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- ENCSR000EMH/cherimoya.fold_0.evaluate.json +78 -0
- ENCSR000EMH/cherimoya.fold_1.log +21 -0
- ENCSR000EMH/cherimoya.fold_2.log +21 -0
- ENCSR000EMH/cherimoya.fold_2.performance.tsv +2 -0
- ENCSR000EMH/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR000EMH/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000EMH/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000EMH/cherimoya.fold_4.fit.json +1 -0
- ENCSR000EMH/cherimoya.fold_4.log +21 -0
- ENCSR000EMR/cherimoya.fold_1.log +21 -0
- ENCSR000EMR/cherimoya.fold_4.fit.json +1 -0
- ENCSR000ENK/cherimoya.fold_0.fit.json +1 -0
- ENCSR000ENK/cherimoya.fold_0.log +21 -0
- ENCSR000ENK/cherimoya.fold_0.performance.tsv +2 -0
- ENCSR000ENK/cherimoya.fold_1.evaluate.json +77 -0
- ENCSR000ENK/cherimoya.fold_2.fit.json +1 -0
- ENCSR000ENK/cherimoya.fold_2.log +21 -0
- ENCSR000ENK/cherimoya.fold_2.performance.tsv +2 -0
- ENCSR000ENK/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR000ENK/cherimoya.fold_3.fit.json +1 -0
- ENCSR000ENK/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000ENK/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000ENK/cherimoya.fold_4.fit.json +1 -0
- ENCSR000ENK/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR000ENV/cherimoya.fold_1.fit.json +1 -0
- ENCSR000ENV/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000ENV/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR000EOR/cherimoya.fold_0.fit.json +1 -0
- ENCSR000EOR/cherimoya.fold_0.log +21 -0
- ENCSR000EOR/cherimoya.fold_1.evaluate.json +77 -0
- ENCSR000EOR/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR000EOR/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR000EOR/cherimoya.fold_3.fit.json +1 -0
- ENCSR000EOR/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000EPH/cherimoya.fold_0.evaluate.json +78 -0
- ENCSR000EPH/cherimoya.fold_0.fit.json +1 -0
- ENCSR000EPH/cherimoya.fold_1.performance.tsv +2 -0
- ENCSR000EPH/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000EPH/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000EPQ/cherimoya.fold_0.performance.tsv +2 -0
- ENCSR000EPQ/cherimoya.fold_1.log +21 -0
- ENCSR000EPQ/cherimoya.fold_1.performance.tsv +2 -0
- ENCSR000EPQ/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR000EPQ/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR000EPQ/cherimoya.fold_3.fit.json +1 -0
- ENCSR000EPQ/cherimoya.fold_3.log +21 -0
- ENCSR000EPQ/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000EPQ/cherimoya.fold_4.log +21 -0
- ENCSR000EPQ/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR000EQD/cherimoya.fold_0.evaluate.json +78 -0
ENCSR000EMH/cherimoya.fold_0.evaluate.json
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{
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"chr8",
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"dtype": "bfloat16",
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"early_stopping": 20,
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],
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"in_window": 2114,
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"loci": [
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"lw_lr": 0.001,
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"lw_momentum": 0.9,
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"name": "cherimoya.fold_0",
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"negative_ratio": 0.25,
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"negatives": [
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],
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"num_workers": 1,
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"out_window": 1000,
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"performance_filename": "cherimoya.fold_0.performance.tsv",
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"reverse_complement": false,
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"sequences": "hg38.fa",
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"training_chroms": [
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ENCSR000EMH/cherimoya.fold_1.log
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| 1 |
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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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| 2 |
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ENCSR000EMH/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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| 2 |
+
0 2878 36.20756983757019 3.336087465286255 320.4326171875 1.9383864402770996 535.1150512695312 0.2371436357498169 0.3689139 4.829574108123779 True
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ENCSR000EMH/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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388.3386535644531 0.37186747789382935 0.47250816226005554 0.15026921033859253 0.6428695917129517 0.6176119446754456 0.7529056072235107
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ENCSR000EMH/cherimoya.fold_3.evaluate.json
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| 1 |
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|
| 2 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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"name": "cherimoya.fold_3",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
|
| 36 |
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"train_nonpeaks.fold_3.bed",
|
| 37 |
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"valid_nonpeaks.fold_3.bed"
|
| 38 |
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],
|
| 39 |
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"num_workers": 1,
|
| 40 |
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"out_window": 1000,
|
| 41 |
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"performance_filename": "cherimoya.fold_3.performance.tsv",
|
| 42 |
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|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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"ENCFF269OGN.bigWig"
|
| 49 |
+
],
|
| 50 |
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"skip": false,
|
| 51 |
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"summits": false,
|
| 52 |
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"training_chroms": [
|
| 53 |
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"chr1",
|
| 54 |
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"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
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"chr7",
|
| 58 |
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"chr8",
|
| 59 |
+
"chr9",
|
| 60 |
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"chr11",
|
| 61 |
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"chr12",
|
| 62 |
+
"chr13",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr16",
|
| 65 |
+
"chr17",
|
| 66 |
+
"chr19",
|
| 67 |
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"chrX",
|
| 68 |
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"chrY"
|
| 69 |
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],
|
| 70 |
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"validation_chroms": [
|
| 71 |
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"chr6",
|
| 72 |
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"chr21"
|
| 73 |
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|
| 74 |
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"verbose": true
|
| 75 |
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}
|
ENCSR000EMH/cherimoya.fold_3.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
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|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
400.01373291015625 0.3718898594379425 0.46977299451828003 0.15035952627658844 0.660731315612793 0.6373956799507141 0.7221590876579285
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ENCSR000EMH/cherimoya.fold_4.evaluate.json
ADDED
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@@ -0,0 +1,75 @@
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|
| 1 |
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{
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| 13 |
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| 14 |
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| 20 |
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|
| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 26 |
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| 27 |
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| 28 |
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|
| 29 |
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| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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"name": "cherimoya.fold_4",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
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| 36 |
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|
| 37 |
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|
| 38 |
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| 39 |
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|
| 40 |
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| 44 |
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| 45 |
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| 46 |
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"sequences": "hg38.fa",
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| 47 |
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"signals": [
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| 48 |
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"ENCFF269OGN.bigWig"
|
| 49 |
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],
|
| 50 |
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"skip": false,
|
| 51 |
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|
| 52 |
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| 55 |
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| 56 |
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| 57 |
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"chr5",
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| 58 |
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"chr6",
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| 59 |
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"chr8",
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| 60 |
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| 61 |
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"chr11",
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| 62 |
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"chr12",
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| 63 |
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"chr14",
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| 64 |
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"chr15",
|
| 65 |
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"chr16",
