AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier: Supervised GTEx splicing-outlier prediction
Fit an Explainable Boosting Classifier on the training/validation data and evaluate the held-out variants.
Evaluation procedure
Fit an Explainable Boosting Classifier on the training/validation data and evaluate the held-out variants.
- Model
- AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- Benchmark
- Supervised GTEx splicing-outlier prediction (AlphaGenome paper)
- Dataset
- Supervised GTEx splicing-outlier prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- protocol id
- alphagenome-2026-t4-protocol-6
- dataset version
- Not reported
- split
- Supervised training chromosomes are 1,4,7,8,10,13,15; validation chromosomes 2,5,11,14,17,20,22,X; test chromosomes 3,6,9,12,16,18,19,21. This is downstream evaluation separation, not a held-out reference-genome claim for the distilled backbone.
- 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
- AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- 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 |
|---|---|---|
| AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier: Supervised GTEx splicing-outlier prediction Model: AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier · Benchmark: Supervised GTEx splicing-outlier prediction (AlphaGenome paper) · Dataset: Supervised GTEx splicing-outlier prediction: evaluated data subset Fit an Explainable Boosting Classifier on the training/validation data and evaluate the held-out variants. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.28 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'!M7 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 variant scores plus expressed-splice-site feature → Explainable Boosting Classifier 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 variant scores plus expressed-splice-site feature → Explainable Boosting Classifier 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 variant scores plus expressed-splice-site feature → Explainable Boosting Classifier 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-fbfed6fa50e72dce
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Fit an Explainable Boosting Classifier on the training/validation data and evaluate the held-out variants.
- version
- AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- source evaluation index
- 6
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-6; dataset version: Not reported; split: Supervised training chromosomes are 1,4,7,8,10,13,15; validation chromosomes 2,5,11,14,17,20,22,X; test chromosomes 3,6,9,12,16,18,19,21. This is downstream evaluation separation, not a held-out reference-genome claim for the distilled backbone.; 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: AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier; 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: AlphaGenome splicing/RNA variant-score features plus a tissue-specific splice-site expression indicator; AbSplice is retrained on the same split.; 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
Related records
- model: AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- benchmark: Supervised GTEx splicing-outlier prediction (AlphaGenome paper)
- dataset: Supervised GTEx splicing-outlier prediction: evaluated data subset
- evaluation: AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier: Supervised GTEx splicing-outlier prediction, auprc