Method

ChromBPNet (ab initio)

Baseline trained from scratch by the DART-Eval authors, evaluated ab initio.

Overview

Baseline trained from scratch by the DART-Eval authors, evaluated ab initio.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

14 evaluations · 14 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.94 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Separating positive GM12878 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-GM12878)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.952 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Separating positive H1ESC peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-H1ESC)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.91 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Separating positive HEPG2 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-HEPG2)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.975 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Separating positive IMR90 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-IMR90)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.917 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Separating positive K562 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-K562)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.54 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Rank correlation with measured accessibility among positive GM12878 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-GM12878)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.754 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Rank correlation with measured accessibility among positive H1ESC peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-H1ESC)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.534 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Rank correlation with measured accessibility among positive HEPG2 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-HEPG2)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.549 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Rank correlation with measured accessibility among positive IMR90 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-IMR90)
Method: ChromBPNet (ab initio)	Task: DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.574 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Rank correlation with measured accessibility among positive K562 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-K562)
Method: ChromBPNet (ab initio)	Task: DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	0.772 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African ChromBPNet), column(ab initio auroc)
Method: ChromBPNet (ab initio)	Task: DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	0.671 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African ChromBPNet), column(ab initio pearson_r)
Method: ChromBPNet (ab initio)	Task: DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.892 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban ChromBPNet), column(ab initio auroc)
Method: ChromBPNet (ab initio)	Task: DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.738 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban ChromBPNet), column(ab initio pearson_r)

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