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- ENCSR000ENA/cherimoya.fold_0.evaluate.json +78 -0
- ENCSR000ENA/cherimoya.fold_0.fit.json +1 -0
- ENCSR000ENA/cherimoya.fold_0.log +21 -0
- ENCSR000ENA/cherimoya.fold_0.performance.tsv +2 -0
- ENCSR000ENA/cherimoya.fold_1.evaluate.json +77 -0
- ENCSR000ENA/cherimoya.fold_1.fit.json +1 -0
- ENCSR000ENA/cherimoya.fold_1.log +21 -0
- ENCSR000ENA/cherimoya.fold_1.performance.tsv +2 -0
- ENCSR000ENA/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR000ENA/cherimoya.fold_2.fit.json +1 -0
- ENCSR000ENA/cherimoya.fold_2.log +21 -0
- ENCSR000ENA/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR000ENA/cherimoya.fold_3.fit.json +1 -0
- ENCSR000ENA/cherimoya.fold_3.log +21 -0
- ENCSR000ENA/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000ENA/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR000ENA/cherimoya.fold_4.fit.json +1 -0
- ENCSR000ENA/cherimoya.fold_4.log +21 -0
- ENCSR000ENA/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR000EOP/cherimoya.fold_0.evaluate.json +78 -0
- ENCSR000EOP/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR000EOP/cherimoya.fold_2.fit.json +1 -0
- ENCSR000EOP/cherimoya.fold_2.log +21 -0
- ENCSR000EOP/cherimoya.fold_2.performance.tsv +2 -0
- ENCSR000EOP/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR000EOP/cherimoya.fold_4.fit.json +1 -0
- ENCSR000EOP/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR044ATC/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR082XEU/cherimoya.fold_0.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_0.evaluate.json +78 -0
- ENCSR121ZSL/cherimoya.fold_0.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_0.log +21 -0
- ENCSR121ZSL/cherimoya.fold_0.performance.tsv +2 -0
- ENCSR121ZSL/cherimoya.fold_1.evaluate.json +77 -0
- ENCSR121ZSL/cherimoya.fold_1.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_1.log +21 -0
- ENCSR121ZSL/cherimoya.fold_1.performance.tsv +2 -0
- ENCSR121ZSL/cherimoya.fold_2.evaluate.json +76 -0
- ENCSR121ZSL/cherimoya.fold_2.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_2.log +21 -0
- ENCSR121ZSL/cherimoya.fold_2.performance.tsv +2 -0
- ENCSR121ZSL/cherimoya.fold_3.evaluate.json +75 -0
- ENCSR121ZSL/cherimoya.fold_3.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_3.log +21 -0
- ENCSR121ZSL/cherimoya.fold_3.performance.tsv +2 -0
- ENCSR121ZSL/cherimoya.fold_4.evaluate.json +75 -0
- ENCSR121ZSL/cherimoya.fold_4.fit.json +1 -0
- ENCSR121ZSL/cherimoya.fold_4.log +21 -0
- ENCSR121ZSL/cherimoya.fold_4.performance.tsv +2 -0
- ENCSR148MFM/cherimoya.fold_0.evaluate.json +78 -0
ENCSR000ENA/cherimoya.fold_0.evaluate.json
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{
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"name": "cherimoya.fold_0",
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"negative_ratio": 0.25,
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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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ENCSR000ENA/cherimoya.fold_0.fit.json
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{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF943QQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
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ENCSR000ENA/cherimoya.fold_0.log
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Epoch Iteration Training Time Validation Time Training MNLL Training Count MSE Validation MNLL Validation Profile Pearson Validation Count Pearson Validation Count MSE Saved?
