Configuration

HyenaDNA (DNALONGBENCH)

Configuration of HyenaDNA: HyenaDNA medium-450k; fine-tuned per task.

5 evaluations · 27 results 1 open disagreement between studies involves its model

Overview

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

Evaluations and results

5 evaluations · 27 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUPRC	AUROC	AUROC (AS (Adipose_Subcutaneous))	AUROC (AT (Artery_Tibial))	AUROC (average over eQTLP conditions as printed)	AUROC (CCF (Cells_Cultured_fibroblasts))	AUROC (MS (Muscle Skeletal))	AUROC (NT (Nerve Tibial))	AUROC (SNSES (Skin_Not_Sun_Exposed_Suprapubic))	AUROC (SSELL (Skin_Sun_Exposed_Lower_leg))	AUROC (Thyroid)	AUROC (WB (Whole_Blood))	Pearson (average over RSAP conditions as printed)	Pearson (average over TISP conditions as printed)	Pearson (EC (ENCODE CAGE))	Pearson (ER (ENCODE RAMPAGE))	Pearson (FC (FANTOM CAGE))	Pearson (GC (GRO-cap))	Pearson (Human)	Pearson (Mouse)	Pearson (PC (PRO-cap))	Stratum adjusted correlation coefficient (average over CMP conditions as printed)	Stratum adjusted correlation coefficient (GM12878)	Stratum adjusted correlation coefficient (H1hESC)	Stratum adjusted correlation coefficient (HCT116)	Stratum adjusted correlation coefficient (HFF)	Stratum adjusted correlation coefficient (IMR90)
HyenaDNA (DNALONGBENCH)Evaluation	DNALONGBENCH Enhancer-target gene prediction (Table 3), DNALONGBENCH Enhancer-target gene prediction test set	0.249	0.828	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
HyenaDNA (DNALONGBENCH)Evaluation	DNALONGBENCH Contact map prediction (Table 4), DNALONGBENCH Contact map prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.115	0.099	0.122	0.118	0.139	0.097
HyenaDNA (DNALONGBENCH)Evaluation	DNALONGBENCH Expression quantitative trait loci prediction (Table 7), DNALONGBENCH Expression quantitative trait loci prediction test set	Not reported	Not reported	0.513	0.479	0.514	0.584	0.487	0.511	0.471	0.544	0.529	0.512	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
HyenaDNA (DNALONGBENCH)Evaluation	DNALONGBENCH Regulatory sequence activity prediction (Table 5), DNALONGBENCH Regulatory sequence activity prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.347	Not reported	Not reported	Not reported	Not reported	Not reported	0.298	0.396	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
HyenaDNA (DNALONGBENCH)Evaluation	DNALONGBENCH Transcription initiation signal prediction (Table 6), DNALONGBENCH Transcription initiation signal prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.132	0.124	0.118	0.138	0.112	Not reported	Not reported	0.168	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 27 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.115 Stratum adjusted correlation coefficient (average over CMP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'Avg'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.099 Stratum adjusted correlation coefficient (GM12878) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'GM12878'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.122 Stratum adjusted correlation coefficient (H1hESC) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'H1hESC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.118 Stratum adjusted correlation coefficient (HCT116) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'HCT116'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.139 Stratum adjusted correlation coefficient (HFF) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'HFF'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.097 Stratum adjusted correlation coefficient (IMR90) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'IMR90'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.513 AUROC (AS (Adipose_Subcutaneous)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'AS'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.479 AUROC (AT (Artery_Tibial)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'AT'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.514 AUROC (average over eQTLP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'Avg'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.584 AUROC (CCF (Cells_Cultured_fibroblasts)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'CCF'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.487 AUROC (MS (Muscle Skeletal)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'MS'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.511 AUROC (NT (Nerve Tibial)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'NT'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.471 AUROC (SNSES (Skin_Not_Sun_Exposed_Suprapubic)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'SNSES'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.544 AUROC (SSELL (Skin_Sun_Exposed_Lower_leg)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'SSELL'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.529 AUROC (Thyroid) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'Thyroid'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.512 AUROC (WB (Whole_Blood)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'HyenaDNA', column 'WB'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.249 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'HyenaDNA', column 'AUPRC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.828 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'HyenaDNA', column 'AUROC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.347 Pearson (average over RSAP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'HyenaDNA', column 'Avg'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.298 Pearson (Human) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'HyenaDNA', column 'Human'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.396 Pearson (Mouse) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'HyenaDNA', column 'Mouse'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.132 Pearson (average over TISP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'HyenaDNA', column 'Avg'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.124 Pearson (EC (ENCODE CAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'HyenaDNA', column 'EC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.118 Pearson (ER (ENCODE RAMPAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'HyenaDNA', column 'ER'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.138 Pearson (FC (FANTOM CAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'HyenaDNA', column 'FC'

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Release 2026-10-23-5347695500ed · Record review: source checked

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DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Original source · Nature Communications 16, published 2025-11-18; PMC12627797 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-dnalongbench-config-hyenadna

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: HyenaDNA
foundation model eligible: true
parameters: HyenaDNA medium-450k; fine-tuned per task
access reuse: Public model code and weights
source locator: Methods 'Expert model', 'CNN' and 'DNA Foundation Model'
missing metadata: version: reason: unreported; note: Checkpoint or release not printed beyond the model name
provenance note: HyenaDNA as evaluated in DNALONGBENCH.

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