Task

DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90

Cell-type-specific element classification, IMR90. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. One-against-rest AUROC for IMR90 accessible elements.

14 evaluations · 14 metric rows

Overview

Cell-type-specific element classification, IMR90. Scored with AUROC on ENCODE chromatin accessibility peaks in five cell lines. One-against-rest AUROC for IMR90 accessible elements.

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Evaluation design

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Benchmarks

DART-Eval

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Recorded evaluations

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Run instructions

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Published comparisons

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Comparison and metric

DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90

auroc (fraction) · Higher values are better for this metric.

Every method DART-Eval reports on Cell-type-specific element classification, IMR90, 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 evaluation0.576
DNABERT-2 (probed) · Configuration · Author-reported evaluation0.691
GENA-LM (probed) · Configuration · Author-reported evaluation0.714
HyenaDNA (probed) · Configuration · Author-reported evaluation0.882
Mistral-DNA (probed) · Configuration · Author-reported evaluation0.643
Nucleotide Transformer (probed) · Configuration · Author-reported evaluation0.779
Caduceus (fine-tuned) · Configuration · Author-reported evaluation0.929
DNABERT-2 (fine-tuned) · Configuration · Author-reported evaluation0.922
GENA-LM (fine-tuned) · Configuration · Author-reported evaluation0.911
HyenaDNA (fine-tuned) · Configuration · Author-reported evaluation0.908
Mistral-DNA (fine-tuned) · Configuration · Author-reported evaluation0.748
Nucleotide Transformer (fine-tuned) · Configuration · Author-reported evaluation0.920
Probing-head-like (ab initio) · Method · Author-reported evaluation0.807
ChromBPNet-like (ab initio) · Method · Author-reported evaluation0.921

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(IMR90 AUROC)

Values, uncertainty and evidence

auroc: original source values
Tested entity	Printed value	Uncertainty	Evidence
Caduceus (probed) · Configuration	0.576 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed Caduceus), column(CTS-IMR90)
DNABERT-2 (probed) · Configuration	0.691 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed DNABERT-2), column(CTS-IMR90)
GENA-LM (probed) · Configuration	0.714 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed GENA-LM), column(CTS-IMR90)
HyenaDNA (probed) · Configuration	0.882 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed HyenaDNA), column(CTS-IMR90)
Mistral-DNA (probed) · Configuration	0.643 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed Mistral-DNA), column(CTS-IMR90)
Nucleotide Transformer (probed) · Configuration	0.779 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Probed Nucleotide Transformer), column(CTS-IMR90)
Caduceus (fine-tuned) · Configuration	0.929 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Caduceus), column(CTS-IMR90)
DNABERT-2 (fine-tuned) · Configuration	0.922 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned DNABERT-2), column(CTS-IMR90)
GENA-LM (fine-tuned) · Configuration	0.911 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned GENA-LM), column(CTS-IMR90)
HyenaDNA (fine-tuned) · Configuration	0.908 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned HyenaDNA), column(CTS-IMR90)
Mistral-DNA (fine-tuned) · Configuration	0.748 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Mistral-DNA), column(CTS-IMR90)
Nucleotide Transformer (fine-tuned) · Configuration	0.920 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Fine-Tuned Nucleotide Transformer), column(CTS-IMR90)
Probing-head-like (ab initio) · Method	0.807 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-IMR90)
ChromBPNet-like (ab initio) · Method	0.921 fraction	Not reported	Author-reported evaluation · source checkedDART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio ChromBPNet-like), column(CTS-IMR90)

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.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
Caduceus (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Caduceus (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 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(Fine-Tuned Caduceus), column(CTS-IMR90) Source checking is not independent reproduction.
Caduceus (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Caduceus (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.576 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-IMR90) Source checking is not independent reproduction.
ChromBPNet-like (ab initio) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Method: ChromBPNet-like (ab initio)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.921 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-IMR90) Source checking is not independent reproduction.
DNABERT-2 (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: DNABERT-2 (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.922 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-IMR90) Source checking is not independent reproduction.
DNABERT-2 (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: DNABERT-2 (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.691 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-IMR90) Source checking is not independent reproduction.
GENA-LM (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: GENA-LM (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.911 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-IMR90) Source checking is not independent reproduction.
GENA-LM (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: GENA-LM (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.714 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-IMR90) Source checking is not independent reproduction.
HyenaDNA (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: HyenaDNA (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.908 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-IMR90) Source checking is not independent reproduction.
HyenaDNA (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: HyenaDNA (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.882 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-IMR90) Source checking is not independent reproduction.
Mistral-DNA (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Mistral-DNA (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.748 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-IMR90) Source checking is not independent reproduction.
Mistral-DNA (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Mistral-DNA (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.643 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-IMR90) Source checking is not independent reproduction.
Nucleotide Transformer (fine-tuned) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Nucleotide Transformer (fine-tuned)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.920 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-IMR90) Source checking is not independent reproduction.
Nucleotide Transformer (probed) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Configuration: Nucleotide Transformer (probed)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.779 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-IMR90) Source checking is not independent reproduction.
Probing-head-like (ab initio) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Method: Probing-head-like (ab initio)Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split) One-against-rest AUROC for IMR90 accessible elements. Author-reported evaluation · Evaluation metadata: source checked
0.807 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-IMR90) 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

Claims, original sources and review scope · Release 2026-09-17-134cd1815de8
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 Original source ↗ Table 4, column(IMR90 AUROC) Version: 2412.05430v1 Retrieved: 2026-09-17T07:56:09.182117+00:00	source checked automated source review · 2026-09-18 Audit details Primary-source transcription with no human sign-off and no independent reproduction. Field: `links:part_of:discovery-benchmark-dart-eval` Claim: dart-eval-association-cts-imr90 Source artifact SHA-256: `4194b137ba55c9a2c269d119a9afec6ae1bb0feaf17d91433ae483c41221a56b` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: dart-eval-task-cts-imr90

areas: dna-genomes
tasks: Cell-type-specific element classification, IMR90
metric: AUROC
metric direction: higher
dataset: ENCODE chromatin accessibility peaks in five cell lines
protocol: One-against-rest AUROC for IMR90 accessible elements.
source locator: Table 4, column(IMR90 AUROC)
comparison panels: id: dart-eval-panel-cts-imr90; title: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90; protocol id: dart-eval-task-cts-imr90; 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-imr90-auroc; dart-eval-result-dnabert-2-probed-cts-imr90-auroc; dart-eval-result-gena-lm-probed-cts-imr90-auroc; dart-eval-result-hyenadna-probed-cts-imr90-auroc; dart-eval-result-mistral-dna-probed-cts-imr90-auroc; dart-eval-result-nucleotide-transformer-probed-cts-imr90-auroc; dart-eval-result-caduceus-fine-tuned-cts-imr90-auroc; dart-eval-result-dnabert-2-fine-tuned-cts-imr90-auroc; dart-eval-result-gena-lm-fine-tuned-cts-imr90-auroc; dart-eval-result-hyenadna-fine-tuned-cts-imr90-auroc; dart-eval-result-mistral-dna-fine-tuned-cts-imr90-auroc; dart-eval-result-nucleotide-transformer-fine-tuned-cts-imr90-auroc; dart-eval-result-probing-head-like-ab-initio-cts-imr90-auroc; dart-eval-result-chrombpnet-like-ab-initio-cts-imr90-auroc; source ids: evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55; source locator: Table 4, column(IMR90 AUROC); context: Every method DART-Eval reports on Cell-type-specific element classification, IMR90, 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

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