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RESM

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.

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

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43 evaluations · 43 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-resm

areas: rna-transcriptomes
source locator: Table 7, row(RESM)
missing metadata: checkpoint revision: unreported; parameters: unextracted

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: RESM	Task: NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Dataset subset: NABench aptamer assays (NABench split)	0.221 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(aptamer)
Configuration: RESM	Task: NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation Dataset subset: NABench enhancer assays (NABench split)	0.123 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(enhancer)
Configuration: RESM	Task: NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation Dataset subset: NABench mRNA assays (NABench split)	0.2 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(mRNA)
Configuration: RESM	Task: NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation Dataset subset: NABench promoter assays (NABench split)	0.169 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(promoter)
Configuration: RESM	Task: NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.232 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(ribozyme)
Configuration: RESM	Task: NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation Dataset subset: NABench tRNA assays (NABench split)	0.448 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(tRNA)
Configuration: RESM	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)	0.251 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Contiguous cross validation Spearman ρ)
Configuration: RESM	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)	0.19 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Few-shot Spearman ρ)
Configuration: RESM	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)	0.579 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Random cross validation Spearman ρ)
Configuration: RESM	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)	0.557 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Zero-shot AUC)
Configuration: RESM	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)	0.172 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Zero-shot Spearman ρ)
Configuration: RESM	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)	0.084 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Zero-shot MCC)
Configuration: RESM	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)	0.408 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(Zero-shot NDCG)
Configuration: RESM	Task: NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot Dataset subset: NABench aptamer assays (NABench split)	0.209 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(aptamer)
Configuration: RESM	Task: NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot Dataset subset: NABench enhancer assays (NABench split)	0.055 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(enhancer)
Configuration: RESM	Task: NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot Dataset subset: NABench mRNA assays (NABench split)	0.339 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(mRNA)
Configuration: RESM	Task: NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot Dataset subset: NABench promoter assays (NABench split)	0.138 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(promoter)
Configuration: RESM	Task: NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot Dataset subset: NABench ribozyme assays (NABench split)	0.159 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(ribozyme)
Configuration: RESM	Task: NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot Dataset subset: NABench tRNA assays (NABench split)	0.329 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(tRNA)
Configuration: RESM	Task: NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation Dataset subset: NABench aptamer assays (NABench split)	0.589 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(aptamer)
Configuration: RESM	Task: NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation Dataset subset: NABench enhancer assays (NABench split)	0.291 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(enhancer)
Configuration: RESM	Task: NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation Dataset subset: NABench mRNA assays (NABench split)	0.679 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(mRNA)
Configuration: RESM	Task: NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation Dataset subset: NABench promoter assays (NABench split)	0.61 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(promoter)
Configuration: RESM	Task: NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.587 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(ribozyme)
Configuration: RESM	Task: NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation Dataset subset: NABench tRNA assays (NABench split)	0.595 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RESM 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(RESM), column(tRNA)