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ENCSR000ENA/cherimoya.fold_0.performance.tsv
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profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
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| 2 |
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1255.7059326171875 0.25237366557121277 0.547177255153656 0.2995665967464447 0.7492042183876038 0.7091129422187805 0.4002588093280792
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ENCSR000ENA/cherimoya.fold_1.evaluate.json
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{
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"adam_lr": 0.001,
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| 3 |
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| 4 |
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| 5 |
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"chr17"
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"early_stopping": 20,
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| 13 |
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"exclusion_lists": [
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| 14 |
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"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
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| 15 |
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],
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| 16 |
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"expansion": 2,
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| 17 |
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"in_window": 2114,
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| 18 |
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"loci": [
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| 19 |
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"train_peaks.fold_1.bed",
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| 20 |
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"valid_peaks.fold_1.bed"
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],
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| 22 |
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"lw_lr": 0.001,
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"lw_momentum": 0.9,
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| 24 |
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"lw_wd": 0.0,
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"max_epochs": 20,
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"max_jitter": 0,
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| 27 |
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"model": "cherimoya.fold_1.torch",
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"muon_lr": 0.025,
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| 30 |
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"n_filters": 128,
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"n_layers": 9,
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| 32 |
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"n_warmup_epochs": 2,
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| 33 |
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"name": "cherimoya.fold_1",
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
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"train_nonpeaks.fold_1.bed",
|
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"valid_nonpeaks.fold_1.bed"
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| 38 |
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],
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| 39 |
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"num_workers": 1,
|
| 40 |
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"out_window": 1000,
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| 41 |
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"performance_filename": "cherimoya.fold_1.performance.tsv",
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"random_state": null,
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| 43 |
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"residual_scale": 0.15,
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| 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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"ENCFF943QQZ.bigWig"
|
| 49 |
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],
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| 50 |
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"skip": false,
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| 51 |
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"summits": false,
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| 52 |
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"training_chroms": [
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| 53 |
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"chr1",
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"chr3",
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"chr4",
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"chr5",
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"chr6",
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"chr7",
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"chr10",
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"chr13",
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"chr14",
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"chr18",
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"chr19",
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| 66 |
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"chr20",
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"chr21",
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"chr22",
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| 69 |
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"chrX",
|
| 70 |
+
"chrY"
|
| 71 |
+
],
|
| 72 |
+
"validation_chroms": [
|
| 73 |
+
"chr12",
|
| 74 |
+
"chr17"
|
| 75 |
+
],
|
| 76 |
+
"verbose": true
|
| 77 |
+
}
|
ENCSR000ENA/cherimoya.fold_1.fit.json
ADDED
|
@@ -0,0 +1 @@
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|
| 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": ["ENCFF943QQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENA/cherimoya.fold_1.log
ADDED
|
@@ -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 |
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0 2716 35.03730654716492 4.1047327518463135 1113.66943359375 0.7181588411331177 1875.39306640625 0.3024795353412628 0.58292896 10.14134407043457 True
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|
ENCSR000ENA/cherimoya.fold_1.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 |
+
1379.8419189453125 0.2427656203508377 0.5518447160720825 0.31594735383987427 0.7698750495910645 0.7462645769119263 0.4255494475364685
|
ENCSR000ENA/cherimoya.fold_2.evaluate.json
ADDED
|
@@ -0,0 +1,76 @@
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|
| 1 |
+
{
|
| 2 |
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"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
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"chroms": [
|
| 6 |
+
"chr22",
|
| 7 |
+
"chr7"
|
| 8 |
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],
|
| 9 |
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"controls": null,
|
| 10 |
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"device": "cuda",
|
| 11 |
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"dtype": "bfloat16",
|
| 12 |
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"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 |
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"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 |
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"valid_nonpeaks.fold_2.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_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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|
| 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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"ENCFF943QQZ.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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}
|
ENCSR000ENA/cherimoya.fold_2.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF943QQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENA/cherimoya.fold_2.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 2872 35.37055993080139 3.6718554496765137 1169.32470703125 1.0530102252960205 1723.5904541015625 0.31215089559555054 0.5738261 5.780245304107666 True
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|
ENCSR000ENA/cherimoya.fold_3.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
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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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"chr6",
|
| 7 |
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"chr21"
|
| 8 |
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|
| 9 |
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"controls": null,
|
| 10 |
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"device": "cuda",
|
| 11 |
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"dtype": "bfloat16",
|
| 12 |
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"early_stopping": 20,
|
| 13 |
+
"exclusion_lists": [
|
| 14 |
+
"https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
|
| 15 |
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| 33 |
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| 35 |
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| 47 |
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| 48 |
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| 50 |
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| 53 |
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| 56 |
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| 71 |
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| 74 |
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|
| 75 |
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|
ENCSR000ENA/cherimoya.fold_3.fit.json
ADDED
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@@ -0,0 +1 @@
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{"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": ["ENCFF943QQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
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ENCSR000ENA/cherimoya.fold_3.log
ADDED
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ENCSR000ENA/cherimoya.fold_3.performance.tsv
ADDED
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| 1 |
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profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
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ENCSR000ENA/cherimoya.fold_4.evaluate.json
ADDED
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"name": "cherimoya.fold_4",
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|
ENCSR000ENA/cherimoya.fold_4.fit.json
ADDED
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@@ -0,0 +1 @@
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|
|
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|
| 1 |
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{"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": ["ENCFF943QQZ.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000ENA/cherimoya.fold_4.log
ADDED
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@@ -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?
|
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19 57240 30.95947551727295 0.5620057582855225 864.248779296875 0.3886055648326874 1250.5390625 0.5441135764122009 0.74431074 0.40038689970970154 False
|
ENCSR000ENA/cherimoya.fold_4.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 |
+
1251.99609375 0.2538040280342102 0.5424677133560181 0.29600173234939575 0.7450581789016724 0.7076519131660461 0.39865127205848694
|
ENCSR000EOP/cherimoya.fold_0.evaluate.json
ADDED
|
@@ -0,0 +1,78 @@
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| 1 |
+
{
|
| 2 |
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"adam_lr": 0.001,
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| 3 |
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"adam_wd": 0.0,
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| 4 |
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"batch_size": 64,
|
| 5 |
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"chroms": [
|
| 6 |
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"chr8",
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| 7 |
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"chr20"
|
| 8 |
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| 9 |
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"controls": null,
|
| 10 |
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"device": "cuda",
|
| 11 |
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"dtype": "bfloat16",
|
| 12 |
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"early_stopping": 20,
|
| 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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"expansion": 2,
|
| 17 |
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"in_window": 2114,
|
| 18 |
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"loci": [
|
| 19 |
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"train_peaks.fold_0.bed",
|
| 20 |
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"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 |
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"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_0.torch",
|
| 28 |
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"muon_lr": 0.025,
|
| 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 |
+
"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 |
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"residual_scale": 0.15,
|
| 44 |
+
"reverse_complement": false,
|
| 45 |
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"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF300QSN.bigWig"
|
| 49 |
+
],
|
| 50 |
+
"skip": false,
|
| 51 |
+
"summits": false,
|
| 52 |
+
"training_chroms": [
|
| 53 |
+
"chr2",
|
| 54 |
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"chr4",
|
| 55 |
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"chr5",
|
| 56 |
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"chr7",
|
| 57 |
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"chr9",
|
| 58 |
+
"chr10",
|
| 59 |
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"chr11",
|
| 60 |
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"chr12",
|
| 61 |
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"chr13",
|
| 62 |
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"chr14",
|
| 63 |
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"chr15",
|
| 64 |
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"chr16",
|
| 65 |
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"chr17",
|
| 66 |
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"chr18",
|
| 67 |
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"chr19",
|
| 68 |
+
"chr21",
|
| 69 |
+
"chr22",
|
| 70 |
+
"chrX",
|
| 71 |
+
"chrY"
|
| 72 |
+
],
|
| 73 |
+
"validation_chroms": [
|
| 74 |
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"chr8",
|
| 75 |
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"chr20"
|
| 76 |
+
],
|
| 77 |
+
"verbose": true
|
| 78 |
+
}
|
ENCSR000EOP/cherimoya.fold_2.evaluate.json
ADDED
|
@@ -0,0 +1,76 @@
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|
|
|
|
| 1 |
+
{
|
| 2 |
+
"adam_lr": 0.001,
|
| 3 |
+
"adam_wd": 0.0,
|
| 4 |
+
"batch_size": 64,
|
| 5 |
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"chroms": [
|
| 6 |
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"chr22",
|
| 7 |
+
"chr7"
|
| 8 |
+
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|
| 9 |
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|
| 10 |
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"device": "cuda",
|
| 11 |
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"dtype": "bfloat16",
|
| 12 |
+
"early_stopping": 20,
