DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
Chromatin activity prediction, H1ESC, positives against negatives. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. Separating positive H1ESC peaks from matched negatives.
Overview
Chromatin activity prediction, H1ESC, positives against negatives. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. Separating positive H1ESC peaks from matched negatives.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
auroc (fraction) · Higher values are better.
DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives · ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)
Evidence origin: Author-reported evaluation.
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, column(AUROC H1ESC)- The evaluation setting is part of the method name: a zero-shot, probed and fine-tuned run of the same model are different entries.
- Metrics and datasets differ between tasks, so these figures cannot be averaged into one score.
Comparison details and limitations
Every method DART-Eval reports on Chromatin activity prediction, H1ESC, positives against negatives, scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines.
- Author-reported numbers, source checked but not independently reproduced.
Automated source review: 2026-09-19. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 12 of 13 matching rows.
- Nucleotide Transformer (fine-tuned)0.958
- Caduceus (fine-tuned)0.954
- ChromBPNet (ab initio)0.952
- GENA-LM (fine-tuned)0.942
- DNABERT-2 (fine-tuned)0.94
- HyenaDNA (fine-tuned)0.927
- Mistral-DNA (fine-tuned)0.838
- GENA-LM (probed)0.809
- Nucleotide Transformer (probed)0.765
- DNABERT-2 (probed)0.763
- HyenaDNA (probed)0.728
- Mistral-DNA (probed)0.644
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Caduceus (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- Caduceus (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- ChromBPNet (ab initio) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- DNABERT-2 (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- DNABERT-2 (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- GENA-LM (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- GENA-LM (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- HyenaDNA (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- Mistral-DNA (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- Mistral-DNA (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- Nucleotide Transformer (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Evidence
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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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-dart-eval Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA Table 5, column(AUROC H1ESC) Version: 2412.05430v1 | source checked automated source review · 2026-09-19 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: dart-eval-association-ca-auroc-h1esc Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · 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-task-ca-auroc-h1esc
- areas
- dna-genomes
- tasks
- Chromatin activity prediction, H1ESC, positives against negatives
- metric
- AUROC
- metric direction
- higher
- dataset
- ENCODE chromatin accessibility peaks in five cell lines
- protocol
- Separating positive H1ESC peaks from matched negatives.
- source locator
- Table 5, column(AUROC H1ESC)
- comparison panels
- id: dart-eval-panel-ca-auroc-h1esc; title: DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives; protocol id: dart-eval-task-ca-auroc-h1esc; dataset id: dart-eval-dataset-encode-chromatin-accessibility-peaks-in-five-cell-lines; metric: auroc; unit: fraction; direction: higher; result ids: dart-eval-result-caduceus-probed-ca-auroc-h1esc-auroc; dart-eval-result-dnabert-2-probed-ca-auroc-h1esc-auroc; dart-eval-result-gena-lm-probed-ca-auroc-h1esc-auroc; dart-eval-result-hyenadna-probed-ca-auroc-h1esc-auroc; dart-eval-result-mistral-dna-probed-ca-auroc-h1esc-auroc; dart-eval-result-nucleotide-transformer-probed-ca-auroc-h1esc-auroc; dart-eval-result-caduceus-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-dnabert-2-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-gena-lm-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-hyenadna-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-mistral-dna-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-nucleotide-transformer-fine-tuned-ca-auroc-h1esc-auroc; dart-eval-result-chrombpnet-ab-initio-ca-auroc-h1esc-auroc; source ids: evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55; source locator: Table 5, column(AUROC H1ESC); context: Every method DART-Eval reports on Chromatin activity prediction, H1ESC, positives against negatives, scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines.; caveats: Author-reported numbers, source checked but not independently reproduced.; The evaluation setting is part of the method name: a zero-shot, probed and fine-tuned run of the same model are different entries.; Metrics and datasets differ between tasks, so these figures cannot be averaged into one score.; review: method: automated_source_review; date: 2026-09-19
Related records
- part of: DART-Eval
- subject: DART-Eval CA-AUROC-H1ESC: part of discovery-benchmark-dart-eval
- benchmark: Caduceus (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: Caduceus (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: ChromBPNet (ab initio) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: DNABERT-2 (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: DNABERT-2 (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: GENA-LM (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: GENA-LM (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: HyenaDNA (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: Mistral-DNA (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: Mistral-DNA (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: Nucleotide Transformer (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives
- benchmark: Nucleotide Transformer (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives