borzoi-ensemble (paper Table 4): Polyadenylation-QTL causality
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.
Evaluation procedure
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.
- Model
- borzoi-ensemble (paper Table 4)
- Benchmark
- Polyadenylation-QTL causality (AlphaGenome paper)
- Dataset
- Polyadenylation-QTL causality: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- borzoi-ensemble (paper Table 4)
- protocol id
- alphagenome-2026-t4-protocol-8
- 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
- Borzoi tissue-pooled fine-mapped 3-prime QTL dataset, with negative controls matched for cleavage-site distance and expression.
- inputs
- Not reported
- adaptation
- borzoi-ensemble (paper Table 4)
- metric implementation
- Not reported
- aggregation
- Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000.
- 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 |
|---|---|---|
| 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.
63 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation borzoi-ensemble (paper Table 4) 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 borzoi-ensemble (paper Table 4) 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 borzoi-ensemble (paper Table 4) 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 Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. 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 Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. 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 Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. 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-ae1b488d90c1b10f
- areas
- dna-genomes
- origin
- author_reported
- protocol
- 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.
- version
- borzoi-ensemble (paper Table 4)
- source evaluation index
- 8
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-8; 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: Borzoi tissue-pooled fine-mapped 3-prime QTL dataset, with negative controls matched for cleavage-site distance and expression.; inputs: Not reported; adaptation: borzoi-ensemble (paper Table 4); metric implementation: Not reported; aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000.; budget: Not reported
- context
- allowed inputs: REF/ALT RNA predictions and annotated polyadenylation sites; pooled track score.; limitations: The100 permutations quantify sensitivity to negative matching, not100 independent experiments. Variants beyond the threshold and incomplete PAS context are not equivalent populations. This paQTL variant endpoint is separate from the quarantined Table3 coverage-ratio conflict.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported