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ENCSR000EOJ/cherimoya.fold_0.evaluate.json

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+{
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+    "verbose": true
+}

ENCSR000EOJ/cherimoya.fold_0.fit.json

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ENCSR000EOJ/cherimoya.fold_0.log

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ENCSR000EOJ/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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ENCSR000EOJ/cherimoya.fold_1.evaluate.json

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+{
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+}

ENCSR000EOJ/cherimoya.fold_1.fit.json

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ENCSR000EOJ/cherimoya.fold_1.log

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ENCSR000EOJ/cherimoya.fold_1.performance.tsv

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ENCSR000EOJ/cherimoya.fold_2.fit.json

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ENCSR000EOJ/cherimoya.fold_2.log

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ENCSR000EOJ/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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ENCSR000EOJ/cherimoya.fold_3.evaluate.json

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+    "exclusion_lists": [
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+    "loci": [
+        "train_peaks.fold_3.bed",
+        "valid_peaks.fold_3.bed"
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+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_3.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_3",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_3.bed",
+        "valid_nonpeaks.fold_3.bed"
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+    "num_workers": 1,
+    "out_window": 1000,
+    "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": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr4",
+        "chr7",
+        "chr8",
+        "chr9",
+        "chr11",
+        "chr12",
+        "chr13",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr19",
+        "chrX",
+        "chrY"
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+        "chr6",
+        "chr21"
+    ],
+    "verbose": true
+}

ENCSR000EOJ/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": ["ENCFF765MQQ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR000EOJ/cherimoya.fold_3.performance.tsv

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ENCSR000EOJ/cherimoya.fold_4.evaluate.json

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+{
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+    "model": "cherimoya.fold_4.torch",
+    "muon_lr": 0.025,
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+    "n_filters": 128,
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+    "performance_filename": "cherimoya.fold_4.performance.tsv",
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+    "skip": false,
+    "summits": false,
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+        "chr10",
+        "chr18"
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+    "verbose": true
+}

ENCSR000EOJ/cherimoya.fold_4.fit.json

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ENCSR000EOJ/cherimoya.fold_4.log

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ENCSR000EOJ/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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ENCSR180HEL/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": ["ENCFF888XOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR180HEL/cherimoya.fold_1.evaluate.json

@@ -0,0 +1,77 @@
+{
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+    "loci": [
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+    "lw_wd": 0.0,
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+    "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": [
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+        "valid_nonpeaks.fold_1.bed"
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+    "num_workers": 1,
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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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+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr10",
+        "chr11",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr12",
+        "chr17"
+    ],
+    "verbose": true
+}

ENCSR180HEL/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": ["ENCFF888XOD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR180HEL/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR180HEL/cherimoya.fold_2.log

@@ -0,0 +1,21 @@
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ENCSR180HEL/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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ENCSR180HEL/cherimoya.fold_4.fit.json

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ENCSR208DMX/cherimoya.fold_0.log

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ENCSR208DMX/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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ENCSR208DMX/cherimoya.fold_1.fit.json

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ENCSR208DMX/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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ENCSR208DMX/cherimoya.fold_2.fit.json

@@ -0,0 +1 @@
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ENCSR208DMX/cherimoya.fold_3.log

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ENCSR208DMX/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
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ENCSR208DMX/cherimoya.fold_4.evaluate.json

@@ -0,0 +1,75 @@
+{
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+        "chr22",
+        "chrY"
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+    "validation_chroms": [
+        "chr10",
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+    "verbose": true
+}

ENCSR208DMX/cherimoya.fold_4.fit.json

@@ -0,0 +1 @@
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ENCSR208DMX/cherimoya.fold_4.log

@@ -0,0 +1,21 @@
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ENCSR235OZX/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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ENCSR248ZAC/cherimoya.fold_0.evaluate.json

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+}

ENCSR248ZAC/cherimoya.fold_0.fit.json

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ENCSR248ZAC/cherimoya.fold_0.log

@@ -0,0 +1,21 @@
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ENCSR248ZAC/cherimoya.fold_0.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR248ZAC/cherimoya.fold_1.evaluate.json

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+{
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+}

