AlphaGenome distilled all-fold student: Coronary smooth-muscle caQTL effect-size prediction
Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.
Evaluation procedure
Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.
- Model
- AlphaGenome distilled all-fold student
- Benchmark
- Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper)
- Dataset
- Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- AlphaGenome distilled all-fold student
- protocol id
- alphagenome-2026-t4-protocol-24
- dataset version
- Not reported
- split
- Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.
- population
- Coronary smooth-muscle caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity.
- inputs
- Not reported
- adaptation
- AlphaGenome distilled all-fold student
- metric implementation
- Not reported
- aggregation
- Pearson correlation against reported effect sizes of the causal/significant QTL set.
- budget
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-a757f4af4277 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AlphaGenome distilled all-fold student: Coronary smooth-muscle caQTL effect-size prediction Model: AlphaGenome distilled all-fold student · Benchmark: Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper) · Dataset: Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.69 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M33; 'Suppl Table 4 Variant performan'!M34 Source checking is not independent reproduction. |
Evidence table
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.
63 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation AlphaGenome distilled all-fold student Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.adaptation AlphaGenome distilled all-fold student Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.adaptation AlphaGenome distilled all-fold student Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.aggregation Pearson correlation against reported effect sizes of the causal/significant QTL set. Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.aggregation Pearson correlation against reported effect sizes of the causal/significant QTL set. Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.aggregation Pearson correlation against reported effect sizes of the causal/significant QTL set. Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.budget No value recorded Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.budget No value recorded Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.budget No value recorded Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.dataset_version No value recorded Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-a757f4af4277 · Record review: needs review
- AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
- AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
- alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Technical metadata and extraction receipts
Stable ID: alphagenome-2026-evaluation-09990d4d1a6a0155
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.
- version
- AlphaGenome distilled all-fold student
- source evaluation index
- 24
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-24; dataset version: Not reported; split: Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.; population: Coronary smooth-muscle caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity.; inputs: Not reported; adaptation: AlphaGenome distilled all-fold student; metric implementation: Not reported; aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.; budget: Not reported
- context
- allowed inputs: REF/ALT sequence and local predicted assay-signal changes. Track selection performed on validation data: AlphaGenome left-cardiac-atrium ATAC; Borzoi vascular-smooth-muscle ATAC.; limitations: Proxy tracks differ across models and are part of the evaluation configuration. ChromBPNet is specialized by cell type; AlphaGenome/Borzoi are evaluated without task-label training. The inspected paper delegates detailed QTL preprocessing to ChromBPNet and does not enumerate final row-level sample counts.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: AlphaGenome distilled all-fold student
- benchmark: Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper)
- dataset: Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset
- evaluation: AlphaGenome distilled all-fold student: Coronary smooth-muscle caQTL effect-size prediction, pearsonr