Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Supervised GTEx splicing-outlier prediction (AlphaGenome paper)
Can rare variants associated with abnormal splicing be distinguished from other rare variants?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7At a glance
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Dataset and biological context | GTEx RNA-seq reprocessed with FRASER2.0/DROP1.3.3; rare variants near aberrant junctions paired by individual, following AbSplice processing.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| 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.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| Allowed inputs and adaptation | AlphaGenome splicing/RNA variant-score features plus a tissue-specific splice-site expression indicator; AbSplice is retrained on the same split.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| Metrics as reported | auprcAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| Aggregation | Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 |
| Entity type | protocol |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
How it works
Conceptual summary of the cited procedure; model-specific conditions are given below.
Read the diagram as text
- Pair rare variants with outlier labels
- Apply chromosome partition
- Fit score-feature classifier
- Evaluate pooled tissue-assigned auPRC
What is tested
Can rare variants associated with abnormal splicing be distinguished from other rare variants?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7Procedure
Fit an Explainable Boosting Classifier on the training/validation data and evaluate the held-out variants.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7Tested models and 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 |
|---|---|---|
| AbSplice: retrained AbSplice (paper Table 4): Supervised GTEx splicing-outlier prediction Model: AbSplice: retrained AbSplice (paper Table 4) · 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 | ||
| 0.251 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'!L7 Source checking is not independent reproduction. |
| 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. |
Strengths and limitations
Limitations and conditions
- 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.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7
- This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-t4-protocol-6Evidence 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.
42 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram steps ["Pair rare variants with outlier labels","Apply chromosome partition","Fit score-feature classifier","Evaluate pooled tissue-assigned auPRC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Pair rare variants with outlier labels","Apply chromosome partition","Fit score-feature classifier","Evaluate pooled tissue-assigned auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram steps ["Pair rare variants with outlier labels","Apply chromosome partition","Fit score-feature classifier","Evaluate pooled tissue-assigned auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram title Supervised GTEx splicing-outlier prediction: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title Supervised GTEx splicing-outlier prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram title Supervised GTEx splicing-outlier prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Dataset and biological context GTEx RNA-seq reprocessed with FRASER2.0/DROP1.3.3; rare variants near aberrant junctions paired by individual, following AbSplice processing. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A7:P7; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.31, Splicing Outliers from GTEx; methods: p.31, Splicing Outliers from GTEx; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 6; sheet rows 7 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: 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-protocol-6
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 6
- source table
- 4
- reference levels
- metric: auprc; printed value: 0.0054; numeric value: 5.4000000000000003E-3; source locator: Suppl Table 4 Variant performan!J7; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
Related records
- benchmark: AbSplice: retrained AbSplice (paper Table 4): Supervised GTEx splicing-outlier prediction
- benchmark: AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier: Supervised GTEx splicing-outlier prediction
- benchmark: Supervised GTEx splicing-outlier prediction: evaluated data subset