|
| 13 |
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"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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|
| 18 |
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|
| 19 |
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"train_peaks.fold_2.bed",
|
| 20 |
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"valid_peaks.fold_2.bed"
|
| 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 |
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"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_2.torch",
|
| 28 |
+
"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 |
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"negative_ratio": 0.25,
|
| 35 |
+
"negatives": [
|
| 36 |
+
"train_nonpeaks.fold_2.bed",
|
| 37 |
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"valid_nonpeaks.fold_2.bed"
|
| 38 |
+
],
|
| 39 |
+
"num_workers": 1,
|
| 40 |
+
"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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"reverse_complement_average": false,
|
| 46 |
+
"sequences": "hg38.fa",
|
| 47 |
+
"signals": [
|
| 48 |
+
"ENCFF300QSN.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 |
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"chr10",
|
| 61 |
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"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 |
+
}
|
ENCSR000EOP/cherimoya.fold_2.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 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": ["ENCFF300QSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EOP/cherimoya.fold_2.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 2905 36.696879625320435 4.82893967628479 308.645751953125 0.8299853205680847 448.5950927734375 0.20383358001708984 0.44115576 3.842801570892334 True
|
| 3 |
+
1 5810 31.296478271484375 0.5275030136108398 339.9698486328125 0.9908617734909058 404.7143249511719 0.32792356610298157 0.51779944 1.6351735591888428 True
|
| 4 |
+
2 8715 31.938859462738037 0.5211136341094971 241.04010009765625 1.3455308675765991 395.61614990234375 0.34661075472831726 0.56720775 0.6755671501159668 True
|
| 5 |
+
3 11620 31.93765425682068 0.5200991630554199 244.4082794189453 0.9225303530693054 392.0897521972656 0.35413309931755066 0.5835727 0.6144713759422302 True
|
| 6 |
+
4 14525 31.940343141555786 0.5171995162963867 324.74432373046875 0.6867685317993164 390.5304260253906 0.3571523427963257 0.5864545 0.6065757870674133 True
|
| 7 |
+
5 17430 31.940049409866333 0.5169839859008789 290.4232177734375 0.7590000629425049 388.63543701171875 0.36220782995224 0.5924422 0.6038181185722351 True
|
| 8 |
+
6 20335 31.92116904258728 8.529507160186768 310.23126220703125 0.5244883894920349 387.2676086425781 0.3652571141719818 0.60827416 0.5706258416175842 True
|
| 9 |
+
7 23240 31.959012746810913 0.5179798603057861 282.449951171875 0.8539235591888428 385.59332275390625 0.3696773648262024 0.6198714 0.5340000987052917 True
|
| 10 |
+
8 26145 32.029048442840576 2.1339666843414307 290.5522155761719 0.5316425561904907 384.9464111328125 0.3705700933933258 0.63418186 0.507108211517334 True
|
| 11 |
+
9 29050 32.39292240142822 33.18335175514221 304.8990478515625 0.5641017556190491 383.789794921875 0.37385842204093933 0.6424865 0.4812874495983124 True
|
| 12 |
+
10 31955 31.94348168373108 0.5229706764221191 281.00970458984375 0.5252759456634521 382.4446716308594 0.377358078956604 0.6556725 0.4587307572364807 True
|
| 13 |
+
11 34860 31.984742641448975 0.519700288772583 267.9996337890625 0.528480052947998 381.9937438964844 0.3776312470436096 0.66403896 0.44046977162361145 True
|
| 14 |
+
12 37765 31.90759015083313 0.5104308128356934 351.22613525390625 0.4890839755535126 380.9935607910156 0.3799431025981903 0.67297065 0.4272385835647583 True
|
| 15 |
+
13 40670 31.88069176673889 0.5419042110443115 272.2882995605469 0.4506552815437317 380.04150390625 0.3832775354385376 0.6832886 0.41879788041114807 True
|
| 16 |
+
14 43575 31.97965145111084 0.5201733112335205 334.207275390625 0.35121414065361023 379.491455078125 0.38417842984199524 0.6905022 0.42228901386260986 True
|
| 17 |
+
15 46480 32.00248718261719 0.510676383972168 345.2022705078125 0.36224251985549927 378.51544189453125 0.3867645263671875 0.69918704 0.4112620949745178 True
|
| 18 |
+
16 49385 31.9524245262146 0.5241584777832031 364.8284606933594 0.6601070165634155 378.21533203125 0.38708925247192383 0.7057581 0.4069535434246063 True
|
| 19 |
+
17 52290 31.862041473388672 0.5175673961639404 310.3089294433594 0.4131876826286316 378.4003601074219 0.38624125719070435 0.7072029 0.4130244553089142 True
|
| 20 |
+
