Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
European-ancestry LCL caQTL classification (AlphaGenome paper)
Can local sequence changes predict which variants affect the measured molecular trait?
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22At a glance
Inputs, training, access and other details
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 | European-ancestry LCL caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| 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.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| Allowed inputs and adaptation | REF/ALT sequence and local predicted assay-signal changes. AlphaGenome DNase GM12878; Borzoi averages its two DNase GM12878 tracks.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| Metrics as reported | auPRCSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| Aggregation | auPRC over causal/noncausal labels.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 |
| 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
How it worksEuropean-ancestry LCL caQTL classification: evaluation procedure
Conceptual summary of the cited procedure; model-specific conditions are given below.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22What is tested
Can local sequence changes predict which variants affect the measured molecular trait?
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22Procedure
Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22Recorded evaluations
Each evaluation records what was tested and under which conditions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
European-ancestry LCL caQTL classification (AlphaGenome paper)
auPRC (dimensionless) · Higher values are better for this metric.
Can local sequence changes predict which variants affect the measured molecular trait?
Evaluation protocol · European-ancestry LCL caQTL classification: evaluated data subset
- chrombpnet (paper Table 4) · Configuration · Author-reported evaluation0.27872
- AlphaGenome distilled all-fold student · Configuration · Author-reported evaluation0.36
- borzoi-ensemble (paper Table 4) · Configuration · Author-reported evaluation0.311657
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L22; 'Suppl Table 4 Variant performan'!M21; 'Suppl Table 4 Variant performan'!M22; 'Suppl Table 4 Variant performan'!L21Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| chrombpnet (paper Table 4) · Configuration | 0.27872 dimensionless | Not reported | Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L22 |
| AlphaGenome distilled all-fold student · Configuration | 0.36 dimensionless | Not reported | Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M21; 'Suppl Table 4 Variant performan'!M22 |
| borzoi-ensemble (paper Table 4) · Configuration | 0.311657 dimensionless | Not reported | Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L21 |
Scope and limitations
- This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.
- Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.
- Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 3 evaluations · 3 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| chrombpnet (paper Table 4): European-ancestry LCL caQTL classification Configuration: chrombpnet (paper Table 4)Protocol: European-ancestry LCL caQTL classification (AlphaGenome paper)Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.27872 auPRC Unit: dimensionless · Direction: higher Aggregation: auPRC over causal/noncausal labels. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L22 Source checking is not independent reproduction. |
| AlphaGenome distilled all-fold student: European-ancestry LCL caQTL classification Configuration: AlphaGenome distilled all-fold studentProtocol: European-ancestry LCL caQTL classification (AlphaGenome paper)Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.36 auPRC Unit: dimensionless · Direction: higher Aggregation: auPRC over causal/noncausal labels. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M21; 'Suppl Table 4 Variant performan'!M22 Source checking is not independent reproduction. |
| borzoi-ensemble (paper Table 4): European-ancestry LCL caQTL classification Configuration: borzoi-ensemble (paper Table 4)Protocol: European-ancestry LCL caQTL classification (AlphaGenome paper)Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.311657 auPRC Unit: dimensionless · Direction: higher Aggregation: auPRC over causal/noncausal labels. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L21 Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.
| Paper or primary resource | Version | Reference |
|---|---|---|
| alphagenome: Journal full-text XML | Retrieved page snapshot; no immutable publisher revision supplied | Read source |
| AlphaGenome Nature 2026 supplementary comparison tables | Nature version of record, 28 January 2026 | Read source DOI: 10.1038/s41586-025-10014-0 |
| AlphaGenome Nature 2026 supplementary methods | Supplement to Nature version of record, 28 January 2026; content hash pinned | Read source |
What is still missing
- Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.
- Subsequent studies use different datasets and are not pooled with this paper.
Search and extraction details
complete comparison extracted
Searches
- AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction
- AlphaGenome independent evaluation benchmark 2026 variant effects
Evidence locations
- 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22
Strengths and limitations
Limitations and conditions
- Proxy tracks differ across models and are part of the evaluation configuration. ChromBPNet is specialized by cell type; AlphaGenome/Borzoi are evaluated without task-label training. The inspected paper delegates detailed QTL preprocessing to ChromBPNet and does not enumerate final row-level sample counts.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 - This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22
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-18Evidence table
Inspect claims, sources and review details
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'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 ["Select ancestry/cell-specific QTL test set","Match the reported assay tracks","Score local REF/ALT signal change","Compute classification auPRC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 ["Select ancestry/cell-specific QTL test set","Match the reported assay tracks","Score local REF/ALT signal change","Compute classification auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 ["Select ancestry/cell-specific QTL test set","Match the reported assay tracks","Score local REF/ALT signal change","Compute classification auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 European-ancestry LCL caQTL classification: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 European-ancestry LCL caQTL classification: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 European-ancestry LCL caQTL classification: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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 European-ancestry LCL caQTL data reused from the ChromBPNet evaluation; retain this ancestry/cell-type/trait identity. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22 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-d277315f7d76 · Record review: needs review
3 source records and release history
- 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-18
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 18
- source table
- 4
- reference levels
- metric: auPRC; printed value: 0.082793; numeric value: 8.2793000000000005E-2; source locator: Suppl Table 4 Variant performan!J21; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: auPRC; printed value: 0.082793; numeric value: 8.2793000000000005E-2; source locator: Suppl Table 4 Variant performan!J22; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
- comparison panels
- id: paper-figure-56bba3b3474752c6e2; title: European-ancestry LCL caQTL classification (AlphaGenome paper); protocol id: alphagenome-2026-t4-protocol-18; dataset id: alphagenome-2026-t4-dataset-18; metric: auPRC; unit: dimensionless; direction: higher; result ids: alphagenome-2026-result-35e4b376addbf942; alphagenome-2026-result-7e24ef3d4d0d5f52; alphagenome-2026-result-9c17a0c84b32f939; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 4 Variant performan'!L22; 'Suppl Table 4 Variant performan'!M21; 'Suppl Table 4 Variant performan'!M22; 'Suppl Table 4 Variant performan'!L21; context: Can local sequence changes predict which variants affect the measured molecular trait?; caveats: This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.; Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.; Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_extracted; primary sources: evidence-official-56e5abfb5f12f1cd3b20; source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; inspected locators: 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22; searched queries: AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction; AlphaGenome independent evaluation benchmark 2026 variant effects; gaps: Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.; Subsequent studies use different datasets and are not pooled with this paper.; claim scope: Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 4 Variant performan'!A21:P21; 'Suppl Table 4 Variant performan'!A22:P22; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs; methods: pp.36–37, Chromatin accessibility variants & bQTLs; paper: Sec10; Fig.5a–c; Supplementary Fig.9; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 18; sheet rows 21, 22; ambiguities: None recorded
Related records
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- benchmark: European-ancestry LCL caQTL classification: evaluated data subset