ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)
The split of ENCODE cCREs against dinucleotide-shuffled backgrounds that DART-Eval evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.
Subset and evaluation context
This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.
Evaluation results
Release 2026-09-17-134cd1815de8 · 32 evaluations · 32 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 REI-ABS: Regulatory element identification, absolute accuracy Configuration: Caduceus (fine-tuned)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.903 absolute_accuracy 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 3, row(Caduceus), column(fine-tuned absolute_accuracy) Source checking is not independent reproduction. |
| Caduceus (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: Caduceus (fine-tuned)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.971 paired_accuracy 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 3, row(Caduceus), column(fine-tuned paired_accuracy) Source checking is not independent reproduction. |
| Caduceus (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: Caduceus (probed)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.726 absolute_accuracy 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 3, row(Caduceus), column(probed absolute_accuracy) Source checking is not independent reproduction. |
| Caduceus (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: Caduceus (probed)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.896 paired_accuracy 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 3, row(Caduceus), column(probed paired_accuracy) Source checking is not independent reproduction. |
| Caduceus (zero-shot) on DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy Configuration: Caduceus (zero-shot)Task: DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences, scored zero-shot from model likelihood. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.971 accuracy 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 3, row(Caduceus), column(zero-shot accuracy) Source checking is not independent reproduction. |
| DNABERT-2 (fine-tuned) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: DNABERT-2 (fine-tuned)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.913 absolute_accuracy 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 3, row(DNABERT-2), column(fine-tuned absolute_accuracy) Source checking is not independent reproduction. |
| DNABERT-2 (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: DNABERT-2 (fine-tuned)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.973 paired_accuracy 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 3, row(DNABERT-2), column(fine-tuned paired_accuracy) Source checking is not independent reproduction. |
| DNABERT-2 (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: DNABERT-2 (probed)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.847 absolute_accuracy 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 3, row(DNABERT-2), column(probed absolute_accuracy) Source checking is not independent reproduction. |
| DNABERT-2 (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: DNABERT-2 (probed)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.943 paired_accuracy 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 3, row(DNABERT-2), column(probed paired_accuracy) Source checking is not independent reproduction. |
| DNABERT-2 (zero-shot) on DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy Configuration: DNABERT-2 (zero-shot)Task: DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences, scored zero-shot from model likelihood. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.876 accuracy 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 3, row(DNABERT-2), column(zero-shot accuracy) Source checking is not independent reproduction. |
| GENA-LM (fine-tuned) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: GENA-LM (fine-tuned)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.909 absolute_accuracy 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 3, row(GENA-LM), column(fine-tuned absolute_accuracy) Source checking is not independent reproduction. |
| GENA-LM (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: GENA-LM (fine-tuned)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.972 paired_accuracy 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 3, row(GENA-LM), column(fine-tuned paired_accuracy) Source checking is not independent reproduction. |
| GENA-LM (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: GENA-LM (probed)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.887 absolute_accuracy 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 3, row(GENA-LM), column(probed absolute_accuracy) Source checking is not independent reproduction. |
| GENA-LM (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: GENA-LM (probed)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.959 paired_accuracy 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 3, row(GENA-LM), column(probed paired_accuracy) Source checking is not independent reproduction. |
| GENA-LM (zero-shot) on DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy Configuration: GENA-LM (zero-shot)Task: DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences, scored zero-shot from model likelihood. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.947 accuracy 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 3, row(GENA-LM), column(zero-shot accuracy) Source checking is not independent reproduction. |
| HyenaDNA (fine-tuned) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: HyenaDNA (fine-tuned)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.877 absolute_accuracy 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 3, row(HyenaDNA), column(fine-tuned absolute_accuracy) Source checking is not independent reproduction. |
| HyenaDNA (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: HyenaDNA (fine-tuned)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.952 paired_accuracy 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 3, row(HyenaDNA), column(fine-tuned paired_accuracy) Source checking is not independent reproduction. |
| HyenaDNA (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: HyenaDNA (probed)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.847 absolute_accuracy 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 3, row(HyenaDNA), column(probed absolute_accuracy) Source checking is not independent reproduction. |
| HyenaDNA (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: HyenaDNA (probed)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.935 paired_accuracy 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 3, row(HyenaDNA), column(probed paired_accuracy) Source checking is not independent reproduction. |
| HyenaDNA (zero-shot) on DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy Configuration: HyenaDNA (zero-shot)Task: DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences, scored zero-shot from model likelihood. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.891 accuracy 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 3, row(HyenaDNA), column(zero-shot accuracy) Source checking is not independent reproduction. |
| Mistral-DNA (fine-tuned) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: Mistral-DNA (fine-tuned)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.817 absolute_accuracy 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 3, row(Mistral-DNA), column(fine-tuned absolute_accuracy) Source checking is not independent reproduction. |
| Mistral-DNA (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: Mistral-DNA (fine-tuned)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.905 paired_accuracy 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 3, row(Mistral-DNA), column(fine-tuned paired_accuracy) Source checking is not independent reproduction. |
| Mistral-DNA (probed) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Configuration: Mistral-DNA (probed)Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.759 absolute_accuracy 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 3, row(Mistral-DNA), column(probed absolute_accuracy) Source checking is not independent reproduction. |
| Mistral-DNA (probed) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Configuration: Mistral-DNA (probed)Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.859 paired_accuracy 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 3, row(Mistral-DNA), column(probed paired_accuracy) Source checking is not independent reproduction. |
| Mistral-DNA (zero-shot) on DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracy Configuration: Mistral-DNA (zero-shot)Task: DART-Eval REI-ACC: Regulatory element identification, zero-shot accuracyDataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split) Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences, scored zero-shot from model likelihood. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.863 accuracy 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 3, row(Mistral-DNA), column(zero-shot accuracy) 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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of ENCODE cCREs against dinucleotide-shuffled backgrounds 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 cCREs against dinucleotide-shuffled backgrounds (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. |
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-dataset-encode-ccres-against-dinucleotide-shuffled-backgrounds
- areas
- dna-genomes
- missing metadata
- version: unreported; url: unextracted
Related records
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