Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Zero-shot enhancer–gene linking (AlphaGenome paper)
Can the model identify which candidate regulatory elements affect a target gene?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17At 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 | ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| Split | Zero-shot evaluation on the annotated ENCODE-rE2G pairs; do not invent a downstream supervised training split.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| Allowed inputs and adaptation | Reference sequence centred on the target gene, K562 RNA-seq predictions and candidate element coordinates.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| Metrics as reported | auprcAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| Aggregation | auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 |
| 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
- Filter annotated element–gene pairs
- Compute gene-linked model evidence
- Normalize element scores
- Evaluate pair-label auPRC
What is tested
Can the model identify which candidate regulatory elements affect a target gene?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17Procedure
Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17Tested 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 |
|---|---|---|
| AlphaGenome distilled all-fold student: Zero-shot enhancer–gene linking Model: AlphaGenome distilled all-fold student · Benchmark: Zero-shot enhancer–gene linking (AlphaGenome paper) · Dataset: Zero-shot enhancer–gene linking: evaluated data subset Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.75 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'!M17 Source checking is not independent reproduction. |
| borzoi-ensemble (paper Table 4): Zero-shot enhancer–gene linking Model: borzoi-ensemble (paper Table 4) · Benchmark: Zero-shot enhancer–gene linking (AlphaGenome paper) · Dataset: Zero-shot enhancer–gene linking: evaluated data subset Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.668 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'!L17 Source checking is not independent reproduction. |
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.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
- 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
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-15Evidence 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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","Normalize element scores","Evaluate pair-label auPRC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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","Normalize element scores","Evaluate pair-label auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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","Normalize element scores","Evaluate pair-label auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 enhancer–gene linking: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 enhancer–gene linking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 enhancer–gene linking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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-15
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 15
- source table
- 4
- reference levels
- metric: auprc; printed value: 0.045; numeric value: 4.4999999999999998E-2; source locator: Suppl Table 4 Variant performan!J17; note: Source reference quantity for relative-performance calculation, not a measured baseline run.