ENCSR248ZAC/cherimoya.fold_1.fit.json

@@ -0,0 +1 @@
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ENCSR248ZAC/cherimoya.fold_1.log

@@ -0,0 +1,21 @@
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ENCSR248ZAC/cherimoya.fold_1.performance.tsv

@@ -0,0 +1,2 @@
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ENCSR248ZAC/cherimoya.fold_2.evaluate.json

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+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_2.bed",
+        "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": [
+        "ENCFF822CVH.bigWig"
+    ],
+    "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
+}

ENCSR248ZAC/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": ["ENCFF822CVH.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}

ENCSR248ZAC/cherimoya.fold_2.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+260.7802734375	0.320593923330307	0.6146851778030396	0.18322108685970306	0.848995566368103	0.8089035749435425	0.28351259231567383

ENCSR248ZAC/cherimoya.fold_3.evaluate.json

@@ -0,0 +1,75 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr6",
+        "chr21"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_3.bed",
+        "valid_peaks.fold_3.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_3.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_3",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_3.bed",
+        "valid_nonpeaks.fold_3.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "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": [
+        "ENCFF822CVH.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr4",
+        "chr7",
+        "chr8",
+        "chr9",
+        "chr11",
+        "chr12",
+        "chr13",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr19",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr6",
+        "chr21"
+    ],
+    "verbose": true
+}

ENCSR248ZAC/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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+4	5665	12.594257831573486	0.25188469886779785	237.3714141845703	0.4144243597984314	266.3628234863281	0.5896422266960144	0.7610525	0.7282185554504395	True
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+7	9064	12.604356527328491	0.26180219650268555	192.06546020507812	0.30417075753211975	262.4828796386719	0.5990577936172485	0.773642	0.3946422338485718	True
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+9	11330	12.578272581100464	0.24684858322143555	207.45663452148438	0.291856050491333	261.3867492675781	0.6027645468711853	0.7813082	0.37075427174568176	True
+10	12463	12.593608856201172	0.2495429515838623	199.47557067871094	0.344894140958786	260.4752502441406	0.6047654151916504	0.7843169	0.3608074188232422	True
+11	13596	12.60586667060852	0.29660797119140625	232.85333251953125	0.2699727416038513	259.6962890625	0.606954038143158	0.79125625	0.3435884118080139	True
+12	14729	12.597962141036987	0.24776148796081543	210.86102294921875	0.35636037588119507	259.2337341308594	0.6082519292831421	0.79770714	0.33741840720176697	True
+13	15862	12.579761981964111	0.24648141860961914	201.56008911132812	0.32093629240989685	258.57696533203125	0.6094968318939209	0.8046682	0.33206671476364136	True
+14	16995	12.573567390441895	0.24911141395568848	204.72171020507812	0.3293163776397705	258.11834716796875	0.6101924777030945	0.8112359	0.3277796804904938	True
+15	18128	12.575305700302124	0.2505028247833252	207.9258575439453	0.2387683391571045	257.9061584472656	0.6105707883834839	0.8153739	0.3242895007133484	True
+16	19261	12.572090864181519	0.24686121940612793	219.59014892578125	0.20134471356868744	257.95257568359375	0.6101873517036438	0.81552374	0.3254184126853943	True
+17	20394	12.759129762649536	8.005731344223022	212.7267303466797	0.11979669332504272	258.22100830078125	0.6092549562454224	0.8151602	0.32852593064308167	False
+18	21527	12.5983145236969	0.24890398979187012	218.15322875976562	0.1485946923494339	258.32196044921875	0.6084523797035217	0.81562865	0.3314944803714752	True
+19	22660	12.598896026611328	0.25478434562683105	190.19305419921875	0.13657230138778687	258.5638122558594	0.6078137755393982	0.8144099	0.33433836698532104	False

ENCSR248ZAC/cherimoya.fold_3.performance.tsv

@@ -0,0 +1,2 @@
+profile_mnll	profile_jsd	profile_pearson	profile_spearman	count_pearson	count_spearman	count_mse
+258.32196044921875	0.3235012888908386	0.6084523797035217	0.18267066776752472	0.8156286478042603	0.7675588726997375	0.3314944803714752