borzoi-ensemble (paper Table 4): Zero-shot enhancer–gene linking
Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context.
Evaluation procedure
Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context.
- Model
- borzoi-ensemble (paper Table 4)
- Benchmark
- Zero-shot enhancer–gene linking (AlphaGenome paper)
- Dataset
- Zero-shot enhancer–gene linking: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- borzoi-ensemble (paper Table 4)
- protocol id
- alphagenome-2026-t4-protocol-15
- dataset version
- Not reported
- split
- Zero-shot evaluation on the annotated ENCODE-rE2G pairs; do not invent a downstream supervised training split.
- population
- ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities.
- inputs
- Not reported
- adaptation
- borzoi-ensemble (paper Table 4)
- metric implementation
- Not reported
- aggregation
- auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.
- budget
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-a757f4af4277 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| 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. |
Evidence 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.
63 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation borzoi-ensemble (paper Table 4) Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.adaptation borzoi-ensemble (paper Table 4) Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded 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 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.adaptation borzoi-ensemble (paper Table 4) Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.aggregation auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.aggregation auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded 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 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.aggregation auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.budget No value recorded Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.budget No value recorded Context-only references | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded 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 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.comparison.budget No value recorded Context-only references | AlphaGenome Nature 2026 supplementary comparison tables No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.comparison.dataset_version No value recorded Context-only references | alphagenome: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | missing or unspecified No individual claim review recorded author reported Audit detailsField: 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-evaluation-a0d48fa9d5e0fe36
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context.
- version
- borzoi-ensemble (paper Table 4)
- source evaluation index
- 15
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-15; dataset version: Not reported; split: Zero-shot evaluation on the annotated ENCODE-rE2G pairs; do not invent a downstream supervised training split.; population: ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities.; inputs: Not reported; adaptation: borzoi-ensemble (paper Table 4); metric implementation: Not reported; aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.; budget: Not reported
- context
- allowed inputs: Reference sequence centred on the target gene, K562 RNA-seq predictions and candidate element coordinates.; limitations: 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.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported