The split of ENCODE chromatin accessibility peaks in five cell lines that DART-Eval evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.
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214 evaluations · 214 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus (fine-tuned) | 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) | 0.935 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive GM12878 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Fine-Tuned Caduceus), column(CA-AUROC-GM12878) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.954 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive H1ESC peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Fine-Tuned Caduceus), column(CA-AUROC-H1ESC) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.896 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive HEPG2 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Fine-Tuned Caduceus), column(CA-AUROC-HEPG2) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.976 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive IMR90 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Fine-Tuned Caduceus), column(CA-AUROC-IMR90) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.933 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive K562 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Fine-Tuned Caduceus), column(CA-AUROC-K562) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.503 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Fine-Tuned Caduceus), column(CA-SPEARMAN-GM12878) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.744 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Fine-Tuned Caduceus), column(CA-SPEARMAN-H1ESC) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.454 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Fine-Tuned Caduceus), column(CA-SPEARMAN-HEPG2) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.479 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Fine-Tuned Caduceus), column(CA-SPEARMAN-IMR90) |
| Configuration: Caduceus (fine-tuned) | 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) | 0.57 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Fine-Tuned Caduceus), column(CA-SPEARMAN-K562) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.671 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceClassify which of five cell lines a accessible element belongs to. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-ACC) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.9 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus (fine-tuned) on DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 One-against-rest AUROC for GM12878 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-GM12878) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.937 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC One-against-rest AUROC for H1ESC accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-H1ESC) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.901 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus (fine-tuned) on DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 One-against-rest AUROC for HEPG2 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-HEPG2) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.929 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 One-against-rest AUROC for IMR90 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-IMR90) |
| Configuration: Caduceus (fine-tuned) | Task: DART-Eval CTS-K562: Cell-type-specific element classification, K562 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) | 0.878 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus (fine-tuned) on DART-Eval CTS-K562: Cell-type-specific element classification, K562 One-against-rest AUROC for K562 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-K562) |
| Configuration: Caduceus (probed) | 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) | 0.605 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive GM12878 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed Caduceus), column(CA-AUROC-GM12878) |
| Configuration: Caduceus (probed) | 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) | 0.608 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive H1ESC peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed Caduceus), column(CA-AUROC-H1ESC) |
| Configuration: Caduceus (probed) | 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) | 0.611 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive HEPG2 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed Caduceus), column(CA-AUROC-HEPG2) |
| Configuration: Caduceus (probed) | 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) | 0.61 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive IMR90 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed Caduceus), column(CA-AUROC-IMR90) |
| Configuration: Caduceus (probed) | 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) | 0.616 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparating positive K562 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed Caduceus), column(CA-AUROC-K562) |
| Configuration: Caduceus (probed) | 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) | 0.251 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Probed Caduceus), column(CA-SPEARMAN-GM12878) |
| Configuration: Caduceus (probed) | 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) | 0.371 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Probed Caduceus), column(CA-SPEARMAN-H1ESC) |
| Configuration: Caduceus (probed) | 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) | 0.312 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Probed Caduceus), column(CA-SPEARMAN-HEPG2) |
| Configuration: Caduceus (probed) | 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) | 0.149 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRank 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(Probed Caduceus), column(CA-SPEARMAN-IMR90) |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of ENCODE chromatin accessibility peaks in five cell lines that DART-Eval evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits. Context-only references | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA No field-specific location recorded Version: 2412.05430v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) Context-only references | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA No field-specific location recorded Version: 2412.05430v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: dart-eval-dataset-encode-chromatin-accessibility-peaks-in-five-cell-lines