Pangolin (paper Table 4): Zero-shot GTEx splicing-outlier prediction
Evaluate the sequence-derived scores directly on the held-out variants.
Evaluation procedure
Evaluate the sequence-derived scores directly on the held-out variants.
- Model
- Pangolin (paper Table 4)
- Benchmark
- Zero-shot GTEx splicing-outlier prediction (AlphaGenome paper)
- Dataset
- Zero-shot GTEx splicing-outlier prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- Pangolin (paper Table 4)
- protocol id
- alphagenome-2026-t4-protocol-5
- 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
- GTEx RNA-seq reprocessed with FRASER2.0/DROP1.3.3; rare variants near aberrant junctions paired by individual, following AbSplice processing.
- inputs
- Not reported
- adaptation
- Pangolin (paper Table 4)
- metric implementation
- Not reported
- aggregation
- Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution.
- 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 |
|---|---|---|
| Pangolin (paper Table 4): Zero-shot GTEx splicing-outlier prediction Model: Pangolin (paper Table 4) · Benchmark: Zero-shot GTEx splicing-outlier prediction (AlphaGenome paper) · Dataset: Zero-shot GTEx splicing-outlier prediction: evaluated data subset Evaluate the sequence-derived scores directly on the held-out variants. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.139737 auprc Unit: dimensionless · Direction: higher Aggregation: Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L6 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 Pangolin (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 Pangolin (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 Pangolin (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 Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution. 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 Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution. 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 Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution. 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-040f7ade49d57ea3
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Evaluate the sequence-derived scores directly on the held-out variants.
- version
- Pangolin (paper Table 4)
- source evaluation index
- 5
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-5; 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: GTEx RNA-seq reprocessed with FRASER2.0/DROP1.3.3; rare variants near aberrant junctions paired by individual, following AbSplice processing.; inputs: Not reported; adaptation: Pangolin (paper Table 4); metric implementation: Not reported; aggregation: Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution.; budget: Not reported
- context
- allowed inputs: REF/ALT sequence and directly aggregated AlphaGenome splicing/junction scores.; limitations: Rare-variant/junction proximity and outlier calls provide association labels, not proof every nearby variant causes the outlier. Supervised and zero-shot scores use the same test subset but different allowed inputs.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported