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best_params_len2_5120_by_task.csv
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multicls_len2_5120_allchr_csv_lr3ebenchmark,task,metric,best_score,lr,weight_decay,warmup_ratio,num_train_epochs,selected_epoch,seed,run_name,eval_results_json
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| 2 |
+
GENOMIC_BENCH,demo_coding_vs_intergenomic_seqs,eval_matthews_correlation,0.814177750,3e-5,0.0,0.06,6,3,42,lr3e-5_wd0.0_wr0.06_ep6_seed42,
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| 3 |
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GENOMIC_BENCH,demo_human_or_worm,eval_matthews_correlation,0.921426297,3e-5,0.03,0.06,8,8,42,lr3e-5_wd0.03_wr0.06_ep8_seed42,
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| 4 |
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GENOMIC_BENCH,drosophila_enhancers_stark,eval_matthews_correlation,0.548676023,3e-5,0.05,0.15,10,4,42,lr3e-5_wd0.05_wr0.15_ep10_seed42,
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| 5 |
+
GENOMIC_BENCH,dummy_mouse_enhancers_ensembl,eval_matthews_correlation,0.638409278,3e-5,0.01,0.10,12,8,42,lr3e-5_wd0.01_wr0.10_ep12_seed42,
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| 6 |
+
GENOMIC_BENCH,human_enhancers_cohn,eval_matthews_correlation,0.497260847,3e-5,0.0,0.03,6,1,42,lr3e-5_wd0.0_wr0.03_ep6_seed42,
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| 7 |
+
GENOMIC_BENCH,human_enhancers_ensembl,eval_matthews_correlation,0.783029985,3e-5,0.0,0.05,5,5,42,lr3e-5_wd0.0_wr0.05_ep5_seed42,
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| 8 |
+
GENOMIC_BENCH,human_ensembl_regulatory,eval_matthews_correlation,0.843082003,3e-5,0.0,0.03,5,5,42,lr3e-5_wd0.0_wr0.03_ep5_seed42,
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| 9 |
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GENOMIC_BENCH,human_nontata_promoters,eval_matthews_correlation,0.891402882,3e-5,0.03,0.06,10,10,42,lr3e-5_wd0.03_wr0.06_ep10_seed42,
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| 10 |
+
GENOMIC_BENCH,human_ocr_ensembl,eval_matthews_correlation,0.499659893,3e-5,0.01,0.05,3,3,42,lr3e-5_wd0.01_wr0.05_ep3_seed42,
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| 11 |
+
GUE,EMP/H3,eval_matthews_correlation,0.739485578,3e-5,0.05,0.06,10,8,42,lr3e-5_wd0.05_wr0.06_ep10_seed42,
|
| 12 |
+
GUE,EMP/H3K14ac,eval_matthews_correlation,0.401359108,3e-5,0.0,0.10,8,4,42,lr3e-5_wd0.0_wr0.10_ep8_seed42,
|
| 13 |
+
GUE,EMP/H3K36me3,eval_matthews_correlation,0.445057920,3e-5,0.05,0.10,8,5,42,lr3e-5_wd0.05_wr0.10_ep8_seed42,
|
| 14 |
+
GUE,EMP/H3K4me1,eval_matthews_correlation,0.362808915,3e-5,0.05,0.06,8,3,42,lr3e-5_wd0.05_wr0.06_ep8_seed42,
|
| 15 |
+
GUE,EMP/H3K4me2,eval_matthews_correlation,0.304098333,3e-5,0.0,0.10,6,1,42,lr3e-5_wd0.0_wr0.10_ep6_seed42,
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| 16 |
+
GUE,EMP/H3K4me3,eval_matthews_correlation,0.260940070,3e-5,0.01,0.03,10,3,42,lr3e-5_wd0.01_wr0.03_ep10_seed42,
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| 17 |
+
GUE,EMP/H3K79me3,eval_matthews_correlation,0.589779325,3e-5,0.0,0.06,10,4,42,lr3e-5_wd0.0_wr0.06_ep10_seed42,
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| 18 |
+
GUE,EMP/H3K9ac,eval_matthews_correlation,0.492805066,3e-5,0.05,0.03,6,3,42,lr3e-5_wd0.05_wr0.03_ep6_seed42,
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| 19 |
+
GUE,EMP/H4,eval_matthews_correlation,0.738651438,3e-5,0.01,0.06,8,3,42,lr3e-5_wd0.01_wr0.06_ep8_seed42,
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| 20 |
+
GUE,EMP/H4ac,eval_matthews_correlation,0.345970992,3e-5,0.05,0.03,10,6,42,lr3e-5_wd0.05_wr0.03_ep10_seed42,
|
| 21 |
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GUE,mouse/0,eval_matthews_correlation,0.430893758,3e-5,0.05,0.10,8,5,42,lr3e-5_wd0.05_wr0.10_ep8_seed42,
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| 22 |
+
GUE,mouse/1,eval_matthews_correlation,0.790509468,3e-5,0.01,0.06,4,4,42,lr3e-5_wd0.01_wr0.06_ep4_seed42,
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| 23 |
+
GUE,mouse/2,eval_matthews_correlation,0.756604084,3e-5,0.0,0.10,12,5,42,lr3e-5_wd0.0_wr0.10_ep12_seed42,
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| 24 |
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GUE,mouse/3,eval_matthews_correlation,0.607150704,3e-5,0.05,0.15,12,12,42,lr3e-5_wd0.05_wr0.15_ep12_seed42,
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| 25 |
+
GUE,mouse/4,eval_matthews_correlation,0.352368365,3e-5,0.05,0.10,8,8,42,lr3e-5_wd0.05_wr0.10_ep8_seed42,
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| 26 |
+
GUE,prom/prom_300_all,eval_matthews_correlation,0.827198799,3e-5,0.01,0.04,4,4,42,lr3e-5_wd0.01_wr0.04_ep4_seed42,
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| 27 |
+
GUE,prom/prom_300_notata,eval_matthews_correlation,0.906924800,3e-5,0.0,0.06,4,4,42,lr3e-5_wd0.0_wr0.06_ep4_seed42,
|
| 28 |
+
GUE,prom/prom_300_tata,eval_matthews_correlation,0.621412621,3e-5,0.0,0.06,12,3,42,lr3e-5_wd0.0_wr0.06_ep12_seed42,
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| 29 |
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GUE,prom/prom_core_all,eval_matthews_correlation,0.626901998,3e-5,0.0,0.06,6,3,42,lr3e-5_wd0.0_wr0.06_ep6_seed42,
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| 30 |
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GUE,prom/prom_core_notata,eval_matthews_correlation,0.659776208,3e-5,0.0,0.04,4,2,42,lr3e-5_wd0.0_wr0.04_ep4_seed42,
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| 31 |
+
GUE,prom/prom_core_tata,eval_matthews_correlation,0.621541639,3e-5,0.01,0.10,12,11,42,lr3e-5_wd0.01_wr0.10_ep12_seed42,
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| 32 |
+
GUE,splice/reconstructed,eval_matthews_correlation,0.752177085,3e-5,0.0,0.06,8,8,42,lr3e-5_wd0.0_wr0.06_ep8_seed42,
|
| 33 |
+
GUE,tf/0,eval_matthews_correlation,0.655088865,3e-5,0.01,0.02,6,3,42,lr3e-5_wd0.01_wr0.02_ep6_seed42,
|
| 34 |
+
GUE,tf/1,eval_matthews_correlation,0.677573607,3e-5,0.01,0.06,4,2,42,lr3e-5_wd0.01_wr0.06_ep4_seed42,
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| 35 |
+
GUE,tf/2,eval_matthews_correlation,0.571741892,3e-5,0.05,0.06,6,5,42,lr3e-5_wd0.05_wr0.06_ep6_seed42,
|
| 36 |
+
GUE,tf/3,eval_matthews_correlation,0.457033141,3e-5,0.01,0.10,6,4,42,lr3e-5_wd0.01_wr0.10_ep6_seed42,
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| 37 |
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GUE,tf/4,eval_matthews_correlation,0.690864121,3e-5,0.01,0.03,6,5,42,lr3e-5_wd0.01_wr0.03_ep6_seed42,
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| 38 |
+
MULTI_ATAC,human_mouse_superclass_allchr,eval_matthews_correlation,0.133020094,3e-5,0.0,0.03,4,4,42,lr3e-5_wd0.0_wr0.03_ep4_seed42,/home/n5huang/dna_token/mario/HP_Tune_MCC/output_1024_human_mouse_superclass_allchr/human_mouse_superclass_allchr/len2_5120/lr3e-5_wd0.0_wr0.03_ep4_seed42/results/multicls_len2_5120_human_mouse_superclass_allchr_lr3e-5_wd0.0_wr0.03_ep4_seed42/eval_results.json
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| 39 |
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MULTI_SCREEN,allchr_csv,eval_matthews_correlation,0.22125646109513525,3e-5,0.0,0.01,3,3.0,42,lr3e-5_wd0.0_wr0.01_ep3_seed42,/home/n5huang/dna_token/mario/HP_Tune_MCC/output_1024_allchr_csv/allchr_csv/len2_5120/lr3e-5_wd0.0_wr0.01_ep3_seed42/results/multicls_len2_5120_allchr_csv_lr3e-5_wd0.0_wr0.01_ep3_seed42/eval_results.json
|
| 40 |
+
NT,H2AFZ,eval_matthews_correlation,0.49297816292786384,3e-5,0.03,0.03,8,4.0,42,lr3e-5_wd0.03_wr0.03_ep8_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H2AFZ/len2_5120/lr3e-5_wd0.03_wr0.03_ep8_seed42/results/hg38_BPE_len2_5120_H2AFZ_lr3e-5_wd0.03_wr0.03_ep8_seed42/eval_results.json
|
| 41 |
+
NT,H3K27ac,eval_matthews_correlation,0.45972104150433896,3e-5,0.0,0.03,10,2.0,42,lr3e-5_wd0.0_wr0.03_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K27ac/len2_5120/lr3e-5_wd0.0_wr0.03_ep10_seed42/results/hg38_BPE_len2_5120_H3K27ac_lr3e-5_wd0.0_wr0.03_ep10_seed42/eval_results.json
|
| 42 |
+
NT,H3K27me3,eval_matthews_correlation,0.5858685282082379,3e-5,0.01,0.03,6,3.0,42,lr3e-5_wd0.01_wr0.03_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K27me3/len2_5120/lr3e-5_wd0.01_wr0.03_ep6_seed42/results/hg38_BPE_len2_5120_H3K27me3_lr3e-5_wd0.01_wr0.03_ep6_seed42/eval_results.json
|
| 43 |
+
NT,H3K36me3,eval_matthews_correlation,0.6166431331477378,3e-5,0.03,0.10,6,3.0,42,lr3e-5_wd0.03_wr0.10_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K36me3/len2_5120/lr3e-5_wd0.03_wr0.10_ep6_seed42/results/hg38_BPE_len2_5120_H3K36me3_lr3e-5_wd0.03_wr0.10_ep6_seed42/eval_results.json
|
| 44 |
+
NT,H3K4me1,eval_matthews_correlation,0.47800002204568415,3e-5,0.01,0.06,6,3.0,42,lr3e-5_wd0.01_wr0.06_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K4me1/len2_5120/lr3e-5_wd0.01_wr0.06_ep6_seed42/results/hg38_BPE_len2_5120_H3K4me1_lr3e-5_wd0.01_wr0.06_ep6_seed42/eval_results.json
|
| 45 |
+
NT,H3K4me2,eval_matthews_correlation,0.5845596755459171,3e-5,0.01,0.10,8,4.0,42,lr3e-5_wd0.01_wr0.10_ep8_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K4me2/len2_5120/lr3e-5_wd0.01_wr0.10_ep8_seed42/results/hg38_BPE_len2_5120_H3K4me2_lr3e-5_wd0.01_wr0.10_ep8_seed42/eval_results.json
|
| 46 |
+
NT,H3K4me3,eval_matthews_correlation,0.6511689742592186,3e-5,0.01,0.10,8,3.0,42,lr3e-5_wd0.01_wr0.10_ep8_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K4me3/len2_5120/lr3e-5_wd0.01_wr0.10_ep8_seed42/results/hg38_BPE_len2_5120_H3K4me3_lr3e-5_wd0.01_wr0.10_ep8_seed42/eval_results.json
|
| 47 |
+
NT,H3K9ac,eval_matthews_correlation,0.5455677494927541,3e-5,0.03,0.10,10,2.0,42,lr3e-5_wd0.03_wr0.10_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K9ac/len2_5120/lr3e-5_wd0.03_wr0.10_ep10_seed42/results/hg38_BPE_len2_5120_H3K9ac_lr3e-5_wd0.03_wr0.10_ep10_seed42/eval_results.json
|
| 48 |
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NT,H3K9me3,eval_matthews_correlation,0.42022477415719994,3e-5,0.01,0.03,6,3.0,42,lr3e-5_wd0.01_wr0.03_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H3K9me3/len2_5120/lr3e-5_wd0.01_wr0.03_ep6_seed42/results/hg38_BPE_len2_5120_H3K9me3_lr3e-5_wd0.01_wr0.03_ep6_seed42/eval_results.json
|
| 49 |
+
NT,H4K20me1,eval_matthews_correlation,0.6603541800239333,3e-5,0.01,0.06,10,2.0,42,lr3e-5_wd0.01_wr0.06_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/H4K20me1/len2_5120/lr3e-5_wd0.01_wr0.06_ep10_seed42/results/hg38_BPE_len2_5120_H4K20me1_lr3e-5_wd0.01_wr0.06_ep10_seed42/eval_results.json
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| 50 |
+
NT,enhancers,eval_matthews_correlation,0.5274541131798851,3e-5,0.03,0.03,6,3.0,42,lr3e-5_wd0.03_wr0.03_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/enhancers/len2_5120/lr3e-5_wd0.03_wr0.03_ep6_seed42/results/hg38_BPE_len2_5120_enhancers_lr3e-5_wd0.03_wr0.03_ep6_seed42/eval_results.json
|
| 51 |
+
NT,enhancers_types,eval_matthews_correlation,0.4650204511524491,3e-5,0.0,0.03,6,1.0,42,lr3e-5_wd0.0_wr0.03_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/enhancers_types/len2_5120/lr3e-5_wd0.0_wr0.03_ep6_seed42/results/hg38_BPE_len2_5120_enhancers_types_lr3e-5_wd0.0_wr0.03_ep6_seed42/eval_results.json
|
| 52 |
+
NT,promoter_all,eval_matthews_correlation,0.7437106907764638,3e-5,0.01,0.10,6,4.0,42,lr3e-5_wd0.01_wr0.10_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/promoter_all/len2_5120/lr3e-5_wd0.01_wr0.10_ep6_seed42/results/hg38_BPE_len2_5120_promoter_all_lr3e-5_wd0.01_wr0.10_ep6_seed42/eval_results.json
|
| 53 |
+
NT,promoter_no_tata,eval_matthews_correlation,0.7747538361222879,3e-5,0.0,0.03,6,2.0,42,lr3e-5_wd0.0_wr0.03_ep6_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/promoter_no_tata/len2_5120/lr3e-5_wd0.0_wr0.03_ep6_seed42/results/hg38_BPE_len2_5120_promoter_no_tata_lr3e-5_wd0.0_wr0.03_ep6_seed42/eval_results.json
