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HyenaDNA

HyenaDNA: Nucleotide foundation 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

43 evaluations · 43 results. Different protocols are not a single leaderboard.

Sorted by Spearman (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	Spearman	AUROC	MCC	NDCG (cutoff not stated)
HyenaDNAEvaluation	NABench SELEX-RCV: Overall fitness prediction on NABench SELEX assays, Random cross validation Spearman ρ, NABench SELEX assays (NABench split)	0.656 (best in column)	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation, NABench mRNA assays (NABench split)	0.599	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench SELEX-FS: Overall fitness prediction on NABench SELEX assays, Few-shot Spearman ρ, NABench SELEX assays (NABench split)	0.585	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation, NABench promoter assays (NABench split)	0.576	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation, NABench tRNA assays (NABench split)	0.571	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation, NABench aptamer assays (NABench split)	0.562	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-RCV: Overall fitness prediction on NABench deep mutational scanning assays, Random cross validation Spearman ρ, NABench deep mutational scanning assays (NABench split)	0.561	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation, NABench ribozyme assays (NABench split)	0.556	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot, NABench mRNA assays (NABench split)	0.298	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation, NABench enhancer assays (NABench split)	0.238	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation, NABench mRNA assays (NABench split)	0.232	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot, NABench aptamer assays (NABench split)	0.216	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation, NABench ribozyme assays (NABench split)	0.215	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation, NABench tRNA assays (NABench split)	0.187	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-CCV: Overall fitness prediction on NABench deep mutational scanning assays, Contiguous cross validation Spearman ρ, NABench deep mutational scanning assays (NABench split)	0.186	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation, NABench aptamer assays (NABench split)	0.143	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-FS: Overall fitness prediction on NABench deep mutational scanning assays, Few-shot Spearman ρ, NABench deep mutational scanning assays (NABench split)	0.132	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot, NABench ribozyme assays (NABench split)	0.13	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-PROMOTER: Fitness prediction on promoter assays, zero-shot, NABench promoter assays (NABench split)	0.13	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, zero-shot, NABench ribozyme assays (NABench split)	0.111	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-ZS-CORR: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot Spearman ρ, NABench deep mutational scanning assays (NABench split)	0.094	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-MRNA: Fitness prediction on mRNA assays, zero-shot, NABench mRNA assays (NABench split)	0.082	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench SELEX-ZS-CORR: Overall fitness prediction on NABench SELEX assays, Zero-shot Spearman ρ, NABench SELEX assays (NABench split)	0.08	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot, NABench promoter assays (NABench split)	0.079	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-TRNA: Fitness prediction on tRNA assays, zero-shot, NABench tRNA assays (NABench split)	0.075	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot, NABench tRNA assays (NABench split)	0.058	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-APTAMER: Fitness prediction on aptamer assays, zero-shot, NABench aptamer assays (NABench split)	0.058	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot, NABench enhancer assays (NABench split)	0.05	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation, NABench enhancer assays (NABench split)	0.049	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation, NABench promoter assays (NABench split)	0.037	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-CORR-ENHANCER: Fitness prediction on enhancer assays, zero-shot, NABench enhancer assays (NABench split)	0.023	Not reported	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-ZS-AUC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot AUC, NABench deep mutational scanning assays (NABench split)	Not reported	0.483	Not reported	Not reported
HyenaDNAEvaluation	NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC, NABench deep mutational scanning assays (NABench split)	Not reported	Not reported	0.047 (best in column)	Not reported
HyenaDNAEvaluation	NABench DMS-ZS-NDCG: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot NDCG, NABench deep mutational scanning assays (NABench split)	Not reported	Not reported	Not reported	0.334 (best in column)
HyenaDNAEvaluation	NABench SELEX-ZS-AUC: Overall fitness prediction on NABench SELEX assays, Zero-shot AUC, NABench SELEX assays (NABench split)	Not reported	0.543	Not reported	Not reported
HyenaDNAEvaluation	NABench SELEX-ZS-MCC: Overall fitness prediction on NABench SELEX assays, Zero-shot MCC, NABench SELEX assays (NABench split)	Not reported	Not reported	0.043	Not reported
HyenaDNAEvaluation	NABench SELEX-ZS-NDCG: Overall fitness prediction on NABench SELEX assays, Zero-shot NDCG, NABench SELEX assays (NABench split)	Not reported	Not reported	Not reported	0.279
HyenaDNAEvaluation	NABench ZS-AUC-APTAMER: Fitness prediction on aptamer assays, zero-shot, NABench aptamer assays (NABench split)	Not reported	0.514	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-AUC-ENHANCER: Fitness prediction on enhancer assays, zero-shot, NABench enhancer assays (NABench split)	Not reported	0.511	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-AUC-MRNA: Fitness prediction on mRNA assays, zero-shot, NABench mRNA assays (NABench split)	Not reported	0.558	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-AUC-PROMOTER: Fitness prediction on promoter assays, zero-shot, NABench promoter assays (NABench split)	Not reported	0.571 (best in column)	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-AUC-RIBOZYME: Fitness prediction on ribozyme assays, zero-shot, NABench ribozyme assays (NABench split)	Not reported	0.556	Not reported	Not reported
HyenaDNAEvaluation	NABench ZS-AUC-TRNA: Fitness prediction on tRNA assays, zero-shot, NABench tRNA assays (NABench split)	Not reported	0.546	Not reported	Not reported

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NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256

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Technical metadata and extraction receipts

