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Dataset subset

NABench deep mutational scanning assays (NABench split)

The split of NABench deep mutational scanning assays that NABench evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.

Subset and evaluation context

This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.

Evaluation results

Release 2026-09-17-134cd1815de8 · 175 evaluations · 175 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
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.

Author-reported evaluation · Evaluation metadata: source checked

0.207 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(AIDO.RNA), column(Contiguous cross validation Spearman ρ)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.201 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(AIDO.RNA), column(Few-shot Spearman ρ)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.486 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(AIDO.RNA), column(Random cross validation Spearman ρ)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.472 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(AIDO.RNA), column(Zero-shot AUC)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.098 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(AIDO.RNA), column(Zero-shot Spearman ρ)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.049 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(AIDO.RNA), column(Zero-shot MCC)

Source checking is not independent reproduction.

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.

Author-reported evaluation · Evaluation metadata: source checked

0.324 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(AIDO.RNA), column(Zero-shot NDCG)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.167 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(BiRNA-BERT), column(Contiguous cross validation Spearman ρ)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.186 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(BiRNA-BERT), column(Few-shot Spearman ρ)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.493 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(BiRNA-BERT), column(Random cross validation Spearman ρ)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.518 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(BiRNA-BERT), column(Zero-shot AUC)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.093 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(BiRNA-BERT), column(Zero-shot Spearman ρ)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.042 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(BiRNA-BERT), column(Zero-shot MCC)

Source checking is not independent reproduction.

BiRNA-BERT 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

0.369 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(BiRNA-BERT), column(Zero-shot NDCG)

Source checking is not independent reproduction.

Crafts 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

0.174 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(Crafts), column(Contiguous cross validation Spearman ρ)

Source checking is not independent reproduction.

Crafts 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

0.141 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(Crafts), column(Few-shot Spearman ρ)

Source checking is not independent reproduction.

Crafts 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

0.525 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(Crafts), column(Random cross validation Spearman ρ)

Source checking is not independent reproduction.

Crafts 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

0.488 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(Crafts), column(Zero-shot AUC)

Source checking is not independent reproduction.

Crafts 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

0.128 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(Crafts), column(Zero-shot Spearman ρ)

Source checking is not independent reproduction.

Crafts 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

0.057 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(Crafts), column(Zero-shot MCC)

Source checking is not independent reproduction.

Crafts 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

0.322 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(Crafts), column(Zero-shot NDCG)

Source checking is not independent reproduction.

Dnabert_6 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

0.163 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(Dnabert_6), column(Contiguous cross validation Spearman ρ)

Source checking is not independent reproduction.

Dnabert_6 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

0.111 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(Dnabert_6), column(Few-shot Spearman ρ)

Source checking is not independent reproduction.

Dnabert_6 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

0.322 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(Dnabert_6), column(Random cross validation Spearman ρ)

Source checking is not independent reproduction.

Dnabert_6 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

0.482 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(Dnabert_6), column(Zero-shot AUC)

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.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-134cd1815de8
Property and statementOriginal source and locationReview and provenance
description

The split of NABench deep mutational scanning assays that NABench evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.

Context-only references
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction

Original source ↗

No field-specific location recorded

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.183421+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: fefd48d53b1a7eadf9e14db96adacc8e646304c1b592562d9f136f4508941350

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

name

NABench deep mutational scanning assays (NABench split)

Context-only references
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction

Original source ↗

No field-specific location recorded

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.183421+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: fefd48d53b1a7eadf9e14db96adacc8e646304c1b592562d9f136f4508941350

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

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-dataset-nabench-deep-mutational-scanning-assays

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rna-transcriptomes
missing metadata
version: unreported; url: unextracted
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