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| 66 |
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"chr20",
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| 67 |
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"chr22",
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| 68 |
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|
| 69 |
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|
| 70 |
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"validation_chroms": [
|
| 71 |
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"chr10",
|
| 72 |
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|
| 73 |
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|
| 74 |
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"verbose": true
|
| 75 |
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}
|
ENCSR000EMH/cherimoya.fold_4.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
{"n_filters": 128, "name": "cherimoya.fold_4", "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", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF269OGN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EMH/cherimoya.fold_4.log
ADDED
|
@@ -0,0 +1,21 @@
|
|
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|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 2883 36.36002516746521 4.105833530426025 347.1907043457031 2.0974478721618652 535.2734375 0.22915460169315338 0.3613506 4.536887168884277 True
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| 3 |
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1 5766 31.62566351890564 1.2135608196258545 279.392333984375 1.179816484451294 433.794677734375 0.40110886096954346 0.44837058 2.2848851680755615 True
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| 4 |
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2 8649 31.78545379638672 19.52534246444702 300.2642822265625 1.4574682712554932 425.768310546875 0.41164255142211914 0.45453912 1.0029774904251099 True
|
| 5 |
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3 11532 31.746756076812744 26.673705339431763 309.05938720703125 0.9022760987281799 419.3341979980469 0.4209877848625183 0.4753104 0.900092363357544 True
|
| 6 |
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4 14415 31.79728102684021 0.8644633293151855 289.3771667480469 0.9591305255889893 415.478515625 0.42954087257385254 0.47826695 0.9221096634864807 True
|
| 7 |
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5 17298 31.65303349494934 0.562952995300293 269.6591796875 0.8574283123016357 413.7703552246094 0.4307694435119629 0.49991512 0.8925978541374207 True
|
| 8 |
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6 20181 31.653214931488037 0.5903639793395996 294.201904296875 1.0679150819778442 409.8392639160156 0.4389973282814026 0.50525916 0.8957478404045105 True
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| 9 |
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7 23064 31.691351890563965 0.5465593338012695 383.07855224609375 1.000535011291504 407.84820556640625 0.4429364800453186 0.51738584 0.8766514658927917 True
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| 10 |
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8 25947 31.709836721420288 0.5605239868164062 316.0511474609375 0.7656831741333008 406.4525451660156 0.44492053985595703 0.53341234 0.8446964621543884 True
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| 11 |
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9 28830 31.628710746765137 0.555955171585083 269.5433349609375 1.0047835111618042 403.1633605957031 0.45077404379844666 0.5422696 0.8556678295135498 True
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| 12 |
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10 31713 31.65881323814392 0.5568010807037354 308.8232421875 1.1493911743164062 401.2433776855469 0.45380648970603943 0.55703634 0.8166574835777283 True
|
| 13 |
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11 34596 31.679895162582397 0.559072732925415 326.4631042480469 0.7598891258239746 398.8174743652344 0.4596749544143677 0.5736021 0.810926616191864 True
|
| 14 |
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12 37479 31.66209840774536 0.5594966411590576 303.5620422363281 0.9332448244094849 396.8850402832031 0.46148887276649475 0.59200937 0.7667292952537537 True
|
| 15 |
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13 40362 31.17741584777832 0.5536932945251465 308.337890625 0.8572614192962646 395.1632995605469 0.46459469199180603 0.6100125 0.7348178625106812 True
|
| 16 |
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14 43245 31.14313793182373 0.5548889636993408 227.96060180664062 0.7558194994926453 393.8251647949219 0.4667050540447235 0.6220993 0.7267264723777771 True
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| 17 |
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15 46128 31.078023672103882 0.550950288772583 311.0299987792969 0.7268311381340027 392.6986389160156 0.4692838788032532 0.6354622 0.7153612375259399 True
|
| 18 |
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16 49011 31.05071783065796 0.540351390838623 328.5240478515625 0.5647130012512207 391.8663024902344 0.47015711665153503 0.6433624 0.7025546431541443 True
|
| 19 |
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17 51894 31.090720653533936 0.5535886287689209 349.51397705078125 0.5942155122756958 391.9639892578125 0.469343900680542 0.6498115 0.698232114315033 True
|
| 20 |
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18 54777 31.0698721408844 0.5400238037109375 348.58154296875 0.7205489873886108 392.64129638671875 0.4673442244529724 0.6493649 0.7067158222198486 False
|
| 21 |
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19 57660 31.02342462539673 0.5408980846405029 259.8232116699219 0.750738799571991 391.625732421875 0.47070756554603577 0.6479895 0.7161760926246643 False
|
ENCSR000EMR/cherimoya.fold_1.log
ADDED
|
@@ -0,0 +1,21 @@
|
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|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 944 14.85985541343689 3.0892765522003174 273.9824523925781 1.3586431741714478 409.01788330078125 0.14882919192314148 0.28962737 17.689376831054688 True
|
| 3 |
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1 1888 10.265307664871216 0.29323530197143555 228.57420349121094 1.0082159042358398 386.59185791015625 0.2234707772731781 0.40821165 9.470619201660156 True
|
| 4 |
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2 2832 10.256781101226807 0.2758505344390869 234.90142822265625 0.9447590112686157 353.7644348144531 0.3122543692588806 0.4990318 9.275177001953125 True
|
| 5 |
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3 3776 10.247742652893066 0.276519775390625 263.7594299316406 1.1461741924285889 327.2459411621094 0.37554290890693665 0.4734026 5.993135452270508 False
|
| 6 |
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4 4720 10.253017663955688 0.27703857421875 220.98037719726562 0.9753820300102234 317.5213317871094 0.39963826537132263 0.45443895 3.275862693786621 False
|
| 7 |
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5 5664 10.266690492630005 13.812167644500732 263.3959045410156 0.9082911014556885 313.88470458984375 0.4055899679660797 0.4765066 2.126004219055176 False
|
| 8 |
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6 6608 10.610820293426514 0.27874231338500977 203.57757568359375 0.8939011096954346 311.8324890136719 0.4098920226097107 0.49987343 1.692667007446289 True
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| 9 |
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7 7552 10.290426969528198 0.2904505729675293 192.55206298828125 0.7864999771118164 309.71868896484375 0.41570964455604553 0.52733755 1.3821171522140503 True
|
| 10 |
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8 8496 10.252726316452026 0.279888391494751 231.3142852783203 0.622020959854126 308.3104553222656 0.41968464851379395 0.54225385 1.1854909658432007 True
|
| 11 |
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9 9440 10.28304123878479 0.27938389778137207 234.00820922851562 0.5153480768203735 306.6639099121094 0.4242601692676544 0.555513 1.005205750465393 True
|
| 12 |
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10 10384 10.297310829162598 0.27897095680236816 229.87060546875 0.5724303722381592 305.6004333496094 0.42695990204811096 0.56355184 0.8828398585319519 True
|
| 13 |
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11 11328 10.273160457611084 0.2762305736541748 237.08126831054688 0.6250860691070557 305.0143127441406 0.4283944070339203 0.5759377 0.7888731360435486 True
|
| 14 |
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12 12272 10.273183822631836 0.2765047550201416 242.60003662109375 0.46196991205215454 304.4078063964844 0.4301065504550934 0.58843356 0.7366577982902527 True
|
| 15 |
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13 13216 10.275833129882812 0.27843523025512695 221.6864013671875 0.659842848777771 303.88092041015625 0.43093475699424744 0.603929 0.6726111173629761 True
|
| 16 |
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14 14160 10.307110071182251 1.0390830039978027 231.2847900390625 0.47808897495269775 303.1611328125 0.43238794803619385 0.6209461 0.6206148862838745 True
|
| 17 |
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15 15104 10.27124309539795 0.2775247097015381 214.54173278808594 0.5979618430137634 303.1622009277344 0.4310366213321686 0.6294252 0.5895079970359802 True
|
| 18 |
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16 16048 10.248489379882812 0.28157854080200195 193.22903442382812 0.4232455790042877 303.4756164550781 0.4289025664329529 0.6376812 0.5616180896759033 True
|
| 19 |
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17 16992 10.297852754592896 9.274157285690308 222.21115112304688 0.5533275604248047 303.11065673828125 0.4306575357913971 0.64371413 0.5413572192192078 True
|
| 20 |
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18 17936 10.826558828353882 13.534093141555786 190.67617797851562 0.4496059715747833 302.8695983886719 0.43175238370895386 0.6456412 0.5378203392028809 True
|
| 21 |
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19 18880 10.755742311477661 0.28737926483154297 233.1892547607422 0.3733765482902527 302.8374328613281 0.43193602561950684 0.6433433 0.5363395810127258 False
|
ENCSR000EMR/cherimoya.fold_4.fit.json
ADDED
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| 1 |
+
{"n_filters": 128, "name": "cherimoya.fold_4", "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", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF398FTI.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENK/cherimoya.fold_0.fit.json
ADDED
|
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| 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": ["ENCFF067TKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENK/cherimoya.fold_0.log
ADDED
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@@ -0,0 +1,21 @@
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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?
|
| 2 |
+
0 2667 33.755863428115845 3.8572492599487305 288.5946350097656 0.9685482978820801 467.0762939453125 0.23001284897327423 0.3771579 5.56597375869751 True
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| 3 |
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1 5334 29.458614826202393 0.858950138092041 332.2065734863281 1.1018565893173218 389.11376953125 0.36287757754325867 0.5206736 3.1236305236816406 True
|
| 4 |
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2 8001 29.668556928634644 0.5613882541656494 277.0324401855469 0.7722659111022949 381.52813720703125 0.3744506239891052 0.5170646 2.1755552291870117 False
|
| 5 |
+
3 10668 29.40027666091919 0.6613082885742188 295.3372802734375 0.7527800798416138 373.26470947265625 0.3827812969684601 0.5391913 1.7072603702545166 True
|
| 6 |
+
4 13335 29.118650197982788 0.790353536605835 311.0370788574219 1.0205588340759277 368.2007751464844 0.3887671232223511 0.55908465 1.3770673274993896 True
|
| 7 |
+
5 16002 28.845803260803223 0.5587489604949951 341.4901123046875 1.0820326805114746 364.2305908203125 0.3956308960914612 0.5684253 1.2557463645935059 True
|
| 8 |
+
6 18669 28.88396644592285 0.5482277870178223 278.11962890625 0.8101660013198853 361.7564392089844 0.40073224902153015 0.575269 1.1773478984832764 True
|
| 9 |
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7 21336 28.81329917907715 0.5698165893554688 286.12054443359375 0.80912846326828 358.6970520019531 0.40711110830307007 0.587198 1.0675864219665527 True
|
| 10 |
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8 24003 28.811447143554688 0.551567792892456 355.477783203125 0.855770468711853 357.9220275878906 0.406687468290329 0.5981351 1.0362207889556885 True
|
| 11 |
+
9 26670 28.824831247329712 0.5484108924865723 248.61038208007812 0.8794538378715515 355.34539794921875 0.41186845302581787 0.60706997 0.929746687412262 True
|
| 12 |
+
10 29337 28.841965913772583 1.8346846103668213 269.0950012207031 0.7725647687911987 355.22503662109375 0.4113765060901642 0.61837727 0.8973484039306641 True
|
| 13 |
+
11 32004 28.85454034805298 1.2457897663116455 306.8975524902344 0.7147544622421265 352.3388671875 0.41762709617614746 0.6271535 0.8482998609542847 True
|
| 14 |
+
12 34671 28.821082592010498 0.5579743385314941 253.2112579345703 0.6432582139968872 351.00103759765625 0.420116662979126 0.6369521 0.8056564927101135 True
|
| 15 |
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13 37338 28.812183141708374 0.5359892845153809 253.4320068359375 0.6097066402435303 348.47137451171875 0.425498902797699 0.6541754 0.7277995944023132 True
|
| 16 |
+
14 40005 28.885140657424927 0.5511894226074219 315.60174560546875 0.6043848991394043 347.6416931152344 0.425432413816452 0.6604421 0.6955926418304443 True
|
| 17 |
+
15 42672 28.873677015304565 0.5408420562744141 227.274169921875 0.54421466588974 347.0425720214844 0.42590975761413574 0.670549 0.6550572514533997 True
|
| 18 |
+
16 45339 28.832077980041504 0.5675842761993408 241.96434020996094 0.47929584980010986 346.4461364746094 0.4273390769958496 0.67814636 0.6250951886177063 True
|
| 19 |
+
17 48006 28.81246590614319 0.5437850952148438 352.4361877441406 0.608135461807251 346.1530456542969 0.4271126389503479 0.68136436 0.6131812930107117 True
|
| 20 |
+
18 50673 28.86445188522339 0.5543653964996338 275.646728515625 0.5077953338623047 345.4288024902344 0.4296794831752777 0.6818799 0.608568012714386 True
|
| 21 |
+
19 53340 28.82740569114685 0.5585603713989258 247.30490112304688 0.47363948822021484 346.01129150390625 0.4283086359500885 0.68185014 0.6133825182914734 False
|
ENCSR000ENK/cherimoya.fold_0.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
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| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
345.4288024902344 0.41541311144828796 0.4296794831752777 0.1197810247540474 0.6818798780441284 0.6204215884208679 0.608568012714386
|
ENCSR000ENK/cherimoya.fold_1.evaluate.json
ADDED
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@@ -0,0 +1,77 @@
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| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr12",
|
| 7 |
+
"chr17"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_1.bed",
|
| 20 |
+
"valid_peaks.fold_1.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_1.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_1",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_1.bed",
|
| 37 |
+
"valid_nonpeaks.fold_1.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_1.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF067TKB.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr3",
|
| 55 |
+
"chr4",
|
| 56 |
+
"chr5",
|
| 57 |
+
"chr6",
|
| 58 |
+
"chr7",
|
| 59 |
+
"chr10",
|
| 60 |
+
"chr11",
|
| 61 |
+
"chr13",
|
| 62 |
+
"chr14",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr18",
|
| 65 |
+
"chr19",
|
| 66 |
+
"chr20",
|
| 67 |
+
"chr21",
|
| 68 |
+
"chr22",
|
| 69 |
+
"chrX",
|
| 70 |
+
"chrY"
|
| 71 |
+
],
|
| 72 |
+
"validation_chroms": [
|
| 73 |
+
"chr12",
|
| 74 |
+
"chr17"
|
| 75 |
+
],
|
| 76 |
+
"verbose": true
|
| 77 |
+
}
|
ENCSR000ENK/cherimoya.fold_2.fit.json
ADDED
|
@@ -0,0 +1 @@
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|
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|
| 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": ["ENCFF067TKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENK/cherimoya.fold_2.log
ADDED
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@@ -0,0 +1,21 @@
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|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 2843 36.186835289001465 2.5260047912597656 269.2835388183594 1.031495451927185 471.0160217285156 0.2313089817762375 0.36160752 4.354429244995117 True
|
| 3 |
+
1 5686 31.47916340827942 1.8770389556884766 450.02496337890625 1.147947072982788 393.3193054199219 0.3600604832172394 0.534358 3.1220414638519287 True
|
| 4 |
+
2 8529 31.48713254928589 1.2183094024658203 307.255615234375 0.8855488300323486 385.1778869628906 0.3696078360080719 0.54880786 2.306450128555298 True
|
| 5 |
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3 11372 31.401246070861816 0.4567112922668457 347.99176025390625 1.1787936687469482 376.587890625 0.38178104162216187 0.5637114 1.7622088193893433 True
|
| 6 |
+
4 14215 31.437533140182495 0.4563279151916504 241.0594024658203 0.8776891827583313 373.10137939453125 0.38913625478744507 0.57312894 1.6537160873413086 True
|
| 7 |
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5 17058 31.34365439414978 0.4635496139526367 315.712890625 0.751117467880249 369.6256103515625 0.39365914463996887 0.59190726 1.2359455823898315 True
|
| 8 |
+
6 19901 31.336628437042236 0.4609074592590332 274.1287536621094 0.8864656090736389 366.4793701171875 0.3992246389389038 0.59872854 1.115949273109436 True
|
| 9 |
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7 22744 31.31796884536743 0.4519829750061035 246.7063446044922 0.6631035804748535 364.21136474609375 0.4024914503097534 0.61785555 1.027609944343567 True
|
| 10 |
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8 25587 31.31361985206604 0.4606170654296875 248.2010498046875 0.7432874441146851 363.01104736328125 0.4040434956550598 0.6266556 0.9879398345947266 True
|
| 11 |
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9 28430 31.27871608734131 0.45717620849609375 278.3611755371094 0.7053835988044739 359.5047302246094 0.4119035601615906 0.6358716 0.9234618544578552 True
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| 12 |
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10 31273 31.370526552200317 0.4637424945831299 261.5574951171875 0.8685835599899292 358.3436584472656 0.4112555682659149 0.64839303 0.8659517168998718 True
|
| 13 |
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11 34116 30.895556211471558 0.4698193073272705 387.4256591796875 0.7675338983535767 355.8434143066406 0.41551005840301514 0.6581841 0.8265662789344788 True
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| 14 |
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12 36959 30.754565238952637 0.9886715412139893 217.25531005859375 0.5630032420158386 354.0951843261719 0.4178006052970886 0.671641 0.7608516812324524 True
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| 15 |
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13 39802 30.8349506855011 0.45487475395202637 249.62547302246094 0.578464686870575 352.91363525390625 0.4186139702796936 0.682414 0.7478006482124329 True
|
| 16 |
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14 42645 30.800154209136963 0.44853997230529785 244.1209259033203 0.6048245429992676 349.6985168457031 0.4260272681713104 0.6940212 0.6695789694786072 True
|
| 17 |
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15 45488 30.731124877929688 0.8819968700408936 285.4073486328125 0.6611371040344238 348.2605895996094 0.4278363883495331 0.703997 0.6468085050582886 True
|
| 18 |
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16 48331 30.77036190032959 0.4558525085449219 272.47991943359375 0.7282677292823792 348.527099609375 0.4243522882461548 0.71005636 0.614409863948822 True
|
| 19 |
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17 51174 30.775256156921387 0.48021602630615234 278.67474365234375 0.41922658681869507 347.7212829589844 0.4267672002315521 0.71151865 0.5993905067443848 True
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| 20 |
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18 54017 30.771045684814453 0.4418013095855713 296.47747802734375 0.34608709812164307 347.8335876464844 0.42566993832588196 0.71301717 0.5950757265090942 True
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| 21 |
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19 56860 30.76642084121704 0.46208739280700684 304.23876953125 0.420768678188324 349.0002746582031 0.42213746905326843 0.7105473 0.5972870588302612 False
|
ENCSR000ENK/cherimoya.fold_2.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
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| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
347.8335876464844 0.4175051152706146 0.4256698489189148 0.12017029523849487 0.7130171656608582 0.6459612250328064 0.5950757265090942
|
ENCSR000ENK/cherimoya.fold_3.evaluate.json
ADDED
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@@ -0,0 +1,75 @@
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|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
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|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr6",
|
| 7 |
+
"chr21"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
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|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_3.bed",
|
| 20 |
+
"valid_peaks.fold_3.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_3.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_3",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_3.bed",
|
| 37 |
+
"valid_nonpeaks.fold_3.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_3.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
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"residual_scale": 0.15,
|
| 44 |
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"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF067TKB.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
+
"chr7",
|
| 58 |
+
"chr8",
|
| 59 |
+
"chr9",
|
| 60 |
+
"chr11",
|
| 61 |
+
"chr12",
|
| 62 |
+
"chr13",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr16",
|
| 65 |
+
"chr17",
|
| 66 |
+
"chr19",
|
| 67 |
+
"chrX",
|
| 68 |
+
"chrY"
|
| 69 |
+
],
|
| 70 |
+
"validation_chroms": [
|
| 71 |
+
"chr6",
|
| 72 |
+
"chr21"
|
| 73 |
+
],
|
| 74 |
+
"verbose": true
|
| 75 |
+
}
|
ENCSR000ENK/cherimoya.fold_3.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF067TKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENK/cherimoya.fold_3.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
359.5428466796875 0.41220787167549133 0.43295013904571533 0.1202385276556015 0.7002761960029602 0.6464613080024719 0.639423668384552
|
ENCSR000ENK/cherimoya.fold_4.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
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|
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|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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{
|
| 2 |
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"adam_lr": 0.001,
|
| 3 |
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|
| 4 |
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"batch_size": 64,
|
| 5 |
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"chroms": [
|
| 6 |
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"chr10",
|
| 7 |
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"chr18"
|
| 8 |
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|
| 9 |
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|
| 10 |
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"device": "cuda",
|
| 11 |
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|
| 12 |
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|
| 13 |
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"exclusion_lists": [
|
| 14 |
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"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
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],
|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
+
],
|
| 22 |
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"lw_lr": 0.001,
|
| 23 |
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"lw_momentum": 0.9,
|
| 24 |
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"lw_wd": 0.0,
|
| 25 |
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"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_4.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
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"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_4",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
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"train_nonpeaks.fold_4.bed",
|
| 37 |
+
"valid_nonpeaks.fold_4.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
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"out_window": 1000,
|
| 41 |
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"performance_filename": "cherimoya.fold_4.performance.tsv",
|
| 42 |
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"random_state": null,
|
| 43 |
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"residual_scale": 0.15,
|
| 44 |
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"reverse_complement": false,
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| 45 |
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"reverse_complement_average": false,
|
| 46 |
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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"ENCFF067TKB.bigWig"
|
| 49 |
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],
|
| 50 |
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"skip": false,
|
| 51 |
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"summits": false,
|
| 52 |
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"training_chroms": [
|
| 53 |
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"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
+
"chr5",
|
| 58 |
+
"chr6",
|
| 59 |
+
"chr8",
|
| 60 |
+
"chr9",
|
| 61 |
+
"chr11",
|
| 62 |
+
"chr12",
|
| 63 |
+
"chr14",
|
| 64 |
+
"chr15",
|
| 65 |
+
"chr16",
|
| 66 |
+
"chr20",
|
| 67 |
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"chr22",
|
| 68 |
+
"chrY"
|
| 69 |
+
],
|
| 70 |
+
"validation_chroms": [
|
| 71 |
+
"chr10",
|
| 72 |
+
"chr18"
|
| 73 |
+
],
|
| 74 |
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"verbose": true
|
| 75 |
+
}
|
ENCSR000ENK/cherimoya.fold_4.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
{"n_filters": 128, "name": "cherimoya.fold_4", "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", "chr5", "chr6", "chr8", "chr9", "chr11", "chr12", "chr14", "chr15", "chr16", "chr20", "chr22", "chrY"], "validation_chroms": ["chr10", "chr18"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_4.bed", "valid_peaks.fold_4.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_4.bed", "valid_nonpeaks.fold_4.bed"], "signals": ["ENCFF067TKB.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENK/cherimoya.fold_4.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
344.7009582519531 0.41490665078163147 0.43117091059684753 0.11947669833898544 0.6855619549751282 0.6246109008789062 0.6184113621711731
|
ENCSR000ENV/cherimoya.fold_1.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF686TIY.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENV/cherimoya.fold_3.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
367.09466552734375 0.4333118796348572 0.37868186831474304 0.10936946421861649 0.6888483762741089 0.6495220065116882 0.5439686179161072
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ENCSR000ENV/cherimoya.fold_4.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
355.92974853515625 0.43447571992874146 0.3816661238670349 0.11105462163686752 0.6796679496765137 0.635467529296875 0.5403335094451904
|
ENCSR000EOR/cherimoya.fold_0.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF287MCX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EOR/cherimoya.fold_0.log
ADDED
|
@@ -0,0 +1,21 @@
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|
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|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 2746 34.45118570327759 3.5534157752990723 915.8508911132812 1.8939473628997803 1708.2093505859375 0.315344899892807 0.37971646 11.286249160766602 True
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2 8238 30.222514152526855 0.5850553512573242 832.1640625 2.312551736831665 1271.8447265625 0.5130314230918884 0.49954373 2.967759847640991 False
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| 5 |
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3 10984 30.17898678779602 0.5701847076416016 1118.015625 1.4817333221435547 1256.66796875 0.5146921277046204 0.50370485 2.3115997314453125 False
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| 9 |
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| 10 |
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10 30206 30.176331758499146 1.2179088592529297 975.0387573242188 1.4124274253845215 1182.072021484375 0.5538567304611206 0.5654627 1.2354185581207275 True
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| 13 |
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11 32952 30.057295322418213 1.5279061794281006 950.4362182617188 1.6762213706970215 1178.2392578125 0.5533609986305237 0.58115613 1.117282748222351 True
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| 15 |
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13 38444 29.70351505279541 0.5746278762817383 1048.408935546875 0.9477041959762573 1159.1766357421875 0.5613175630569458 0.6053269 0.9475811719894409 True
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14 41190 29.618668794631958 1.1298549175262451 832.4830322265625 1.1390870809555054 1155.8997802734375 0.5630613565444946 0.61771876 0.899402379989624 True
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15 43936 29.608325958251953 1.7650244235992432 965.067626953125 1.3353707790374756 1153.6185302734375 0.5636598467826843 0.63086087 0.8479098677635193 True
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| 18 |
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16 46682 29.566537618637085 0.5646061897277832 909.63623046875 0.784957230091095 1148.9029541015625 0.5651788711547852 0.6389813 0.795829176902771 True
|
| 19 |
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17 49428 29.573811531066895 0.561337947845459 875.9702758789062 0.704182505607605 1147.8077392578125 0.5659155249595642 0.6438005 0.7741154432296753 True
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19 54920 29.770970344543457 27.576485872268677 834.6178588867188 1.3916820287704468 1145.57177734375 0.5682700872421265 0.6479227 0.7553518414497375 True
|
ENCSR000EOR/cherimoya.fold_1.evaluate.json
ADDED
|
@@ -0,0 +1,77 @@
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|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
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|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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"chr12",
|
| 7 |
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"chr17"
|
| 8 |
+
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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"exclusion_lists": [
|
| 14 |
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"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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"valid_peaks.fold_1.bed"
|
| 21 |
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],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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"model": "cherimoya.fold_1.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_1",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_1.bed",
|
| 37 |
+
"valid_nonpeaks.fold_1.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_1.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF287MCX.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr3",
|
| 55 |
+
"chr4",
|
| 56 |
+
"chr5",
|
| 57 |
+
"chr6",
|
| 58 |
+
"chr7",
|
| 59 |
+
"chr10",
|
| 60 |
+
"chr11",
|
| 61 |
+
"chr13",
|
| 62 |
+
"chr14",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr18",
|
| 65 |
+
"chr19",
|
| 66 |
+
"chr20",
|
| 67 |
+
"chr21",
|
| 68 |
+
"chr22",
|
| 69 |
+
"chrX",
|
| 70 |
+
"chrY"
|
| 71 |
+
],
|
| 72 |
+
"validation_chroms": [
|
| 73 |
+
"chr12",
|
| 74 |
+
"chr17"
|
| 75 |
+
],
|
| 76 |
+
"verbose": true
|
| 77 |
+
}
|
ENCSR000EOR/cherimoya.fold_2.evaluate.json
ADDED
|
@@ -0,0 +1,76 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr22",
|
| 7 |
+
"chr7"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_2.bed",
|
| 20 |
+
"valid_peaks.fold_2.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_2.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_2",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_2.bed",
|
| 37 |
+
"valid_nonpeaks.fold_2.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_2.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF287MCX.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr5",
|
| 57 |
+
"chr6",
|
| 58 |
+
"chr8",
|
| 59 |
+
"chr9",
|
| 60 |
+
"chr10",
|
| 61 |
+
"chr13",
|
| 62 |
+
"chr14",
|
| 63 |
+
"chr16",
|
| 64 |
+
"chr17",
|
| 65 |
+
"chr18",
|
| 66 |
+
"chr19",
|
| 67 |
+
"chr20",
|
| 68 |
+
"chr21",
|
| 69 |
+
"chrX"
|
| 70 |
+
],
|
| 71 |
+
"validation_chroms": [
|
| 72 |
+
"chr22",
|
| 73 |
+
"chr7"
|
| 74 |
+
],
|
| 75 |
+
"verbose": true
|
| 76 |
+
}
|
ENCSR000EOR/cherimoya.fold_3.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr6",
|
| 7 |
+
"chr21"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_3.bed",
|
| 20 |
+
"valid_peaks.fold_3.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_3.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_3",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_3.bed",
|
| 37 |
+
"valid_nonpeaks.fold_3.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_3.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF287MCX.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
+
"chr7",
|
| 58 |
+
"chr8",
|
| 59 |
+
"chr9",
|
| 60 |
+
"chr11",
|
| 61 |
+
"chr12",
|
| 62 |
+
"chr13",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr16",
|
| 65 |
+
"chr17",
|
| 66 |
+
"chr19",
|
| 67 |
+
"chrX",
|
| 68 |
+
"chrY"
|
| 69 |
+
],
|
| 70 |
+
"validation_chroms": [
|
| 71 |
+
"chr6",
|
| 72 |
+
"chr21"
|
| 73 |
+
],
|
| 74 |
+
"verbose": true
|
| 75 |
+
}
|
ENCSR000EOR/cherimoya.fold_3.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF287MCX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EOR/cherimoya.fold_4.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr10",
|
| 7 |
+
"chr18"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_4.bed",
|
| 20 |
+
"valid_peaks.fold_4.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_4.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_4",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_4.bed",
|
| 37 |
+
"valid_nonpeaks.fold_4.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_4.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF287MCX.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
+
"chr5",
|
| 58 |
+
"chr6",
|
| 59 |
+
"chr8",
|
| 60 |
+
"chr9",
|
| 61 |
+
"chr11",
|
| 62 |
+
"chr12",
|
| 63 |
+
"chr14",
|
| 64 |
+
"chr15",
|
| 65 |
+
"chr16",
|
| 66 |
+
"chr20",
|
| 67 |
+
"chr22",
|
| 68 |
+
"chrY"
|
| 69 |
+
],
|
| 70 |
+
"validation_chroms": [
|
| 71 |
+
"chr10",
|
| 72 |
+
"chr18"
|
| 73 |
+
],
|
| 74 |
+
"verbose": true
|
| 75 |
+
}
|
ENCSR000EPH/cherimoya.fold_0.evaluate.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr8",
|
| 7 |
+
"chr20"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
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"expansion": 2,
|
| 17 |
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"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
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"train_peaks.fold_0.bed",
|
| 20 |
+
"valid_peaks.fold_0.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
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"lw_momentum": 0.9,
|
| 24 |
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"lw_wd": 0.0,
|
| 25 |
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"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_0.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_0",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_0.bed",
|
| 37 |
+
"valid_nonpeaks.fold_0.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_0.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF732OWD.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr2",
|
| 54 |
+
"chr4",
|
| 55 |
+
"chr5",
|
| 56 |
+
"chr7",
|
| 57 |
+
"chr9",
|
| 58 |
+
"chr10",
|
| 59 |
+
"chr11",
|
| 60 |
+
"chr12",
|
| 61 |
+
"chr13",
|
| 62 |
+
"chr14",
|
| 63 |
+
"chr15",
|
| 64 |
+
"chr16",
|
| 65 |
+
"chr17",
|
| 66 |
+
"chr18",
|
| 67 |
+
"chr19",
|
| 68 |
+
"chr21",
|
| 69 |
+
"chr22",
|
| 70 |
+
"chrX",
|
| 71 |
+
"chrY"
|
| 72 |
+
],
|
| 73 |
+
"validation_chroms": [
|
| 74 |
+
"chr8",
|
| 75 |
+
"chr20"
|
| 76 |
+
],
|
| 77 |
+
"verbose": true
|
| 78 |
+
}
|
ENCSR000EPH/cherimoya.fold_0.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF732OWD.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EPH/cherimoya.fold_1.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
559.1942749023438 0.3463505208492279 0.5092667937278748 0.16757550835609436 0.612389087677002 0.5955588221549988 0.7808120250701904
|
ENCSR000EPH/cherimoya.fold_3.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
489.4029235839844 0.3559707701206207 0.5072622895240784 0.15207773447036743 0.6617958545684814 0.6368720531463623 0.5386223793029785
|
ENCSR000EPH/cherimoya.fold_4.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
