NT-v2 paQTL discrimination evaluation (short window); Feng et al. 2025.
These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.
Release 2026-10-07-1448159e6a81 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 checkedMethods, coverage and sourceNT-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 checkedMethods, coverage and sourceNT-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. |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
Table 6, paQTL column, frozen embeddings + random forest classifier
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Frozen pretrained representation plus a supervised random-forest classifier head fitted for this exact QTL task Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.aggregation Mean of AUC/Cohen's d across the three outer chromosome test folds Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.budget Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.dataset_version Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.inputs Alternate-minus-reference embedding representation around each paQTL variant (short window) Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.metric_implementation Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.population Borzoi-derived GTEx v8 whole-blood putative causal variants paired with matched noncausal variants by distance to functional site/gene expression. paQTL pre-window-filter positives: 142. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.protocol_id amp-feng-20261007-protocol-qtl-paqtl Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.split 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. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.origin independent_paper Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
View linked audit checks and correction history
Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: amp-feng-20261007-eval-qtl-paqtl-nt-v2