AlphaGenome, output tracks* (paQTL discrimination)
AlphaGenome, output tracks* (paQTL 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).
Overview
AlphaGenome, output tracks* (paQTL 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).
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
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* (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 checkedMethods, coverage and sourceAlphaGenome, 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 checkedMethods, coverage and sourceAlphaGenome, 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. |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
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Stable ID: amp-feng-20261007-config-qtl-paqtl-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
- paQTL discrimination
- version
- Not reported
Related records
- configuration: AlphaGenome, output tracks* paQTL discrimination evaluation