Protocol

Feng GTEx whole-blood expression prediction, all genes, 6 kb input

Table 4 gene-expression prediction on all 21,004 genes with ~6 kb input; Feng et al. 2025 source-reported protocol.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

5 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

5 evaluations · 10 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)
GROVER (GTEx whole-blood expression prediction)Evaluation	0.233 (best in column)	0.114
Caduceus-Ph (GTEx whole-blood expression prediction)Evaluation	0.234	0.123 (best in column)
HyenaDNA (GTEx whole-blood expression prediction)Evaluation	0.235	0.122
DNABERT-2 (GTEx whole-blood expression prediction)Evaluation	0.236	0.121
NT-v2 (GTEx whole-blood expression prediction)Evaluation	0.236	0.122

All 10 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ph (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	0.234 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 Caduceus-Ph 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 'Caduceus-Ph', column 'Average Prediction MSE'
Configuration: Caduceus-Ph (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	0.123 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 Caduceus-Ph 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 'Caduceus-Ph', column 'Average Prediction Correlation'
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'
Configuration: GROVER (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	0.233 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 GROVER 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 'GROVER', column 'Average Prediction MSE'
Configuration: GROVER (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	0.114 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 GROVER 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 'GROVER', column 'Average Prediction Correlation'
Configuration: HyenaDNA (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	0.235 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 HyenaDNA 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 'HyenaDNA', column 'Average Prediction MSE'
Configuration: HyenaDNA (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	0.122 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 HyenaDNA 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 'HyenaDNA', column 'Average Prediction Correlation'
Configuration: NT-v2 (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 NT-v2 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 'NT-v2', column 'Average Prediction MSE'
Configuration: NT-v2 (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	0.122 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 NT-v2 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 'NT-v2', column 'Average Prediction Correlation'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations: 5

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-11-02-a7f03c9e55a5. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

4 source records and release history

Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1
Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information · Original source · Nature Communications 16, 10780 (2025); Supplementary Information PDF (MOESM1, 11 pages)
ChongWuLab/dna_foundation_benchmark README.md · Original source · 3f4c81ce066f3c47422a83466b085aac1a6be902
ChongWuLab/dna_foundation_benchmark job_scripts/gtex_hyena.py · Original source · 3f4c81ce066f3c47422a83466b085aac1a6be902

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: feng-dna-fm-20261013-protocol-gtex-wb-expression-6kb

areas: dna-genomes
contexts: research
scope note: Per-gene regression of covariate-corrected GTEx v8 whole-blood expression (residuals after regressing sex, PEER factors and genotype principal components) on frozen zero-shot embeddings of each subject's phased sequence around the transcription start site. One random forest regressor per gene; subjects split 75:25 into training and test; fivefold cross-validation on MSE for hyperparameter tuning. Pearson correlation and MSE between predicted and observed expression are computed per gene and averaged across genes. Random forest was chosen over XGBoost because it was better for every model (Supplementary Table 3). Supervised on expression labels; not label-free prediction.
task: Subject-level gene expression prediction from personal sequence (average per-gene Pearson correlation and MSE)
version: Table 4, rows without asterisk
access note: Individual-level GTEx v8 whole-genome sequences and expression are protected human-participant data: per the Data availability statement, raw individual WGS must be requested through the GTEx Protected Data Access portal, and the processed expression benchmark is not deposited with the other processed datasets on Hugging Face. Only aggregated GTEx releases are public.
reproducibility note: Reproduction requires approved GTEx protected access, the per-model GPU environments described in the author README (pinned at 3f4c81ce066f3c47422a83466b085aac1a6be902), and scheduler-style job scripts that take a job index and placeholder dataset and checkpoint paths. The pinned job_scripts/gtex_hyena.py reads 'long_seqs_by_gene', centre-crops to 6000 bp and writes to an output folder named 'cadph_long'; which script settings produced each Table 4 row cannot be confirmed from the repository. Not attempted by Rewire.
comparison limit: Not comparable with the long-input rows: those cover a 768-gene subset (Table 4 footnote).
hyperparameters: Random forest grid: n_estimators 100, 200, 500; max_depth None, 5, 10 (printed as Supplementary Table 5; the main text cites it as Supplementary Table 6).

Related records

subject: reported_finding: feng-dna-fm-20261013-protocol-gtex-wb-expression-6kb
assessment: Caduceus-Ph GTEx whole-blood expression evaluation
assessment: DNABERT-2 GTEx whole-blood expression evaluation
assessment: GROVER GTEx whole-blood expression evaluation
assessment: HyenaDNA GTEx whole-blood expression evaluation
assessment: NT-v2 GTEx whole-blood expression evaluation
assessed by: Select regulatory variants and genes for functional follow-up

Suggest a correction