Protocol

Feng paQTL discrimination

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

Overview

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

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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.

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Results

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All evaluations

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

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaGenome, output tracks* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.754 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: AlphaGenome, output tracks* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.982 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.508 paQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Caduceus-Ph (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.0456 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.465 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Caduceus-Ph, long sequence (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	−0.1151 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.507 paQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: DNABERT-2 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.024 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.674 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Enformer, hidden states* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.603 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.666 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Enformer, output tracks* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.546 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.449 paQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GROVER paQTL discrimination evaluation Table 6, paQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, GROVER row, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: GROVER (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	−0.1393 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.552 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: HyenaDNA-450K, long sequence (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination long-window dataset	0.207 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.47 paQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA paQTL discrimination evaluation Table 6, paQTL column, frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 6, AUC block, HyenaDNA row, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: HyenaDNA (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	−0.0768 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.525 paQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT-v2 paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: NT-v2 (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.0658 paQTL 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 paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.619 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Sei, hidden states* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.454 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.655 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md).
Configuration: Sei, output tracks* (paQTL discrimination)	Protocol: Feng paQTL discrimination Dataset: Feng paQTL discrimination short-window dataset	0.55 paQTL 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* paQTL discrimination evaluation Table 6, paQTL 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, paQTL 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.

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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: amp-feng-20261007-protocol-qtl-paqtl

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 paQTL: 142 (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: paQTL causal-vs-noncausal variant discrimination (AUC, Cohen's d)
version: Table 6

Related records

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

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