Configuration

AlphaGenome, output tracks* (sQTL discrimination)

AlphaGenome, output tracks* (sQTL discrimination); Feng et al. 2025 source-reported, task-scoped configuration. Printed in the source with an asterisk as a non-DNA-foundation specialised genomic comparator, not one of the paper's own DNA foundation models. Actual DNA input consumed by the model: 131072 bp (a crop of the dataset's generated window where smaller). Output tracks averaged over the central 2048 bp of the model's OUTPUT (not a smaller DNA input crop).

1 evaluation · 2 results

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1 evaluation · 2 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 checked Methods, coverage and source AlphaGenome, 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 checked Methods, coverage and source AlphaGenome, 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.

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

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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-config-qtl-sqtl-alphagenome-output-tracks

method types: conventional_pipeline
actual input bp: 131072
foundation model eligible: false
head: Supervised random forest fitted separately for this task
head revision: Not reported
missing metadata: version: Printed model name and input representation only; immutable checkpoint/head revision is unreported in the inspected primary text.
output aggregation bp: 2048
reported name: AlphaGenome, output tracks*
representation: Alternate-minus-reference frozen representation
task: sQTL discrimination
version: Not reported

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configuration: AlphaGenome, output tracks* sQTL discrimination evaluation

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