Feng sQTL discrimination long-window scored population; Feng et al. 2025.
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5 evaluations · 10 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaGenome, output tracks* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.715 sQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome, output tracks* sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.787 sQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome, output tracks* sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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 (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.57 sQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph, long sequence sQTL discrimination evaluation Table 6, sQTL 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, sQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). |
| Configuration: Caduceus-Ph, long sequence (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.246 sQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph, long sequence sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.666 sQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, hidden states* sQTL discrimination evaluation Table 6, sQTL 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, sQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). |
| Configuration: Enformer, hidden states* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.612 sQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, hidden states* sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.617 sQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, output tracks* sQTL discrimination evaluation Table 6, sQTL 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, sQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). |
| Configuration: Enformer, output tracks* (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.413 sQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer, output tracks* sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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 (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.526 sQTL AUC AUC · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-450K, long sequence sQTL discrimination evaluation Table 6, sQTL 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, sQTL column (deterministic XML extraction; rowspans resolved per data/omics/amp-coverage-20261007/feng/review-notes.md). |
| Configuration: HyenaDNA-450K, long sequence (sQTL discrimination) | Protocol: Feng sQTL discrimination Dataset: Feng sQTL discrimination long-window dataset | 0.0757 sQTL Cohen’s d Cohen's d · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA-450K, long sequence sQTL discrimination evaluation Table 6, sQTL 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, sQTL 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. |
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
5 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population Borzoi-derived GTEx v8 whole-blood putative causal variants paired with matched noncausal variants by distance to functional site/gene expression. sQTL pre-window-filter positive count: 540 (not an established per-model scored denominator; post-filter counts are unreported, recorded as null, not zero; this is a different population from the Table 5 pathogenic/common SNP short/long counts, never copied here). Long generated/chromosome-boundary-filtered window: 196,608 bp. A model's actual_input_bp may crop a smaller region from this generated window (e.g. AlphaGenome and long-sequence Caduceus-Ph each crop the central 131,072 bp); exact realised per-model scored counts after that crop are unextracted, not asserted as zero. 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| description Feng sQTL discrimination long-window scored population; Feng et al. 2025. 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name Feng sQTL discrimination long-window dataset 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 Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: amp-feng-20261007-dataset-qtl-sqtl-long