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
Release 2026-09-17-134cd1815de8 · 14 evaluations · 14 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ChromBPNet (ab initio) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Method: ChromBPNet (ab initio)Task: DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negativesDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Separating positive GM12878 peaks from matched negatives. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.940 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-GM12878) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Method: ChromBPNet (ab initio)Task: DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negativesDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Separating positive H1ESC peaks from matched negatives. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.952 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-H1ESC) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Method: ChromBPNet (ab initio)Task: DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negativesDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Separating positive HEPG2 peaks from matched negatives. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.910 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-HEPG2) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Method: ChromBPNet (ab initio)Task: DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negativesDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Separating positive IMR90 peaks from matched negatives. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.975 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-IMR90) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Method: ChromBPNet (ab initio)Task: DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negativesDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Separating positive K562 peaks from matched negatives. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.917 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-AUROC-K562) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Method: ChromBPNet (ab initio)Task: DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives onlyDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Rank correlation with measured accessibility among positive GM12878 peaks. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.540 spearman_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-GM12878) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Method: ChromBPNet (ab initio)Task: DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives onlyDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Rank correlation with measured accessibility among positive H1ESC peaks. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.754 spearman_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-H1ESC) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Method: ChromBPNet (ab initio)Task: DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives onlyDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Rank correlation with measured accessibility among positive HEPG2 peaks. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.534 spearman_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-HEPG2) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Method: ChromBPNet (ab initio)Task: DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives onlyDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Rank correlation with measured accessibility among positive IMR90 peaks. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.549 spearman_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-IMR90) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Method: ChromBPNet (ab initio)Task: DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives onlyDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Rank correlation with measured accessibility among positive K562 peaks. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.574 spearman_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Ab initio ChromBPNet), column(CA-SPEARMAN-K562) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Method: ChromBPNet (ab initio)Task: DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROCDataset subset: Chromatin QTLs in African LCLs (DART-Eval split) Score the effect of a variant on chromatin accessibility, against the measured QTL call. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.772 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African ChromBPNet), column(ab initio auroc) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Method: ChromBPNet (ab initio)Task: DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson rDataset subset: Chromatin QTLs in African LCLs (DART-Eval split) Score the effect of a variant on chromatin accessibility, against the measured QTL call. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.671 pearson_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African ChromBPNet), column(ab initio pearson_r) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Method: ChromBPNet (ab initio)Task: DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROCDataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split) Score the effect of a variant on chromatin accessibility, against the measured QTL call. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.892 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban ChromBPNet), column(ab initio auroc) Source checking is not independent reproduction. |
| ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Method: ChromBPNet (ab initio)Task: DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson rDataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split) Score the effect of a variant on chromatin accessibility, against the measured QTL call. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.738 pearson_r Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban ChromBPNet), column(ab initio pearson_r) Source checking is not independent reproduction. |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Original source · 2412.05430v1
Technical metadata and extraction receipts
Stable ID: dart-eval-method-chrombpnet-ab-initio
- areas
- dna-genomes
- source locator
- Table 1, row(ChromBPNet)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: ChromBPNet (ab initio) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives
- model: ChromBPNet (ab initio) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- model: ChromBPNet (ab initio) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives
- model: ChromBPNet (ab initio) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives
- model: ChromBPNet (ab initio) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives
- model: ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only
- model: ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only
- model: ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only
- model: ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only
- model: ChromBPNet (ab initio) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only
- model: ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC
- model: ChromBPNet (ab initio) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r
- model: ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC
- model: ChromBPNet (ab initio) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r