|
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|
|
|
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|
|
|
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|
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|
|
|
|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
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|
|
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|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
+
"chroms": [
|
| 6 |
+
"chr10",
|
| 7 |
+
"chr18"
|
| 8 |
+
],
|
| 9 |
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"controls": null,
|
| 10 |
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"device": "cuda",
|
| 11 |
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"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
+
],
|
| 16 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_4.bed",
|
| 20 |
+
"valid_peaks.fold_4.bed"
|
| 21 |
+
],
|
| 22 |
+
"lw_lr": 0.001,
|
| 23 |
+
"lw_momentum": 0.9,
|
| 24 |
+
"lw_wd": 0.0,
|
| 25 |
+
"max_epochs": 20,
|
| 26 |
+
"max_jitter": 0,
|
| 27 |
+
"model": "cherimoya.fold_4.torch",
|
| 28 |
+
"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
+
"n_layers": 9,
|
| 32 |
+
"n_warmup_epochs": 2,
|
| 33 |
+
"name": "cherimoya.fold_4",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_4.bed",
|
| 37 |
+
"valid_nonpeaks.fold_4.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"out_window": 1000,
|
| 41 |
+
"performance_filename": "cherimoya.fold_4.performance.tsv",
|
| 42 |
+
"random_state": null,
|
| 43 |
+
"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
+
"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF732OWD.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr1",
|
| 54 |
+
"chr2",
|
| 55 |
+
"chr3",
|
| 56 |
+
"chr4",
|
| 57 |
+
"chr5",
|
| 58 |
+
"chr6",
|
| 59 |
+
"chr8",
|
| 60 |
+
"chr9",
|
| 61 |
+
"chr11",
|
| 62 |
+
"chr12",
|
| 63 |
+
"chr14",
|
| 64 |
+
"chr15",
|
| 65 |
+
"chr16",
|
| 66 |
+
"chr20",
|
| 67 |
+
"chr22",
|
| 68 |
+
"chrY"
|
| 69 |
+
],
|
| 70 |
+
"validation_chroms": [
|
| 71 |
+
"chr10",
|
| 72 |
+
"chr18"
|
| 73 |
+
],
|
| 74 |
+
"verbose": true
|
| 75 |
+
}
|
ENCSR000EPQ/cherimoya.fold_0.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
269.9356689453125 0.4589698016643524 0.37147271633148193 0.09414173662662506 0.6425240635871887 0.5915403962135315 0.4887496531009674
|
ENCSR000EPQ/cherimoya.fold_1.log
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 2507 30.85050916671753 5.064661741256714 219.58547973632812 0.6814078092575073 355.79913330078125 0.2193847894668579 0.32638878 5.4405741691589355 True
|
| 3 |
+
1 5014 27.493318796157837 0.6814262866973877 227.0580291748047 0.7040629386901855 316.1189270019531 0.3299599289894104 0.42442334 3.1677029132843018 True
|
| 4 |
+
2 7521 27.64250898361206 2.9883930683135986 248.59759521484375 0.6299707889556885 309.1253967285156 0.34213265776634216 0.46207786 1.9037585258483887 True
|
| 5 |
+
3 10028 27.659483432769775 0.6596856117248535 202.8247528076172 0.6288661956787109 305.6856384277344 0.3496394157409668 0.4901525 1.441800594329834 True
|
| 6 |
+
4 12535 27.63766646385193 0.6632802486419678 274.72027587890625 1.1921720504760742 303.6156005859375 0.35520538687705994 0.4946572 1.3415639400482178 True
|
| 7 |
+
5 15042 27.690159797668457 1.0302228927612305 234.42604064941406 0.6017673015594482 302.4851379394531 0.35918521881103516 0.5139629 1.179305911064148 True
|
| 8 |
+
6 17549 27.70085573196411 0.6625039577484131 212.0125732421875 0.6885376572608948 301.4290771484375 0.3616507351398468 0.5313973 1.1092216968536377 True
|
| 9 |
+
7 20056 27.655572652816772 0.6515178680419922 252.371826171875 0.8739756941795349 300.8522033691406 0.3623476028442383 0.54400826 1.105907678604126 True
|
| 10 |
+
8 22563 27.657564878463745 0.6539857387542725 269.63751220703125 0.5783222913742065 299.824462890625 0.3638615906238556 0.570818 0.9760389924049377 True
|
| 11 |
+
9 25070 27.616020917892456 4.272314786911011 233.13528442382812 0.6840600967407227 298.56121826171875 0.36841192841529846 0.58400756 0.9294266104698181 True
|
| 12 |
+
10 27577 27.69230818748474 0.6580891609191895 229.19741821289062 0.7250605821609497 297.3306884765625 0.37160611152648926 0.6000145 0.8790220022201538 True
|
| 13 |
+
11 30084 27.684731006622314 0.6462874412536621 255.3465576171875 0.4017353355884552 296.43408203125 0.3727347254753113 0.61756366 0.7968965172767639 True
|
| 14 |
+
12 32591 27.63409662246704 0.6602792739868164 215.06768798828125 0.541333019733429 295.6476135253906 0.37456491589546204 0.6339498 0.7397342920303345 True
|
| 15 |
+
13 35098 27.66008710861206 0.6830096244812012 249.40667724609375 0.48180854320526123 295.0722961425781 0.37607210874557495 0.64360005 0.6835386157035828 True
|
| 16 |
+
14 37605 27.67548680305481 1.936579704284668 272.4033203125 0.48693448305130005 294.27325439453125 0.37702158093452454 0.65788823 0.6220824122428894 True
|
| 17 |
+
15 40112 27.640050172805786 0.6603922843933105 193.97401428222656 0.5563404560089111 293.73040771484375 0.3795171082019806 0.66656375 0.5769056081771851 True
|
| 18 |
+
16 42619 27.677070140838623 0.6430187225341797 253.053955078125 0.5560356378555298 293.6663513183594 0.3786439597606659 0.6725784 0.5453908443450928 True
|
| 19 |
+
17 45126 27.649123430252075 0.6441504955291748 208.41348266601562 0.36748501658439636 293.3232727050781 0.38019615411758423 0.6716054 0.5210117101669312 False
|
| 20 |
+
18 47633 27.67264437675476 0.6626405715942383 201.05987548828125 0.3356390595436096 293.30523681640625 0.3798712193965912 0.67205423 0.5150779485702515 False
|
| 21 |
+
19 50140 27.671396732330322 0.6570265293121338 186.370361328125 0.2405155897140503 293.3620910644531 0.37949466705322266 0.670427 0.5150659680366516 False
|
ENCSR000EPQ/cherimoya.fold_1.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
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|
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|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
293.6663513183594 0.45105743408203125 0.3786439299583435 0.0975472629070282 0.6725783944129944 0.6271970272064209 0.5453908443450928
|
ENCSR000EPQ/cherimoya.fold_2.evaluate.json
ADDED
|
@@ -0,0 +1,76 @@
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| 1 |
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{
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| 2 |
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"adam_lr": 0.001,
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| 3 |
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| 4 |
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"batch_size": 64,
|
| 5 |
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| 6 |
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"chr22",
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| 7 |
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"chr7"
|
| 8 |
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| 9 |
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| 10 |
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|
| 11 |
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| 12 |
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|
| 13 |
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"exclusion_lists": [
|
| 14 |
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"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
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| 16 |
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|
| 17 |
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|
| 18 |
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"loci": [
|
| 19 |
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"train_peaks.fold_2.bed",
|
| 20 |
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"valid_peaks.fold_2.bed"
|
| 21 |
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],
|
| 22 |
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"lw_lr": 0.001,
|
| 23 |
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"lw_momentum": 0.9,
|
| 24 |
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"lw_wd": 0.0,
|
| 25 |
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"max_epochs": 20,
|
| 26 |
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"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_2.torch",
|
| 28 |
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"muon_lr": 0.025,
|
| 29 |
+
"muon_wd": 0.03,
|
| 30 |
+
"n_filters": 128,
|
| 31 |
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"n_layers": 9,
|
| 32 |
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"n_warmup_epochs": 2,
|
| 33 |
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"name": "cherimoya.fold_2",
|
| 34 |
+
"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
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"train_nonpeaks.fold_2.bed",
|
| 37 |
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"valid_nonpeaks.fold_2.bed"
|
| 38 |
+
],
|
| 39 |
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"num_workers": 1,
|
| 40 |
