Polyadenylation-QTL causality: evaluated data subset
Borzoi tissue-pooled fine-mapped 3-prime QTL dataset, with negative controls matched for cleavage-site distance and expression.
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 |
|---|---|---|
| AlphaGenome distilled all-fold student: Polyadenylation-QTL causality Model: AlphaGenome distilled all-fold student · Benchmark: Polyadenylation-QTL causality (AlphaGenome paper) · Dataset: Polyadenylation-QTL causality: evaluated data subset Summarize predicted RNA coverage near PASs, derive the largest allelic change in proximal-versus-distal usage, average tracks and classify positive versus matched negative variants. Unscored variants receive zero as specified by the paper. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.63 PAS_10000_average_auprc Unit: dimensionless · Direction: higher Aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M9 Source checking is not independent reproduction. |
| borzoi-ensemble (paper Table 4): Polyadenylation-QTL causality Model: borzoi-ensemble (paper Table 4) · Benchmark: Polyadenylation-QTL causality (AlphaGenome paper) · Dataset: Polyadenylation-QTL causality: evaluated data subset Summarize predicted RNA coverage near PASs, derive the largest allelic change in proximal-versus-distal usage, average tracks and classify positive versus matched negative variants. Unscored variants receive zero as specified by the paper. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.620662 PAS_10000_average_auprc Unit: dimensionless · Direction: higher Aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L9 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 [{"positive":613,"negative":1950,"scope":"test-chromosome paQTL pool; negative candidates before matching permutation","source_locator":"Supplementary Methods p.36, Polyadenylation variants"}] 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 [{"positive":613,"negative":1950,"scope":"test-chromosome paQTL pool; negative candidates before matching permutation","source_locator":"Supplementary Methods p.36, Polyadenylation variants"}] 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 [{"positive":613,"negative":1950,"scope":"test-chromosome paQTL pool; negative candidates before matching permutation","source_locator":"Supplementary Methods p.36, Polyadenylation variants"}] 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 GTEx / 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-8
- areas
- dna-genomes
- entity level
- evaluation_subset
- source dataset label
- GTEx / 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
- positive: 613; negative: 1950; scope: test-chromosome paQTL pool; negative candidates before matching permutation; source locator: Supplementary Methods p.36, Polyadenylation variants
- missing metadata
- split manifest: unextracted; per score denominator: unextracted