18 55195 31.88344097137451 0.5200979709625244 305.4507751464844 0.39862197637557983 378.3619689941406 0.386445015668869 0.70934576 0.4153578579425812 True
|
| 21 |
+
19 58100 32.714022397994995 15.85103464126587 271.1173095703125 0.34124940633773804 378.1474609375 0.3873876929283142 0.70706856 0.41891250014305115 False
|
ENCSR000EOP/cherimoya.fold_2.performance.tsv
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
378.3619689941406 0.41640806198120117 0.38644498586654663 0.12195596843957901 0.7093457579612732 0.681119441986084 0.4153578579425812
|
ENCSR000EOP/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 |
+
385.1451416015625 0.41909822821617126 0.3783153295516968 0.11922063678503036 0.7116868495941162 0.6941612362861633 0.4143221378326416
|
ENCSR000EOP/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": ["ENCFF300QSN.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR000EOP/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 |
+
374.3353576660156 0.42063841223716736 0.38040921092033386 0.11801299452781677 0.7043458223342896 0.677139163017273 0.4022374153137207
|
ENCSR044ATC/cherimoya.fold_2.evaluate.json
ADDED
|
@@ -0,0 +1,76 @@
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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 |
+
"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 |
+
"ENCFF493YHE.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 |
+
}
|
ENCSR082XEU/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": ["ENCFF076BWX.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR121ZSL/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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|
|
|
|
|
|
|
|
|
|
|
|
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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 |
+
"expansion": 2,
|
| 17 |
+
"in_window": 2114,
|
| 18 |
+
"loci": [
|
| 19 |
+
"train_peaks.fold_0.bed",
|
| 20 |
+
"valid_peaks.fold_0.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_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 |
+
"ENCFF673FXA.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 |
+
}
|
ENCSR121ZSL/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": ["ENCFF673FXA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR121ZSL/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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|
|
|
|
| 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 2714 34.691097259521484 3.595374345779419 1877.738525390625 0.9639758467674255 3027.235595703125 0.2955748736858368 0.37191117 18.704797744750977 True
|
| 3 |
+
1 5428 29.55256700515747 23.568299055099487 1896.9361572265625 0.7814657092094421 2311.927490234375 0.5317507386207581 0.4398344 8.429429054260254 True
|
| 4 |
+
2 8142 30.732463598251343 0.5733897686004639 1926.254150390625 1.0573747158050537 2263.410400390625 0.542855978012085 0.46150523 3.0155482292175293 True
|
| 5 |
+
3 10856 29.049969911575317 0.549114465713501 1749.218505859375 0.9803704023361206 2235.22900390625 0.5522978901863098 0.4835087 1.8843098878860474 True
|
| 6 |
+
4 13570 29.036290645599365 0.8284251689910889 1639.6484375 0.6378481388092041 2211.512451171875 0.5583824515342712 0.49478537 1.6296477317810059 True
|
| 7 |
+
5 16284 29.042200326919556 27.91094398498535 1724.2681884765625 0.7273198366165161 2187.755615234375 0.5659691095352173 0.505955 1.4604697227478027 True
|
| 8 |
+
6 18998 29.173998832702637 0.5502851009368896 1729.686767578125 0.660115659236908 2178.371826171875 0.569766640663147 0.5125823 1.4480020999908447 True
|
| 9 |
+
7 21712 29.163339138031006 0.5384035110473633 2144.769775390625 0.9200067520141602 2165.942138671875 0.5739414095878601 0.5114567 1.3488469123840332 False
|
| 10 |
+
8 24426 29.218843936920166 0.5429482460021973 1744.690185546875 0.8046427965164185 2155.144287109375 0.5757389664649963 0.51890755 1.1799821853637695 True
|
| 11 |
+
9 27140 29.072164297103882 0.9498887062072754 1524.6649169921875 0.6895876526832581 2136.789794921875 0.5807929039001465 0.5303547 1.086464285850525 True
|
| 12 |
+
10 29854 29.16423201560974 0.553687334060669 1690.8961181640625 0.8866811394691467 2128.202880859375 0.5832437872886658 0.5428857 0.9597762823104858 True
|
| 13 |
+
11 32568 29.3331036567688 0.5461311340332031 1732.882080078125 0.6587599515914917 2111.484375 0.5876626968383789 0.5576989 0.8254739046096802 True
|
| 14 |
+
12 35282 29.213980197906494 1.9803416728973389 1700.3092041015625 0.6257402896881104 2091.426025390625 0.5931551456451416 0.57216805 0.7347974181175232 True
|
| 15 |
+
13 37996 29.14150857925415 0.5472030639648438 1500.044189453125 0.6610411405563354 2084.901123046875 0.5935669541358948 0.58657813 0.6691251397132874 True
|
| 16 |
+
14 40710 29.071751832962036 0.7945232391357422 1667.296142578125 0.4889518618583679 2068.31103515625 0.5975877046585083 0.60465056 0.6005665063858032 True
|
| 17 |
+
15 43424 29.10112977027893 0.535724401473999 1620.337158203125 0.5813551545143127 2065.740966796875 0.5961073040962219 0.62210554 0.53536456823349 True
|
| 18 |
+
16 46138 29.085571765899658 0.5381865501403809 1471.4547119140625 0.5363816618919373 2059.545166015625 0.5971080660820007 0.6315098 0.4853626489639282 True
|
| 19 |
+
17 48852 28.987130403518677 1.5617527961730957 1742.0518798828125 0.5340980291366577 2054.55859375 0.5994581580162048 0.6412847 0.45176416635513306 True
|
| 20 |
+
18 51566 29.236541509628296 10.606262922286987 1473.038818359375 0.26116442680358887 2050.57080078125 0.6000366806983948 0.6471443 0.4349674880504608 True
|
| 21 |
+
19 54280 29.07248330116272 1.3387413024902344 1608.3797607421875 0.6402729749679565 2053.1240234375 0.5993137955665588 0.64735454 0.43305301666259766 True
|
ENCSR121ZSL/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 |
+
2053.1240234375 0.20931752026081085 0.5993138551712036 0.3827143609523773 0.6473545432090759 0.644279956817627 0.43305301666259766
|
ENCSR121ZSL/cherimoya.fold_1.evaluate.json
ADDED
|
@@ -0,0 +1,77 @@
|
|
|
|
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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 |
+
"chr12",
|
| 7 |
+
"chr17"
|
| 8 |
+
],
|
| 9 |
+
"controls": null,
|
| 10 |
+
"device": "cuda",
|
| 11 |
+
"dtype": "bfloat16",
|
| 12 |
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| 13 |
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| 14 |
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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_1",
|
| 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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|
| 46 |
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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"training_chroms": [
|
| 53 |
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"chr1",
|
| 54 |
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|
| 55 |
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"chr4",
|
| 56 |
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"chr5",
|
| 57 |
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"chr6",
|
| 58 |
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"chr7",
|
| 59 |
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|
| 60 |
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"chr11",
|
| 61 |
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"chr13",
|
| 62 |
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"chr14",
|
| 63 |
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"chr15",
|
| 64 |
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"chr18",
|
| 65 |
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"chr19",
|
| 66 |
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"chr20",
|
| 67 |
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"chr21",
|
| 68 |
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"chr22",
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| 69 |
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"chrX",
|
| 70 |
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"chrY"
|
| 71 |
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|
| 72 |
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"validation_chroms": [
|
| 73 |
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|
| 74 |
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|
| 75 |
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|
| 76 |
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"verbose": true
|
| 77 |
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|
ENCSR121ZSL/cherimoya.fold_1.fit.json
ADDED
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@@ -0,0 +1 @@
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| 1 |
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{"n_filters": 128, "name": "cherimoya.fold_1", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr1", "chr3", "chr4", "chr5", "chr6", "chr7", "chr10", "chr11", "chr13", "chr14", "chr15", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr12", "chr17"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_1.bed", "valid_peaks.fold_1.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_1.bed", "valid_nonpeaks.fold_1.bed"], "signals": ["ENCFF673FXA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
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ENCSR121ZSL/cherimoya.fold_1.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?