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"out_window": 1000,
|
| 41 |
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"performance_filename": "cherimoya.fold_2.performance.tsv",
|
| 42 |
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"random_state": null,
|
| 43 |
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"residual_scale": 0.15,
|
| 44 |
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"reverse_complement": false,
|
| 45 |
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|
| 46 |
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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"ENCFF114YPJ.bigWig"
|
| 49 |
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],
|
| 50 |
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"skip": false,
|
| 51 |
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"summits": false,
|
| 52 |
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"training_chroms": [
|
| 53 |
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"chr1",
|
| 54 |
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"chr2",
|
| 55 |
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"chr3",
|
| 56 |
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"chr5",
|
| 57 |
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"chr6",
|
| 58 |
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"chr8",
|
| 59 |
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"chr9",
|
| 60 |
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"chr10",
|
| 61 |
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"chr13",
|
| 62 |
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"chr14",
|
| 63 |
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"chr16",
|
| 64 |
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"chr17",
|
| 65 |
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"chr18",
|
| 66 |
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"chr19",
|
| 67 |
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"chr20",
|
| 68 |
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"chr21",
|
| 69 |
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"chrX"
|
| 70 |
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],
|
| 71 |
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"validation_chroms": [
|
| 72 |
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"chr22",
|
| 73 |
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"chr7"
|
| 74 |
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],
|
| 75 |
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"verbose": true
|
| 76 |
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}
|
ENCSR000EPQ/cherimoya.fold_3.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
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|
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|
|
|
|
|
| 1 |
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{
|
| 2 |
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"adam_lr": 0.001,
|
| 3 |
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"adam_wd": 0.0,
|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
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| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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|
| 26 |
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|
| 27 |
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"model": "cherimoya.fold_3.torch",
|
| 28 |
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|
| 29 |
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"muon_wd": 0.03,
|
| 30 |
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"n_filters": 128,
|
| 31 |
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"n_layers": 9,
|
| 32 |
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"n_warmup_epochs": 2,
|
| 33 |
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"name": "cherimoya.fold_3",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
|
| 36 |
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"train_nonpeaks.fold_3.bed",
|
| 37 |
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"valid_nonpeaks.fold_3.bed"
|
| 38 |
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],
|
| 39 |
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"num_workers": 1,
|
| 40 |
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|
| 41 |
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"performance_filename": "cherimoya.fold_3.performance.tsv",
|
| 42 |
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|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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"ENCFF114YPJ.bigWig"
|
| 49 |
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],
|
| 50 |
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"skip": false,
|
| 51 |
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"summits": false,
|
| 52 |
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"training_chroms": [
|
| 53 |
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"chr1",
|
| 54 |
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"chr2",
|
| 55 |
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"chr3",
|
| 56 |
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"chr4",
|
| 57 |
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"chr7",
|
| 58 |
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"chr8",
|
| 59 |
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"chr9",
|
| 60 |
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"chr11",
|
| 61 |
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"chr12",
|
| 62 |
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"chr13",
|
| 63 |
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"chr15",
|
| 64 |
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"chr16",
|
| 65 |
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"chr17",
|
| 66 |
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"chr19",
|
| 67 |
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"chrX",
|
| 68 |
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"chrY"
|
| 69 |
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],
|
| 70 |
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"validation_chroms": [
|
| 71 |
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"chr6",
|
| 72 |
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"chr21"
|
| 73 |
+
],
|
| 74 |
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"verbose": true
|
| 75 |
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}
|
ENCSR000EPQ/cherimoya.fold_3.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF114YPJ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EPQ/cherimoya.fold_3.log
ADDED
|
@@ -0,0 +1,21 @@
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|
| 1 |
+
Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
|
| 2 |
+
0 2572 32.245500326156616 3.2779831886291504 244.0634765625 0.7337441444396973 332.875732421875 0.2190619856119156 0.32451546 5.523846626281738 True
|
| 3 |
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1 5144 28.354580640792847 0.4931495189666748 195.7598114013672 0.6459639668464661 295.1165771484375 0.3267221450805664 0.38117632 2.710296630859375 True
|
| 4 |
+
2 7716 28.217299699783325 0.5097177028656006 207.9178466796875 0.651492714881897 288.27044677734375 0.34493517875671387 0.43861645 1.8004521131515503 True
|
| 5 |
+
3 10288 27.851092100143433 0.45599842071533203 207.34359741210938 0.5996551513671875 285.9154968261719 0.3500394821166992 0.4583197 1.4194178581237793 True
|
| 6 |
+
4 12860 27.845239877700806 0.4554448127746582 221.82872009277344 0.7370072603225708 284.72467041015625 0.35085541009902954 0.46103334 1.4143953323364258 True
|
| 7 |
+
5 15432 27.838214635849 0.47211217880249023 230.98104858398438 0.7129526138305664 283.4190979003906 0.3547973334789276 0.48475465 1.3598626852035522 True
|
| 8 |
+
6 18004 27.781067371368408 0.4667649269104004 234.6902313232422 0.694933295249939 282.1406555175781 0.3597399890422821 0.49724957 1.2894266843795776 True
|
| 9 |
+
7 20576 27.809310913085938 0.4712660312652588 198.4401092529297 0.8213810324668884 281.72344970703125 0.359779953956604 0.5105665 1.1388559341430664 True
|
| 10 |
+
8 23148 27.77792000770569 0.4632885456085205 194.2813720703125 0.5079885721206665 280.5914001464844 0.3623403310775757 0.527875 1.065756916999817 True
|
| 11 |
+
9 25720 27.797399282455444 0.46909141540527344 185.98348999023438 0.6695368885993958 279.4920959472656 0.3655053377151489 0.54635686 0.9265697002410889 True
|
| 12 |
+
10 28292 27.83170247077942 0.4667515754699707 225.01124572753906 0.7090641260147095 278.48382568359375 0.3681977391242981 0.56529576 0.8347483277320862 True
|
| 13 |
+
11 30864 27.838175535202026 0.46839165687561035 225.0776824951172 0.5794326066970825 277.1452331542969 0.37289899587631226 0.5799864 0.7340198159217834 True
|
| 14 |
+
12 33436 27.777246952056885 3.1185615062713623 195.28482055664062 0.5214170217514038 277.3821716308594 0.36913198232650757 0.60118973 0.680140495300293 True
|
| 15 |
+
