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AIDO.RNA

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.

Evaluations and results

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-aido-rna

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

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AIDO.RNA	Task: NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Dataset subset: NABench aptamer assays (NABench split)	0.218 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(aptamer)
Configuration: AIDO.RNA	Task: NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation Dataset subset: NABench enhancer assays (NABench split)	0.015 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(enhancer)
Configuration: AIDO.RNA	Task: NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation Dataset subset: NABench mRNA assays (NABench split)	0.143 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(mRNA)
Configuration: AIDO.RNA	Task: NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation Dataset subset: NABench promoter assays (NABench split)	0.095 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(promoter)
Configuration: AIDO.RNA	Task: NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.219 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(ribozyme)
Configuration: AIDO.RNA	Task: NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation Dataset subset: NABench tRNA assays (NABench split)	0.309 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(tRNA)
Configuration: AIDO.RNA	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)	0.207 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Contiguous cross validation Spearman ρ)
Configuration: AIDO.RNA	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)	0.201 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Few-shot Spearman ρ)
Configuration: AIDO.RNA	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)	0.486 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Random cross validation Spearman ρ)
Configuration: AIDO.RNA	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)	0.472 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Zero-shot AUC)
Configuration: AIDO.RNA	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)	0.098 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Zero-shot Spearman ρ)
Configuration: AIDO.RNA	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)	0.049 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Zero-shot MCC)
Configuration: AIDO.RNA	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)	0.324 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(Zero-shot NDCG)
Configuration: AIDO.RNA	Task: NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot Dataset subset: NABench aptamer 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 AIDO.RNA 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(AIDO.RNA), column(aptamer)
Configuration: AIDO.RNA	Task: NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot Dataset subset: NABench enhancer assays (NABench split)	0.033 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(enhancer)
Configuration: AIDO.RNA	Task: NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot Dataset subset: NABench mRNA assays (NABench split)	0.297 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(mRNA)
Configuration: AIDO.RNA	Task: NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot Dataset subset: NABench promoter assays (NABench split)	0.126 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(promoter)
Configuration: AIDO.RNA	Task: NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot Dataset subset: NABench ribozyme assays (NABench split)	0.201 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(ribozyme)
Configuration: AIDO.RNA	Task: NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot Dataset subset: NABench tRNA assays (NABench split)	0.256 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(tRNA)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation Dataset subset: NABench aptamer assays (NABench split)	0.48 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(aptamer)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation Dataset subset: NABench enhancer 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 AIDO.RNA 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(AIDO.RNA), column(enhancer)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation Dataset subset: NABench mRNA assays (NABench split)	0.565 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(mRNA)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation Dataset subset: NABench promoter assays (NABench split)	0.481 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(promoter)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation Dataset subset: NABench ribozyme assays (NABench split)	0.495 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(ribozyme)
Configuration: AIDO.RNA	Task: NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation Dataset subset: NABench tRNA assays (NABench split)	0.549 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AIDO.RNA 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(AIDO.RNA), column(tRNA)