Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Zero-shot distance-balanced eQTL causality (AlphaGenome paper)
Can the model distinguish putatively causal expression variants from low-probability variants after balancing distance to the target gene?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13At 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 | Reprocessed GTEx SuSiE eQTL-catalogue SNVs; positives PIP≥0.9, negatives PIP≤0.01, GENCODEv46 genes, controls downsampled within log-distance-to-TSS bins.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| 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.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| Allowed inputs and adaptation | REF/ALT allele predictions and target-gene, tissue-matched RNA-seq log-fold change.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| Metrics as reported | tissue_weighted_mean_aurocAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| Aggregation | auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| 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'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 |
| 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
- Create distance-balanced fine-mapping labels
- Hold out test chromosomes
- Score gene-specific RNA changes
- Aggregate tissue auROC
What is tested
Can the model distinguish putatively causal expression variants from low-probability variants after balancing distance to the target gene?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13Procedure
Evaluate the gene-specific RNA variant score directly on the distance-balanced labels.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13Tested 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 |
|---|---|---|
| borzoi-ensemble (paper Table 4): Zero-shot distance-balanced eQTL causality Model: borzoi-ensemble (paper Table 4) · Benchmark: Zero-shot distance-balanced eQTL causality (AlphaGenome paper) · Dataset: Zero-shot distance-balanced eQTL causality: evaluated data subset Evaluate the gene-specific RNA variant score directly on the distance-balanced labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.702311127873157 tissue_weighted_mean_auroc Unit: dimensionless · Direction: higher Aggregation: auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L13 Source checking is not independent reproduction. |
| AlphaGenome distilled all-fold student: Zero-shot distance-balanced eQTL causality Model: AlphaGenome distilled all-fold student · Benchmark: Zero-shot distance-balanced eQTL causality (AlphaGenome paper) · Dataset: Zero-shot distance-balanced eQTL causality: evaluated data subset Evaluate the gene-specific RNA variant score directly on the distance-balanced labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.71 tissue_weighted_mean_auroc Unit: dimensionless · Direction: higher Aggregation: auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M13 Source checking is not independent reproduction. |
Strengths and limitations
Limitations and conditions
- Fine-mapping labels represent putative causality. Distance balancing changes the sampled population and does not establish calibration to genome-wide prevalence. Do not equate the supervised feature pipeline with the RNA-only scorer.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13
- 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'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13
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-11Evidence 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'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 ["Create distance-balanced fine-mapping labels","Hold out test chromosomes","Score gene-specific RNA changes","Aggregate tissue auROC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 ["Create distance-balanced fine-mapping labels","Hold out test chromosomes","Score gene-specific RNA changes","Aggregate tissue auROC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 ["Create distance-balanced fine-mapping labels","Hold out test chromosomes","Score gene-specific RNA changes","Aggregate tissue auROC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 Zero-shot distance-balanced eQTL causality: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 Zero-shot distance-balanced eQTL causality: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 Zero-shot distance-balanced eQTL causality: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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 Reprocessed GTEx SuSiE eQTL-catalogue SNVs; positives PIP≥0.9, negatives PIP≤0.01, GENCODEv46 genes, controls downsampled within log-distance-to-TSS bins. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 11; sheet rows 13 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-11
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 11
- source table
- 4
- reference levels
- metric: tissue_weighted_mean_auroc; printed value: 0.5; numeric value: 0.5; source locator: Suppl Table 4 Variant performan!J13; note: Source reference quantity for relative-performance calculation, not a measured baseline run.