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GENA-LM-large

Nucleotide foundation model evaluated by the NABench authors under their fitness prediction protocol.

Overview

Nucleotide foundation model evaluated by the NABench authors under their fitness prediction protocol.

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42 evaluations · 42 results. Different protocols are not a single leaderboard.

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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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Stable ID: nabench-method-gena-lm-large

areas: rna-transcriptomes
source locator: Table 7, row(GENA-LM-large)
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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GENA-LM-large	Task: NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Dataset subset: NABench aptamer assays (NABench split)	0.203 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(aptamer)
Configuration: GENA-LM-large	Task: NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation Dataset subset: NABench enhancer assays (NABench split)	0.062 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(enhancer)
Configuration: GENA-LM-large	Task: NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation Dataset subset: NABench mRNA assays (NABench split)	0.105 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(mRNA)
Configuration: GENA-LM-large	Task: NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation Dataset subset: NABench promoter assays (NABench split)	0.592 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(promoter)
Configuration: GENA-LM-large	Task: NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.369 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(ribozyme)
Configuration: GENA-LM-large	Task: NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation Dataset subset: NABench tRNA assays (NABench split)	0.27 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(tRNA)
Configuration: GENA-LM-large	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)	0.271 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Contiguous cross validation Spearman ρ)
Configuration: GENA-LM-large	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)	0.151 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Few-shot Spearman ρ)
Configuration: GENA-LM-large	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)	0.474 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Random cross validation Spearman ρ)
Configuration: GENA-LM-large	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)	0.529 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Zero-shot AUC)
Configuration: GENA-LM-large	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)	0.113 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Zero-shot Spearman ρ)
Configuration: GENA-LM-large	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)	0.045 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Zero-shot MCC)
Configuration: GENA-LM-large	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)	0.364 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(Zero-shot NDCG)
Configuration: GENA-LM-large	Task: NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot Dataset subset: NABench aptamer assays (NABench split)	0.248 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(aptamer)
Configuration: GENA-LM-large	Task: NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot Dataset subset: NABench enhancer assays (NABench split)	0.06 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(enhancer)
Configuration: GENA-LM-large	Task: NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot Dataset subset: NABench mRNA assays (NABench split)	0.349 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(mRNA)
Configuration: GENA-LM-large	Task: NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot Dataset subset: NABench promoter assays (NABench split)	0.11 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(promoter)
Configuration: GENA-LM-large	Task: NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot Dataset subset: NABench ribozyme assays (NABench split)	0.127 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(ribozyme)
Configuration: GENA-LM-large	Task: NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot Dataset subset: NABench tRNA assays (NABench split)	0.131 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(tRNA)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation Dataset subset: NABench aptamer assays (NABench split)	0.444 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(aptamer)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation Dataset subset: NABench enhancer assays (NABench split)	0.217 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(enhancer)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation Dataset subset: NABench mRNA assays (NABench split)	0.594 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(mRNA)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation Dataset subset: NABench promoter assays (NABench split)	0.604 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(promoter)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.475 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(ribozyme)
Configuration: GENA-LM-large	Task: NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation Dataset subset: NABench tRNA assays (NABench split)	0.47 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM-large 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(GENA-LM-large), column(tRNA)