Configuration

Enformer (GTEx whole-blood expression prediction)

Enformer (GTEx whole-blood expression prediction): Enformer final hidden state, mean-pooled over all regions, computed per phased allele and the two allele embeddings 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, 768 genes, long input · Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes

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)
Enformer (GTEx whole-blood expression prediction)Evaluation	0.227	0.129

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Enformer (GTEx whole-blood expression prediction)	Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes	0.227 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 Enformer 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 'Enformer*', column 'Average Prediction MSE'
Configuration: Enformer (GTEx whole-blood expression prediction)	Protocol: Feng GTEx whole-blood expression prediction, 768 genes, long input Dataset: Feng GTEx v8 whole-blood expression, TSS +/- 98 kb, 768 genes	0.129 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 Enformer 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 'Enformer*', 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-enformer

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
foundation model eligible: false
head: Supervised random forest regressor fitted per gene
reported name: Enformer*
task: GTEx whole-blood gene expression prediction
representation: Enformer final hidden state, mean-pooled over all regions, computed per phased allele and the two allele embeddings averaged (Methods, Gene expression prediction benchmark).
limitations: Input length printed as '196K bp'.; Printed with an asterisk; Enformer is a supervised sequence-to-expression model used as a comparator, not one of the paper's DNA foundation models. Official PyTorch implementation (Methods).
missing metadata: actual input bp: reason: unreported; note: Printed as '196K bp'; the exact base-pair count is not printed in Table 4.; head revision: reason: unextracted; version: reason: unreported; note: Immutable checkpoint revision is not stated in the article.
provenance note: Enformer* (GTEx whole-blood expression prediction); Feng et al. 2025 source-reported, task-scoped configuration.

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system: Enformer GTEx whole-blood expression evaluation

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