Configuration

HyenaDNA (fine-tuned)

DNA language model evaluated by the DART-Eval authors in the fine-tuned setting.

Overview

DNA language model evaluated by the DART-Eval authors in the fine-tuned setting.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

22 evaluations · 22 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HyenaDNA (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)	0.853 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Separating 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 HyenaDNA), column(CA-AUROC-GM12878)
Configuration: HyenaDNA (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)	0.927 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Separating 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 HyenaDNA), column(CA-AUROC-H1ESC)
Configuration: HyenaDNA (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)	0.854 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Separating 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 HyenaDNA), column(CA-AUROC-HEPG2)
Configuration: HyenaDNA (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)	0.941 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Separating 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 HyenaDNA), column(CA-AUROC-IMR90)
Configuration: HyenaDNA (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)	0.75 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Separating 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 HyenaDNA), column(CA-AUROC-K562)
Configuration: HyenaDNA (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)	0.435 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Rank 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 HyenaDNA), column(CA-SPEARMAN-GM12878)
Configuration: HyenaDNA (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)	0.672 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Rank 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 HyenaDNA), column(CA-SPEARMAN-H1ESC)
Configuration: HyenaDNA (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)	0.406 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Rank 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 HyenaDNA), column(CA-SPEARMAN-HEPG2)
Configuration: HyenaDNA (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)	0.426 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Rank 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 HyenaDNA), column(CA-SPEARMAN-IMR90)
Configuration: HyenaDNA (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)	0.446 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Rank 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 HyenaDNA), column(CA-SPEARMAN-K562)
Configuration: HyenaDNA (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)	0.61 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Classify 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 HyenaDNA), column(CTS-ACC)
Configuration: HyenaDNA (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)	0.875 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (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 HyenaDNA), column(CTS-GM12878)
Configuration: HyenaDNA (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)	0.906 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (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 HyenaDNA), column(CTS-H1ESC)
Configuration: HyenaDNA (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)	0.873 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (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 HyenaDNA), column(CTS-HEPG2)
Configuration: HyenaDNA (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)	0.908 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (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 HyenaDNA), column(CTS-IMR90)
Configuration: HyenaDNA (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)	0.847 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (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 HyenaDNA), column(CTS-K562)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.877 absolute_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(HyenaDNA), column(fine-tuned absolute_accuracy)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.952 paired_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(HyenaDNA), column(fine-tuned paired_accuracy)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	0.611 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African HyenaDNA), column(fine-tuned auroc)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	0.265 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African HyenaDNA), column(fine-tuned pearson_r)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.573 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban HyenaDNA), column(fine-tuned auroc)
Configuration: HyenaDNA (fine-tuned)	Task: DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.503 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA (fine-tuned) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban HyenaDNA), column(fine-tuned pearson_r)

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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.

0 evidence rows matching the loaded filters