Configuration

HyenaDNA large

DNA language model whose frozen embeddings the BEND authors scored with a downstream head.

Overview

DNA language model whose frozen embeddings the BEND authors scored with a downstream head.

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

Evaluations and results

Release 2026-09-17-134cd1815de8 · 7 evaluations · 7 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
HyenaDNA large on BEND CHROMATIN: Chromatin accessibility Configuration: HyenaDNA largeTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.84 auroc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Chromatin accessibility) Source checking is not independent reproduction.
HyenaDNA large on BEND CPG: CpG methylation Configuration: HyenaDNA largeTask: BEND CPG: CpG methylationDataset subset: ENCODE CpG methylation (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.91 auroc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(CpG methylation) Source checking is not independent reproduction.
HyenaDNA large on BEND ENHANCER: Enhancer annotation Configuration: HyenaDNA largeTask: BEND ENHANCER: Enhancer annotationDataset subset: Fulco 2019, Gasperini 2019 and Enformer enhancer set (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.03 auprc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Enhancer annotation) Source checking is not independent reproduction.
HyenaDNA large on BEND GENE-FINDING: Gene finding Configuration: HyenaDNA largeTask: BEND GENE-FINDING: Gene findingDataset subset: GENCODE (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.35 mcc Unit: correlation · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Gene finding) Source checking is not independent reproduction.
HyenaDNA large on BEND HISTONE: Histone modification Configuration: HyenaDNA largeTask: BEND HISTONE: Histone modificationDataset subset: ENCODE histone modification (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.76 auroc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Histone modification) Source checking is not independent reproduction.
HyenaDNA large on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: HyenaDNA largeTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.45 auroc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Noncoding variant effects on disease) Source checking is not independent reproduction.
HyenaDNA large on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression Configuration: HyenaDNA largeTask: BEND VARIANT-EXPRESSION: Noncoding variant effects on expressionDataset subset: DeepSEA expression variants (BEND split) A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Author-reported evaluation · Evaluation metadata: source checked
0.51 auroc Unit: fraction · Direction: higher	Uncertainty: Not reported Scored: Not reported · Eligible: Not reported	source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Noncoding variant effects on expression) 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.

0 evidence rows matching the loaded filters