Protocol

Feng eQTL discrimination

Table 6 eQTL causal-versus-noncausal variant discrimination; Feng et al. 2025 source-reported protocol.

Overview

Table 6 eQTL causal-versus-noncausal variant discrimination; Feng et al. 2025 source-reported protocol.

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

12 recorded evaluations, 24 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

12 evaluations · 24 results. Different protocols are not a single leaderboard.

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: AlphaGenome, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.803 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, AlphaGenome, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Source Results prose (Sec8) states AlphaGenome's QTL AUC as approximately 0.80, which differs from this exact Table 6 AUC cell (eQTL 0.8029, sQTL 0.7147); the table value is retained and the prose discrepancy is not silently resolved or transposed onto Cohen's d.
Configuration: AlphaGenome, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	1.29 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, AlphaGenome, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Caduceus-Ph (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.649 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Caduceus-Ph row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Caduceus-Ph (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.548 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Caduceus-Ph row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Caduceus-Ph, long sequence (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.626 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph, long sequence eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Caduceus-Ph, long sequence row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Caduceus-Ph, long sequence (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.491 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph, long sequence eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Caduceus-Ph, long sequence row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: DNABERT-2 (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.57 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, DNABERT-2 row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: DNABERT-2 (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.237 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, DNABERT-2 row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Enformer, hidden states* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.774 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer, hidden states* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Enformer, hidden states* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Enformer, hidden states* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	1.11 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer, hidden states* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Enformer, hidden states* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Enformer, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.77 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Enformer, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Enformer, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	1.11 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Enformer, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Enformer, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: GROVER (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.59 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GROVER eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, GROVER row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: GROVER (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.319 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GROVER eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, GROVER row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: HyenaDNA-450K, long sequence (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.603 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA-450K, long sequence eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, HyenaDNA-450K, long sequence row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: HyenaDNA-450K, long sequence (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination long-window dataset	0.36 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA-450K, long sequence eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, HyenaDNA-450K, long sequence row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: HyenaDNA (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.612 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, HyenaDNA row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: HyenaDNA (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.388 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, HyenaDNA row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: NT-v2 (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.609 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT-v2 eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, NT-v2 row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: NT-v2 (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.396 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT-v2 eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, NT-v2 row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Sei, hidden states* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.756 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Sei, hidden states* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Sei, hidden states* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Sei, hidden states* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	1.03 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Sei, hidden states* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Sei, hidden states* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.
Configuration: Sei, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	0.75 eQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Sei, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, Sei, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Sei, output tracks* (eQTL discrimination)	Protocol: Feng eQTL discrimination Dataset: Feng eQTL discrimination short-window dataset	1.01 eQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Sei, output tracks* eQTL discrimination evaluation Table 6, eQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, Cohen’s d block, Sei, output tracks* row, eQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). Signed effect size; no universal desirable sign/direction is stated by the source.

Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.

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: 12

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 · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-10-07-1448159e6a81. 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.

Strengths, limitations and unresolved questions

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 2026-10-07-1448159e6a81
Property and statement	Original source and location	Review and provenance

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

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-10-07-1448159e6a81 · Record review: source checked

1 source records and release history

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

Download this release

Technical metadata and extraction receipts

Stable ID: amp-feng-20261007-protocol-qtl-eqtl

areas: dna-genomes
missing metadata: None recorded
scope note: Alternate-minus-reference embedding representations scored by a supervised random forest classifier. Three disjoint outer chromosome test groups (3/6/9/12/16/18/19/21; 2/5/11/14/17/20/22/X; 1/4/7/8/10/13/15), each held out in turn with fourfold inner-chromosome cross-validation for hyperparameter tuning. Borzoi-derived GTEx v8 whole-blood putative causal variants paired with matched noncausal variants by distance to functional site/gene expression. Pre-window-filter positive count for eQTL: 1896 (not an established per-model scored denominator; post-filter counts are unreported and recorded as null, not zero). Short and long generated-window datasets are separate scored populations, never pooled. AlphaGenome uses the long dataset with a central input crop and separate output averaging.
task: eQTL causal-vs-noncausal variant discrimination (AUC, Cohen's d)
version: Table 6

Related records

protocol: AlphaGenome, output tracks* eQTL discrimination evaluation
protocol: Caduceus-Ph eQTL discrimination evaluation
protocol: Caduceus-Ph, long sequence eQTL discrimination evaluation
protocol: DNABERT-2 eQTL discrimination evaluation
protocol: Enformer, hidden states* eQTL discrimination evaluation
protocol: Enformer, output tracks* eQTL discrimination evaluation
protocol: GROVER eQTL discrimination evaluation
protocol: HyenaDNA eQTL discrimination evaluation
protocol: HyenaDNA-450K, long sequence eQTL discrimination evaluation
protocol: NT-v2 eQTL discrimination evaluation
protocol: Sei, hidden states* eQTL discrimination evaluation
protocol: Sei, output tracks* eQTL discrimination evaluation

Suggest a correction