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RNAernie

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

43 evaluations · 43 metric rows

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

Release 2026-09-17-134cd1815de8 · 43 evaluations · 43 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
RNAernie on NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench aptamer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.076 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(aptamer)

Source checking is not independent reproduction.

RNAernie on NABench CCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench enhancer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.074 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(enhancer)

Source checking is not independent reproduction.

RNAernie on NABench CCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench mRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.247 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(mRNA)

Source checking is not independent reproduction.

RNAernie on NABench CCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench promoter assays.

Author-reported evaluation · Evaluation metadata: source checked

0.081 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(promoter)

Source checking is not independent reproduction.

RNAernie on NABench CCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench ribozyme assays.

Author-reported evaluation · Evaluation metadata: source checked

0.237 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(ribozyme)

Source checking is not independent reproduction.

RNAernie on NABench CCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, contiguous cross validation

Scored supervised, contiguous cross validation across the NABench tRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.185 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNAernie), column(tRNA)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.199 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Contiguous cross validation Spearman ρ)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.102 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Few-shot Spearman ρ)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.387 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Random cross validation Spearman ρ)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.481 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot AUC)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.078 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot Spearman ρ)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.044 mcc

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot MCC)

Source checking is not independent reproduction.

RNAernie 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.

Author-reported evaluation · Evaluation metadata: source checked

0.353 ndcg

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot NDCG)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-APTAMER: Fitness prediction on aptamer assays, few-shot

Scored few-shot across the NABench aptamer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.142 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(aptamer)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-ENHANCER: Fitness prediction on enhancer assays, few-shot

Scored few-shot across the NABench enhancer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.026 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(enhancer)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-MRNA: Fitness prediction on mRNA assays, few-shot

Scored few-shot across the NABench mRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.072 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(mRNA)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-PROMOTER: Fitness prediction on promoter assays, few-shot

Scored few-shot across the NABench promoter assays.

Author-reported evaluation · Evaluation metadata: source checked

0.110 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(promoter)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-RIBOZYME: Fitness prediction on ribozyme assays, few-shot

Scored few-shot across the NABench ribozyme assays.

Author-reported evaluation · Evaluation metadata: source checked

0.102 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(ribozyme)

Source checking is not independent reproduction.

RNAernie on NABench FS-CORR-TRNA: Fitness prediction on tRNA assays, few-shot

Scored few-shot across the NABench tRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.100 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 9, row(RNAernie), column(tRNA)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench aptamer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.390 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(aptamer)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-ENHANCER: Fitness prediction on enhancer assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench enhancer assays.

Author-reported evaluation · Evaluation metadata: source checked

0.129 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(enhancer)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-MRNA: Fitness prediction on mRNA assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench mRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.461 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(mRNA)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-PROMOTER: Fitness prediction on promoter assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench promoter assays.

Author-reported evaluation · Evaluation metadata: source checked

0.348 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(promoter)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-RIBOZYME: Fitness prediction on ribozyme assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench ribozyme assays.

Author-reported evaluation · Evaluation metadata: source checked

0.394 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(ribozyme)

Source checking is not independent reproduction.

RNAernie on NABench RCV-CORR-TRNA: Fitness prediction on tRNA assays, supervised, random cross validation

Scored supervised, random cross validation across the NABench tRNA assays.

Author-reported evaluation · Evaluation metadata: source checked

0.464 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 10, row(RNAernie), column(tRNA)

Source checking is not independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-134cd1815de8
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No evidence rows match these filters. Choose another scope or clear the search.

Sources and history

Release 2026-09-17-134cd1815de8 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: nabench-method-rnaernie

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