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DNABERT-2 (GTEx whole-blood expression prediction)

DNABERT-2 (GTEx whole-blood expression prediction): Frozen zero-shot embeddings computed per phased allele and the two averaged; Supervised random forest regressor fitted per gene.

1 evaluation · 2 results

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1 evaluation · 2 results. Different protocols are not a single leaderboard.

Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input · Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb

Sorted by MSE (mean across genes of per-gene MSE of covariate-corrected expression) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	MSE (mean across genes of per-gene MSE of covariate-corrected expression)	Pearson (mean across genes of per-gene Pearson correlation between predicted and observed expression)
DNABERT-2 (GTEx whole-blood expression prediction)Evaluation	0.236	0.121

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNABERT-2 (GTEx whole-blood expression prediction)	Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb	0.236 MSE (mean across genes of per-gene MSE of covariate-corrected expression) unit-unreported · lower Uncertainty: Not reported by the source: Table 4 prints averages only; per-gene spread is shown only as a histogram (Fig. 3). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 GTEx whole-blood expression evaluation Table 4, frozen embeddings + per-gene random forest regression Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 4, row 'DNABERT-2', column 'Average Prediction MSE'
Configuration: DNABERT-2 (GTEx whole-blood expression prediction)	Protocol: Feng GTEx whole-blood expression prediction, all genes, 6 kb input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 3 kb	0.121 Pearson (mean across genes of per-gene Pearson correlation between predicted and observed expression) unitless · higher Uncertainty: Not reported by the source: Table 4 prints averages only; per-gene spread is shown only as a histogram (Fig. 3). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 GTEx whole-blood expression evaluation Table 4, frozen embeddings + per-gene random forest regression Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 4, row 'DNABERT-2', column 'Average Prediction Correlation'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1

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Technical metadata and extraction receipts

Stable ID: feng-dna-fm-20261013-config-gtex-dnabert-2

areas: dna-genomes
contexts: research
method types: foundation_model
foundation model eligible: true
head: Supervised random forest regressor fitted per gene
reported name: DNABERT-2
task: GTEx whole-blood gene expression prediction
representation: Frozen zero-shot embeddings computed per phased allele and the two averaged (Methods, Gene expression prediction benchmark). Token pooling for this task is not stated; the pinned HyenaDNA author script mean-pools tokens.
limitations: Input length printed as '6000 bp'.
actual input bp: 6000
checkpoint: DNABERT-2, its only published checkpoint (Methods, 'Model configuration selection' paragraph)
missing metadata: head revision: reason: unextracted; version: reason: unreported; note: Immutable checkpoint revision is not stated in the article.
provenance note: DNABERT-2 (GTEx whole-blood expression prediction); Feng et al. 2025 source-reported, task-scoped configuration.

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system: DNABERT-2 GTEx whole-blood expression evaluation

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