13 36008 27.864243268966675 0.4650459289550781 210.93063354492188 0.5310831069946289 276.5753479003906 0.3713209927082062 0.6193789 0.6139722466468811 True
|
| 16 |
+
14 38580 28.21646523475647 0.46854376792907715 238.23672485351562 0.4791708290576935 275.6590881347656 0.3743301033973694 0.634389 0.572997510433197 True
|
| 17 |
+
15 41152 27.76961398124695 1.0973870754241943 220.03219604492188 0.6139910221099854 275.4657287597656 0.3747091293334961 0.6450406 0.5363573431968689 True
|
| 18 |
+
16 43724 27.797606468200684 0.46518683433532715 179.31472778320312 0.33320069313049316 275.2656555175781 0.37401044368743896 0.65538573 0.49735739827156067 True
|
| 19 |
+
17 46296 27.73337435722351 0.46779632568359375 194.74960327148438 0.40770959854125977 274.69677734375 0.3775349259376526 0.6604172 0.4729439914226532 True
|
| 20 |
+
18 48868 27.809180974960327 0.46714115142822266 215.90245056152344 0.5268589854240417 274.5207214355469 0.37792617082595825 0.66136676 0.46778255701065063 True
|
| 21 |
+
19 51440 27.732709407806396 0.87709641456604 219.90614318847656 0.28437429666519165 274.7343444824219 0.3766683042049408 0.66063833 0.4687548279762268 False
|
ENCSR000EPQ/cherimoya.fold_4.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
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|
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|
|
|
|
| 1 |
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{
|
| 2 |
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"adam_lr": 0.001,
|
| 3 |
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|
| 4 |
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"batch_size": 64,
|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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],
|
| 9 |
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"controls": null,
|
| 10 |
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|
| 11 |
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|
| 12 |
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"early_stopping": 20,
|
| 13 |
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"exclusion_lists": [
|
| 14 |
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|
| 15 |
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| 16 |
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| 19 |
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| 20 |
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| 21 |
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| 23 |
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| 26 |
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| 29 |
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| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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"name": "cherimoya.fold_4",
|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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|
| 38 |
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|
| 39 |
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|
| 40 |
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|
| 41 |
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|
| 42 |
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|
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| 47 |
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|
| 48 |
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|
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| 50 |
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|
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| 53 |
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| 60 |
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| 62 |
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|
| 75 |
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ENCSR000EPQ/cherimoya.fold_4.log
ADDED
|
@@ -0,0 +1,21 @@
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| 1 |
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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?
|
| 2 |
+
0 2651 33.020697593688965 4.125022888183594 186.57498168945312 0.6409615278244019 322.6328125 0.21856006979942322 0.2874952 4.274867534637451 True
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| 5 |
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3 10604 29.36940884590149 0.48953676223754883 217.14944458007812 0.799812376499176 276.20135498046875 0.34717607498168945 0.47191837 1.0124248266220093 True
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| 6 |
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4 13255 29.369965314865112 0.48834919929504395 245.23004150390625 0.6807497143745422 274.7402648925781 0.35243016481399536 0.48345616 0.9098888635635376 True
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| 10 |
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|
| 11 |
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9 26510 28.750788688659668 0.4955568313598633 232.97177124023438 0.6909072399139404 269.8503723144531 0.36743471026420593 0.5474116 0.7082645297050476 True
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| 12 |
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10 29161 28.71936845779419 0.49257397651672363 182.4210968017578 0.6198098063468933 269.13720703125 0.36888018250465393 0.56489515 0.6623013615608215 True
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| 13 |
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11 31812 28.73585033416748 0.4977560043334961 197.340087890625 0.4867655634880066 268.263427734375 0.37226957082748413 0.57808673 0.6297916769981384 True
|
| 14 |
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12 34463 28.672990560531616 18.526740074157715 262.2851257324219 0.5162768363952637 267.8006896972656 0.37318965792655945 0.59323436 0.5835382342338562 True
|
| 15 |
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13 37114 28.770195960998535 0.49736905097961426 225.5028076171875 0.3730636239051819 267.43414306640625 0.37405624985694885 0.60474956 0.5498105883598328 True
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| 16 |
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14 39765 28.735187768936157 0.9989945888519287 214.43820190429688 0.6834133863449097 266.7751159667969 0.3767082989215851 0.61342657 0.532045841217041 True
|
| 17 |
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15 42416 28.691091060638428 0.48369717597961426 226.77914428710938 0.5555849075317383 266.42431640625 0.3780551850795746 0.6201145 0.521652102470398 True
|
| 18 |
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16 45067 28.65827965736389 0.48598790168762207 239.97329711914062 0.3610469400882721 266.7939147949219 0.37539786100387573 0.6272595 0.49787554144859314 True
|
| 19 |
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17 47718 28.622888803482056 0.4857783317565918 223.61737060546875 0.38051849603652954 266.2796325683594 0.3779152035713196 0.62991244 0.48724526166915894 True
|
| 20 |
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18 50369 28.713773250579834 0.48569703102111816 246.4102020263672 0.4647563099861145 266.66912841796875 0.3754345178604126 0.629033 0.4873252511024475 False
|
| 21 |
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19 53020 28.643713235855103 0.49350619316101074 206.07058715820312 0.490253210067749 266.3540954589844 0.37724971771240234 0.6278732 0.49101200699806213 False
|
ENCSR000EPQ/cherimoya.fold_4.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
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|
|
|
|
|
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|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
266.2796325683594 0.45749402046203613 0.37791526317596436 0.09152133762836456 0.6299124360084534 0.5815083980560303 0.48724526166915894
|
ENCSR000EQD/cherimoya.fold_0.evaluate.json
ADDED
|
@@ -0,0 +1,78 @@
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|
|
| 1 |
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{
|
| 2 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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| 6 |
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| 7 |
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|
| 8 |
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| 9 |
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| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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| 16 |
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|
| 17 |
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| 18 |
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| 19 |
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| 20 |
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|
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|
| 26 |
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|
| 31 |
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|
| 32 |
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"name": "cherimoya.fold_0",
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"negative_ratio": 0.25,
|
| 35 |
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