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ENCSR121ZSL/cherimoya.fold_1.performance.tsv
ADDED
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@@ -0,0 +1,2 @@
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| 1 |
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profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
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|
ENCSR121ZSL/cherimoya.fold_2.evaluate.json
ADDED
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@@ -0,0 +1,76 @@
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|
| 1 |
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{
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| 4 |
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|
| 5 |
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| 6 |
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| 14 |
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|
| 15 |
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| 19 |
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| 20 |
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|
| 21 |
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],
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| 22 |
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|
| 23 |
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|
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|
| 25 |
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|
| 26 |
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|
| 27 |
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"model": "cherimoya.fold_2.torch",
|
| 28 |
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|
| 29 |
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|
| 30 |
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"n_filters": 128,
|
| 31 |
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"n_layers": 9,
|
| 32 |
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|
| 33 |
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"name": "cherimoya.fold_2",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
|
| 36 |
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|
| 37 |
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|
| 38 |
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],
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"num_workers": 1,
|
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|
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"performance_filename": "cherimoya.fold_2.performance.tsv",
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"sequences": "hg38.fa",
|
| 47 |
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"signals": [
|
| 48 |
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"ENCFF673FXA.bigWig"
|
| 49 |
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],
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| 50 |
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"skip": false,
|
| 51 |
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"summits": false,
|
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"training_chroms": [
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| 53 |
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"chr1",
|
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"chr2",
|
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"chr3",
|
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"chr5",
|
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"chr6",
|
| 58 |
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"chr8",
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"chr9",
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| 60 |
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"chr10",
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"chr14",
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"chr16",
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"chr17",
|
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"chr18",
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"chr19",
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"chr20",
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"chr21",
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|
| 70 |
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|
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"validation_chroms": [
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|
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|
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],
|
| 75 |
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|
| 76 |
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}
|
ENCSR121ZSL/cherimoya.fold_2.fit.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
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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": ["ENCFF673FXA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR121ZSL/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 |
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ENCSR121ZSL/cherimoya.fold_2.performance.tsv
ADDED
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@@ -0,0 +1,2 @@
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| 1 |
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profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
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| 2 |
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ENCSR121ZSL/cherimoya.fold_3.evaluate.json
ADDED
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@@ -0,0 +1,75 @@
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| 1 |
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| 14 |
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| 16 |
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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",
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|
| 35 |
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"negatives": [
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| 36 |
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| 40 |
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| 47 |
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"signals": [
|
| 48 |
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|
| 49 |
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| 50 |
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|
| 51 |
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|
| 52 |
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| 53 |
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| 62 |
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| 66 |
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|
| 69 |
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| 70 |
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"validation_chroms": [
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| 71 |
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| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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}
|
ENCSR121ZSL/cherimoya.fold_3.fit.json
ADDED
|
@@ -0,0 +1 @@
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|
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|
| 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": ["ENCFF673FXA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR121ZSL/cherimoya.fold_3.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 |
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|
ENCSR121ZSL/cherimoya.fold_3.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 |
+
2076.923828125 0.20708519220352173 0.5997540950775146 0.3853289783000946 0.6705491542816162 0.67241370677948 0.42424625158309937
|
ENCSR121ZSL/cherimoya.fold_4.evaluate.json
ADDED
|
@@ -0,0 +1,75 @@
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|
| 1 |
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{
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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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|
| 13 |
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|
| 14 |
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|
| 15 |
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],
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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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],
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| 22 |
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"lw_lr": 0.001,
|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_4.torch",
|
| 28 |
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"muon_lr": 0.025,
|
| 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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|
| 33 |
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"name": "cherimoya.fold_4",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
|
| 36 |
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"train_nonpeaks.fold_4.bed",
|
| 37 |
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"valid_nonpeaks.fold_4.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_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,
|
| 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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"ENCFF673FXA.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 |
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"chr3",
|
| 56 |
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"chr4",
|
| 57 |
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"chr5",
|
| 58 |
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"chr6",
|
| 59 |
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"chr8",
|
| 60 |
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"chr9",
|
| 61 |
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"chr11",
|
| 62 |
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"chr12",
|
| 63 |
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"chr14",
|
| 64 |
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"chr15",
|
| 65 |
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"chr16",
|
| 66 |
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"chr20",
|
| 67 |
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"chr22",
|
| 68 |
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"chrY"
|
| 69 |
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],
|
| 70 |
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"validation_chroms": [
|
| 71 |
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"chr10",
|
| 72 |
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"chr18"
|
| 73 |
+
],
|
| 74 |
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"verbose": true
|
| 75 |
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}
|
ENCSR121ZSL/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": ["ENCFF673FXA.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}
|
ENCSR121ZSL/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 2829 34.92210292816162 4.6726765632629395 1808.592041015625 1.1463111639022827 2968.770263671875 0.2952274680137634 0.38296828 17.30028533935547 True
|
| 3 |
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1 5658 30.77501130104065 0.5585799217224121 1561.41845703125 0.7571945190429688 2304.63134765625 0.5273545980453491 0.40196383 6.215628147125244 True
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2 8487 30.4357647895813 0.519099235534668 1708.164306640625 1.084677815437317 2253.64013671875 0.5404913425445557 0.424026 2.7069854736328125 True
|
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|
ENCSR121ZSL/cherimoya.fold_4.performance.tsv
ADDED
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@@ -0,0 +1,2 @@
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profile_mnll profile_jsd profile_pearson profile_spearman count_pearson count_spearman count_mse
|
| 2 |
+
2027.681640625 0.2088305503129959 0.6014066338539124 0.3813496530056 0.6608721613883972 0.6596991419792175 0.4046650230884552
|
ENCSR148MFM/cherimoya.fold_0.evaluate.json
ADDED
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@@ -0,0 +1,78 @@
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| 1 |
+
{
|
| 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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"chr8",
|
| 7 |
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"chr20"
|
| 8 |
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],
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| 9 |
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"controls": null,
|
| 10 |
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|
| 11 |
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"dtype": "bfloat16",
|
| 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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],
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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_0.bed",
|
| 20 |
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"valid_peaks.fold_0.bed"
|
| 21 |
+
],
|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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"max_epochs": 20,
|
| 26 |
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"max_jitter": 0,
|
| 27 |
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"model": "cherimoya.fold_0.torch",
|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 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_0",
|
| 34 |
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"negative_ratio": 0.25,
|
| 35 |
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"negatives": [
|
| 36 |
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"train_nonpeaks.fold_0.bed",
|
| 37 |
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"valid_nonpeaks.fold_0.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_0.performance.tsv",
|
| 42 |
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| 43 |
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|
| 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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"ENCFF371WIZ.bigWig"
|
| 49 |
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],
|
| 50 |
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|
| 51 |
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|
| 52 |
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"training_chroms": [
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| 53 |
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| 54 |
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| 55 |
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| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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| 65 |
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| 67 |
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| 68 |
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| 69 |
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|
| 70 |
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"chrX",
|
| 71 |
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"chrY"
|
| 72 |
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],
|
| 73 |
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"validation_chroms": [
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| 74 |
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"chr8",
|
| 75 |
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| 76 |
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],
|
| 77 |
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"verbose": true
|
| 78 |
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}
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