Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Supervised enhancer–gene linking (AlphaGenome paper)
Can the model identify which candidate regulatory elements affect a target gene?
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18At 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 | ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| Split | ENCODE-rE2G out-of-fold prediction/training pipeline; reuse the authors’ cross-validated comparison scores and rerun the feature-augmented pipeline. Exact fold assignments are not enumerated in this methods paragraph.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| Allowed inputs and adaptation | ENCODE-rE2G extended features plus one AlphaGenome K562 RNA-seq input×gradient feature, identified by Extended Data Fig.7b. The multimodal K562 variant-feature model in Fig.7c is a different configuration.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| Aggregation | auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 |
| 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 worksSupervised enhancer–gene linking: 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18What is tested
Can the model identify which candidate regulatory elements affect a target gene?
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18Procedure
Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18Recorded 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.
Supervised enhancer–gene linking (AlphaGenome paper)
auprc (dimensionless) · Higher values are better for this metric.
Can the model identify which candidate regulatory elements affect a target gene?
Evaluation protocol · Supervised enhancer–gene linking: evaluated data subset
- ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4) · Pipeline · Author-reported evaluation0.76
- ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature · Pipeline · Author-reported evaluation0.78
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'!L18; 'Suppl Table 4 Variant performan'!M18Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4) · Pipeline | 0.76 dimensionless | Not reported | Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L18 |
| ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature · Pipeline | 0.78 dimensionless | Not reported | Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M18 |
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 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking Pipeline: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)Protocol: Supervised enhancer–gene linking (AlphaGenome paper)Dataset subset: Supervised enhancer–gene linking: evaluated data subset Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.76 auprc Unit: dimensionless · Direction: higher Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L18 Source checking is not independent reproduction. |
| ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature: Supervised enhancer–gene linking Pipeline: ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient featureProtocol: Supervised enhancer–gene linking (AlphaGenome paper)Dataset subset: Supervised enhancer–gene linking: evaluated data subset Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.78 auprc Unit: dimensionless · Direction: higher Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M18 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18
Strengths and limitations
Limitations and conditions
- Restricted to this cell context and filtered pair set. Distant elements outside input context are zero-imputed, and the paper notes that distal effects remain underestimated. Extended Data Fig.7b identifies the single input×gradient addition; do not substitute the multimodal feature bundle from panelc.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 - 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18
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-16Evidence 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Augment out-of-fold feature model","Evaluate pair-label auPRC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Augment out-of-fold feature model","Evaluate pair-label auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Augment out-of-fold feature model","Evaluate pair-label auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 enhancer–gene linking: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 enhancer–gene linking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 enhancer–gene linking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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 ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18 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-16
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 16
- source table
- 4
- reference levels
- metric: auprc; printed value: 0.045; numeric value: 4.4999999999999998E-2; source locator: Suppl Table 4 Variant performan!J18; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
- comparison panels
- id: paper-figure-9041268114c2fda649; title: Supervised enhancer–gene linking (AlphaGenome paper); protocol id: alphagenome-2026-t4-protocol-16; dataset id: alphagenome-2026-t4-dataset-16; metric: auprc; unit: dimensionless; direction: higher; result ids: alphagenome-2026-result-21401786b8288da1; alphagenome-2026-result-5ef7238b75eb48d7; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 4 Variant performan'!L18; 'Suppl Table 4 Variant performan'!M18; context: Can the model identify which candidate regulatory elements affect a target gene?; 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18; 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'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 16; sheet rows 18; ambiguities: None recorded
Related records
- benchmark: ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature: Supervised enhancer–gene linking
- benchmark: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking
- benchmark: Supervised enhancer–gene linking: evaluated data subset