Stable ID: nabench-method-hyenadna

areas: rna-transcriptomes
source locator: Table 7, row(HyenaDNA)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Nucleotide foundation model evaluated by the NABench authors under their fitness prediction protocol.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HyenaDNA	Task: NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Dataset subset: NABench aptamer assays (NABench split)	0.143 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench aptamer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(aptamer)
Configuration: HyenaDNA	Task: NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation Dataset subset: NABench enhancer assays (NABench split)	0.049 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench enhancer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(enhancer)
Configuration: HyenaDNA	Task: NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation Dataset subset: NABench mRNA assays (NABench split)	0.232 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench mRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(mRNA)
Configuration: HyenaDNA	Task: NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation Dataset subset: NABench promoter assays (NABench split)	0.037 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench promoter assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(promoter)
Configuration: HyenaDNA	Task: NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.215 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench ribozyme assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(ribozyme)
Configuration: HyenaDNA	Task: NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation Dataset subset: NABench tRNA assays (NABench split)	0.187 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench tRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(HyenaDNA), column(tRNA)
Configuration: HyenaDNA	Task: NABench DMS-CCV: Overall fitness prediction on NABench deep mutational scanning assays, Contiguous cross validation Spearman ρ Dataset subset: NABench deep mutational scanning assays (NABench split)	0.186 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-CCV: Overall fitness prediction on NABench deep mutational scanning assays, Contiguous cross validation Spearman ρ Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Contiguous cross validation Spearman ρ)
Configuration: HyenaDNA	Task: NABench DMS-FS: Overall fitness prediction on NABench deep mutational scanning assays, Few-shot Spearman ρ Dataset subset: NABench deep mutational scanning assays (NABench split)	0.132 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-FS: Overall fitness prediction on NABench deep mutational scanning assays, Few-shot Spearman ρ Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Few-shot Spearman ρ)
Configuration: HyenaDNA	Task: NABench DMS-RCV: Overall fitness prediction on NABench deep mutational scanning assays, Random cross validation Spearman ρ Dataset subset: NABench deep mutational scanning assays (NABench split)	0.561 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-RCV: Overall fitness prediction on NABench deep mutational scanning assays, Random cross validation Spearman ρ Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Random cross validation Spearman ρ)
Configuration: HyenaDNA	Task: NABench DMS-ZS-AUC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot AUC Dataset subset: NABench deep mutational scanning assays (NABench split)	0.483 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-ZS-AUC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot AUC Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot AUC)
Configuration: HyenaDNA	Task: NABench DMS-ZS-CORR: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot Spearman ρ Dataset subset: NABench deep mutational scanning assays (NABench split)	0.094 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-ZS-CORR: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot Spearman ρ Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot Spearman ρ)
Configuration: HyenaDNA	Task: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Dataset subset: NABench deep mutational scanning assays (NABench split)	0.047 MCC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot MCC)
Configuration: HyenaDNA	Task: NABench DMS-ZS-NDCG: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot NDCG Dataset subset: NABench deep mutational scanning assays (NABench split)	0.334 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench DMS-ZS-NDCG: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot NDCG Aggregated by the NABench authors across NABench deep mutational scanning assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot NDCG)
Configuration: HyenaDNA	Task: NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot Dataset subset: NABench aptamer assays (NABench split)	0.216 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot Scored few-shot across the NABench aptamer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(aptamer)
Configuration: HyenaDNA	Task: NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot Dataset subset: NABench enhancer assays (NABench split)	0.05 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot Scored few-shot across the NABench enhancer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(enhancer)
Configuration: HyenaDNA	Task: NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot Dataset subset: NABench mRNA assays (NABench split)	0.298 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot Scored few-shot across the NABench mRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(mRNA)
Configuration: HyenaDNA	Task: NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot Dataset subset: NABench promoter assays (NABench split)	0.079 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot Scored few-shot across the NABench promoter assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(promoter)
Configuration: HyenaDNA	Task: NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot Dataset subset: NABench ribozyme assays (NABench split)	0.13 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot Scored few-shot across the NABench ribozyme assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(ribozyme)
Configuration: HyenaDNA	Task: NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot Dataset subset: NABench tRNA assays (NABench split)	0.058 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot Scored few-shot across the NABench tRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(HyenaDNA), column(tRNA)
Configuration: HyenaDNA	Task: NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation Dataset subset: NABench aptamer assays (NABench split)	0.562 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation Scored supervised, random cross validation across the NABench aptamer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(aptamer)
Configuration: HyenaDNA	Task: NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation Dataset subset: NABench enhancer assays (NABench split)	0.238 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation Scored supervised, random cross validation across the NABench enhancer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(enhancer)
Configuration: HyenaDNA	Task: NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation Dataset subset: NABench mRNA assays (NABench split)	0.599 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation Scored supervised, random cross validation across the NABench mRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(mRNA)
Configuration: HyenaDNA	Task: NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation Dataset subset: NABench promoter assays (NABench split)	0.576 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation Scored supervised, random cross validation across the NABench promoter assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(promoter)
Configuration: HyenaDNA	Task: NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.556 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation Scored supervised, random cross validation across the NABench ribozyme assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(ribozyme)
Configuration: HyenaDNA	Task: NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation Dataset subset: NABench tRNA assays (NABench split)	0.571 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source HyenaDNA on NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation Scored supervised, random cross validation across the NABench tRNA assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(HyenaDNA), column(tRNA)