|
| 54 |
+
NT,promoter_tata,eval_matthews_correlation,0.776596104778345,3e-5,0.05,0.10,8,6.0,42,lr3e-5_wd0.05_wr0.10_ep8_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/promoter_tata/len2_5120/lr3e-5_wd0.05_wr0.10_ep8_seed42/results/hg38_BPE_len2_5120_promoter_tata_lr3e-5_wd0.05_wr0.10_ep8_seed42/eval_results.json
|
| 55 |
+
NT,splice_sites_acceptors,eval_matthews_correlation,0.6656724198357925,3e-5,0.03,0.03,10,5.0,42,lr3e-5_wd0.03_wr0.03_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/splice_sites_acceptors/len2_5120/lr3e-5_wd0.03_wr0.03_ep10_seed42/results/hg38_BPE_len2_5120_splice_sites_acceptors_lr3e-5_wd0.03_wr0.03_ep10_seed42/eval_results.json
|
| 56 |
+
NT,splice_sites_all,eval_matthews_correlation,0.6797807535374488,3e-5,0.01,0.06,10,10.0,42,lr3e-5_wd0.01_wr0.06_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/splice_sites_all/len2_5120/lr3e-5_wd0.01_wr0.06_ep10_seed42/results/hg38_BPE_len2_5120_splice_sites_all_lr3e-5_wd0.01_wr0.06_ep10_seed42/eval_results.json
|
| 57 |
+
NT,splice_sites_donors,eval_matthews_correlation,0.6887836145033946,3e-5,0.0,0.03,10,8.0,42,lr3e-5_wd0.0_wr0.03_ep10_seed42,/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/output_hg38_1024_multi_nt_rerun/splice_sites_donors/len2_5120/lr3e-5_wd0.0_wr0.03_ep10_seed42/results/hg38_BPE_len2_5120_splice_sites_donors_lr3e-5_wd0.0_wr0.03_ep10_seed42/eval_results.json
|
| 58 |
+
SCREEN,CA,eval_matthews_correlation,0.826488142,1e-5,0.0,0.03,8,,42,lr1e-5_wd0.0_wr0.03_ep8_seed42,
|
| 59 |
+
SCREEN,CA-CTCF,eval_matthews_correlation,0.860197713,1e-5,0.01,0.10,8,,42,lr1e-5_wd0.01_wr0.10_ep8_seed42,
|
| 60 |
+
SCREEN,CA-H3K4me3,eval_matthews_correlation,0.834254863,1e-5,0.01,0.10,10,,42,lr1e-5_wd0.01_wr0.10_ep10_seed42,
|
| 61 |
+
SCREEN,CA-TF,eval_matthews_correlation,0.832562340,1e-5,0.05,0.06,8,,42,lr1e-5_wd0.05_wr0.06_ep8_seed42,
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| 62 |
+
SCREEN,PLS,eval_matthews_correlation,0.897623980,1e-5,0.05,0.03,8,,42,lr1e-5_wd0.05_wr0.03_ep8_seed42,
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| 63 |
+
SCREEN,TF,eval_matthews_correlation,0.832763408,1e-5,0.05,0.10,6,,42,lr1e-5_wd0.05_wr0.10_ep6_seed42,
|
| 64 |
+
SCREEN,dELS,eval_matthews_correlation,0.828497849,1e-5,0.01,0.06,6,,42,lr1e-5_wd0.01_wr0.06_ep6_seed42,
|
| 65 |
+
SCREEN,pELS,eval_matthews_correlation,0.853285402,1e-5,0.01,0.06,8,,42,lr1e-5_wd0.01_wr0.06_ep8_seed42,
|
| 66 |
+
SUPER_BINARY,EXC,eval_matthews_correlation,0.335797204,1e-5,0.01,0.06,8,,42,lr1e-5_wd0.01_wr0.06_ep8_seed42,
|
| 67 |
+
SUPER_BINARY,GLIA,eval_matthews_correlation,0.402840786,1e-5,0.05,0.06,8,,42,lr1e-5_wd0.05_wr0.06_ep8_seed42,
|
| 68 |
+
SUPER_BINARY,INH,eval_matthews_correlation,0.289303920,1e-5,0.05,0.06,8,,42,lr1e-5_wd0.05_wr0.06_ep8_seed42,
|
| 69 |
+
SUPER_BINARY,VASC,eval_matthews_correlation,0.341530572,1e-5,0.0,0.06,10,,42,lr1e-5_wd0.0_wr0.06_ep10_seed42,
|