AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison)
Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.
Evaluation procedure
Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.
- Model
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- Benchmark
- Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) (AlphaGenome paper)
- Dataset
- Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison): evaluated data subset
- origin
- Author-reported evaluation
- configuration
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- protocol id
- alphagenome-2026-t4-protocol-9-row11
- dataset version
- Not reported
- split
- Use the challenge’s evaluation data and reported locus exclusions. Do not replace this locus-based protocol with the generic variant chromosome split.
- population
- CAGI5 challenge effects with hg19 sequence and GENCODEv19 annotations; comparator-specific locus/context sets.
- inputs
- Not reported
- adaptation
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- metric implementation
- Not reported
- aggregation
- Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate.
- 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 |
|---|---|---|
| AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) Model: AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset · Benchmark: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) (AlphaGenome paper) · Dataset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison): evaluated data subset Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.56 mean_pearsonr_all Unit: correlation · Direction: higher Aggregation: Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M11 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 AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset 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 AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset 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 AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset 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 Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. 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 Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. 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 Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. 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-4f66864f98841ad8
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.
- version
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- source evaluation index
- 9
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-9-row11; dataset version: Not reported; split: Use the challenge’s evaluation data and reported locus exclusions. Do not replace this locus-based protocol with the generic variant chromosome split.; population: CAGI5 challenge effects with hg19 sequence and GENCODEv19 annotations; comparator-specific locus/context sets.; inputs: Not reported; adaptation: AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset; metric implementation: Not reported; aggregation: Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate.; budget: Not reported
- context
- allowed inputs: REF/ALT native genomic sequence and DNase scores averaged across cell-type-matched tracks; mappings differ by comparator strategy.; limitations: Native genomic prediction is compared with an MPRA measurement. Track proxies and context exclusions affect comparability; do not merge the two same-index rows into one evaluation population.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- benchmark: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) (AlphaGenome paper)
- dataset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison): evaluated data subset
- evaluation: AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison), mean pearsonr all