12",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr20",
+        "chr22",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr10",
+        "chr18"
+    ],
+    "verbose": true
+}

ENCSR000ENI/cherimoya.fold_4.performance.tsv

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+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+1305.6383056640625	0.23769915103912354	0.6105883121490479	0.32106152176856995	0.6712496280670166	0.6445742845535278	0.6404381394386292

ENCSR000EQH/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": ["ENCFF515HWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EQH/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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ENCSR000EQH/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": ["ENCFF515HWF.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EQH/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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ENCSR000EQH/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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ENCSR000EQH/cherimoya.fold_2.evaluate.json

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+{
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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,
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+}

ENCSR000EQH/cherimoya.fold_2.fit.json

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ENCSR000EQH/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR000EQH/cherimoya.fold_4.fit.json

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ENCSR000EQH/cherimoya.fold_4.log

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ENCSR000EQJ/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
+{
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+    "n_filters": 128,
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+    "name": "cherimoya.fold_2",
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+        "chr22",
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+}

ENCSR000EQJ/cherimoya.fold_4.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR021YFW/cherimoya.fold_0.fit.json

@@ -0,0 +1 @@
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ENCSR021YFW/cherimoya.fold_2.evaluate.json

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

ENCSR021YFW/cherimoya.fold_3.log

@@ -0,0 +1,21 @@
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ENCSR021YFW/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR021YFW/cherimoya.fold_4.performance.tsv

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ENCSR036VRV/cherimoya.fold_0.evaluate.json

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+}

ENCSR036VRV/cherimoya.fold_0.log

@@ -0,0 +1,21 @@
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ENCSR036VRV/cherimoya.fold_2.evaluate.json

@@ -0,0 +1,76 @@
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+    "verbose": true
+}

ENCSR036VRV/cherimoya.fold_2.fit.json

@@ -0,0 +1 @@
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ENCSR036VRV/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
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ENCSR036VRV/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR040DJK/cherimoya.fold_0.evaluate.json

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

ENCSR040DJK/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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ENCSR040DJK/cherimoya.fold_0.performance.tsv

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ENCSR040DJK/cherimoya.fold_1.evaluate.json

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+}

ENCSR040DJK/cherimoya.fold_1.log

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ENCSR040DJK/cherimoya.fold_2.fit.json

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ENCSR040DJK/cherimoya.fold_2.performance.tsv

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ENCSR040DJK/cherimoya.fold_3.evaluate.json

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+}

ENCSR082JCE/cherimoya.fold_0.log

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ENCSR102RXG/cherimoya.fold_1.fit.json

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ENCSR102RXG/cherimoya.fold_4.performance.tsv

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ENCSR122NDR/cherimoya.fold_0.fit.json

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ENCSR122NDR/cherimoya.fold_1.fit.json

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ENCSR122NDR/cherimoya.fold_3.log

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ENCSR122NDR/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+370.5904235839844	0.2875387966632843	0.6472032070159912	0.2442023903131485	0.7082417011260986	0.6773516535758972	0.4881007671356201

ENCSR163KRG/cherimoya.fold_0.evaluate.json

@@ -0,0 +1,78 @@
+{
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+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
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+        "chr20"
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+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
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+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
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+        "valid_peaks.fold_0.bed"
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+    "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": [
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+        "valid_nonpeaks.fold_0.bed"
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+    "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": [
+        "ENCFF595FZS.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
+}

ENCSR163KRG/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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ENCSR163KRG/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+264.039306640625	0.3352339267730713	0.5929714441299438	0.17089812457561493	0.6511092782020569	0.6232082843780518	0.45282918214797974