DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
Cell-type-specific element classification, H1ESC. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. One-against-rest AUROC for H1ESC accessible elements.
Overview
Cell-type-specific element classification, H1ESC. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. One-against-rest AUROC for H1ESC accessible elements.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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 CTS-H1ESC: Cell-type-specific element classification, H1ESC
- Caduceus (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- ChromBPNet-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- DNABERT-2 (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- DNABERT-2 (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- GENA-LM (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- GENA-LM (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- HyenaDNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- HyenaDNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- Mistral-DNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- Mistral-DNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- Nucleotide Transformer (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
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.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
auroc (fraction) · Higher values are better for this metric.
Every method DART-Eval reports on Cell-type-specific element classification, H1ESC, scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines.
Evaluation protocol · ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)
- Caduceus (probed) · Configuration · Author-reported evaluation0.622
- DNABERT-2 (probed) · Configuration · Author-reported evaluation0.757
- GENA-LM (probed) · Configuration · Author-reported evaluation0.787
- HyenaDNA (probed) · Configuration · Author-reported evaluation0.889
- Mistral-DNA (probed) · Configuration · Author-reported evaluation0.678
- Nucleotide Transformer (probed) · Configuration · Author-reported evaluation0.795
- Caduceus (fine-tuned) · Configuration · Author-reported evaluation0.937
- DNABERT-2 (fine-tuned) · Configuration · Author-reported evaluation0.930
- GENA-LM (fine-tuned) · Configuration · Author-reported evaluation0.923
- HyenaDNA (fine-tuned) · Configuration · Author-reported evaluation0.906
- Mistral-DNA (fine-tuned) · Configuration · Author-reported evaluation0.762
- Nucleotide Transformer (fine-tuned) · Configuration · Author-reported evaluation0.925
- Probing-head-like (ab initio) · Method · Author-reported evaluation0.836
- ChromBPNet-like (ab initio) · Method · Author-reported evaluation0.929
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, column(H1ESC AUROC)Values, uncertainty and evidence
Scope and limitations
- 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.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities 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 |
|---|---|---|
| Caduceus (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Caduceus (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.937 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 4, row(Fine-Tuned Caduceus), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Caduceus (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Caduceus (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.622 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 4, row(Probed Caduceus), column(CTS-H1ESC) Source checking is not independent reproduction. |
| ChromBPNet-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Method: ChromBPNet-like (ab initio)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.929 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 4, row(Ab initio ChromBPNet-like), column(CTS-H1ESC) Source checking is not independent reproduction. |
| DNABERT-2 (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: DNABERT-2 (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.930 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 4, row(Fine-Tuned DNABERT-2), column(CTS-H1ESC) Source checking is not independent reproduction. |
| DNABERT-2 (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: DNABERT-2 (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.757 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 4, row(Probed DNABERT-2), column(CTS-H1ESC) Source checking is not independent reproduction. |
| GENA-LM (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: GENA-LM (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.923 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 4, row(Fine-Tuned GENA-LM), column(CTS-H1ESC) Source checking is not independent reproduction. |
| GENA-LM (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: GENA-LM (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.787 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 4, row(Probed GENA-LM), column(CTS-H1ESC) Source checking is not independent reproduction. |
| HyenaDNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: HyenaDNA (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.906 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 4, row(Fine-Tuned HyenaDNA), column(CTS-H1ESC) Source checking is not independent reproduction. |
| HyenaDNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: HyenaDNA (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.889 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 4, row(Probed HyenaDNA), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Mistral-DNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Mistral-DNA (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.762 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 4, row(Fine-Tuned Mistral-DNA), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Mistral-DNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Mistral-DNA (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.678 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 4, row(Probed Mistral-DNA), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Nucleotide Transformer (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Nucleotide Transformer (fine-tuned)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.925 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 4, row(Fine-Tuned Nucleotide Transformer), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Nucleotide Transformer (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Configuration: Nucleotide Transformer (probed)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.795 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 4, row(Probed Nucleotide Transformer), column(CTS-H1ESC) Source checking is not independent reproduction. |
| Probing-head-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Method: Probing-head-like (ab initio)Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESCDataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for H1ESC accessible elements. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.836 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 4, row(Ab initio Probing-head-like), column(CTS-H1ESC) 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.
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 4, column(H1ESC AUROC) Version: 2412.05430v1 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: dart-eval-association-cts-h1esc Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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-task-cts-h1esc
- areas
- dna-genomes
- tasks
- Cell-type-specific element classification, H1ESC
- metric
- AUROC
- metric direction
- higher
- dataset
- ENCODE chromatin accessibility peaks in five cell lines
- protocol
- One-against-rest AUROC for H1ESC accessible elements.
- source locator
- Table 4, column(H1ESC AUROC)
- comparison panels
- id: dart-eval-panel-cts-h1esc; title: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC; protocol id: dart-eval-task-cts-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-cts-h1esc-auroc; dart-eval-result-dnabert-2-probed-cts-h1esc-auroc; dart-eval-result-gena-lm-probed-cts-h1esc-auroc; dart-eval-result-hyenadna-probed-cts-h1esc-auroc; dart-eval-result-mistral-dna-probed-cts-h1esc-auroc; dart-eval-result-nucleotide-transformer-probed-cts-h1esc-auroc; dart-eval-result-caduceus-fine-tuned-cts-h1esc-auroc; dart-eval-result-dnabert-2-fine-tuned-cts-h1esc-auroc; dart-eval-result-gena-lm-fine-tuned-cts-h1esc-auroc; dart-eval-result-hyenadna-fine-tuned-cts-h1esc-auroc; dart-eval-result-mistral-dna-fine-tuned-cts-h1esc-auroc; dart-eval-result-nucleotide-transformer-fine-tuned-cts-h1esc-auroc; dart-eval-result-probing-head-like-ab-initio-cts-h1esc-auroc; dart-eval-result-chrombpnet-like-ab-initio-cts-h1esc-auroc; source ids: evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55; source locator: Table 4, column(H1ESC AUROC); context: Every method DART-Eval reports on Cell-type-specific element classification, H1ESC, 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: 2026-09-18
Related records
- part of: DART-Eval
- subject: DART-Eval CTS-H1ESC: part of discovery-benchmark-dart-eval
- benchmark: Caduceus (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Caduceus (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: ChromBPNet-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: DNABERT-2 (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: DNABERT-2 (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: GENA-LM (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: GENA-LM (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: HyenaDNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: HyenaDNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Mistral-DNA (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Mistral-DNA (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Nucleotide Transformer (fine-tuned) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Nucleotide Transformer (probed) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC
- benchmark: Probing-head-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC