Zero-shot distance-balanced eQTL causality: evaluated data subset
Reprocessed GTEx SuSiE eQTL-catalogue SNVs; positives PIP≥0.9, negatives PIP≤0.01, GENCODEv46 genes, controls downsampled within log-distance-to-TSS bins.
Evaluation results
Release 2026-09-17-a757f4af4277 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| borzoi-ensemble (paper Table 4): Zero-shot distance-balanced eQTL causality Model: borzoi-ensemble (paper Table 4) · Benchmark: Zero-shot distance-balanced eQTL causality (AlphaGenome paper) · Dataset: Zero-shot distance-balanced eQTL causality: evaluated data subset Evaluate the gene-specific RNA variant score directly on the distance-balanced labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.702311127873157 tissue_weighted_mean_auroc Unit: dimensionless · Direction: higher Aggregation: auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L13 Source checking is not independent reproduction. |
| AlphaGenome distilled all-fold student: Zero-shot distance-balanced eQTL causality Model: AlphaGenome distilled all-fold student · Benchmark: Zero-shot distance-balanced eQTL causality (AlphaGenome paper) · Dataset: Zero-shot distance-balanced eQTL causality: evaluated data subset Evaluate the gene-specific RNA variant score directly on the distance-balanced labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.71 tissue_weighted_mean_auroc Unit: dimensionless · Direction: higher Aggregation: auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M13 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.
24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.entity_level evaluation_subset 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.entity_level evaluation_subset 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.entity_level evaluation_subset 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.reported_dataset_counts [{"total":21948,"positive":10974,"negative":10974,"positive_negative_derivation":"The source reports exactly 50% class balance; the per-class counts are derived as 21,948 / 2.","count_unit":"variant/gene/tissue tuples","scope":"reported balanced test set","source_locator":"Supplementary Methods p.33, Zero-Shot eQTL Causality"}] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.reported_dataset_counts [{"total":21948,"positive":10974,"negative":10974,"positive_negative_derivation":"The source reports exactly 50% class balance; the per-class counts are derived as 21,948 / 2.","count_unit":"variant/gene/tissue tuples","scope":"reported balanced test set","source_locator":"Supplementary Methods p.33, Zero-Shot eQTL Causality"}] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.reported_dataset_counts [{"total":21948,"positive":10974,"negative":10974,"positive_negative_derivation":"The source reports exactly 50% class balance; the per-class counts are derived as 21,948 / 2.","count_unit":"variant/gene/tissue tuples","scope":"reported balanced test set","source_locator":"Supplementary Methods p.33, Zero-Shot eQTL Causality"}] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.source_dataset_label EMS1 eQTLs & Borzoi paper 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 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-t4-dataset-11
- areas
- dna-genomes
- entity level
- evaluation_subset
- source dataset label
- EMS1 eQTLs & Borzoi paper
- source subset scope
- 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.
- exact manifest
- Not reported
- reported dataset counts
- total: 21948; positive: 10974; negative: 10974; positive negative derivation: The source reports exactly 50% class balance; the per-class counts are derived as 21,948 / 2.; count unit: variant/gene/tissue tuples; scope: reported balanced test set; source locator: Supplementary Methods p.33, Zero-Shot eQTL Causality
- missing metadata
- split manifest: unextracted; per score denominator: unextracted