AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: DNase track prediction at 32 bp
Align predicted and experimental values on the same 32-bp tracks and test intervals.
Evaluation procedure
Align predicted and experimental values on the same 32-bp tracks and test intervals.
- Model
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- Benchmark
- DNase track prediction at 32 bp (AlphaGenome paper)
- Dataset
- DNase track prediction at 32 bp: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- protocol id
- alphagenome-2026-t3-protocol-14
- dataset version
- Not reported
- split
- Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.
- population
- Original Borzoi TFRecords, retaining their scaling and 32-bp target bins.
- inputs
- Not reported
- adaptation
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- metric implementation
- Not reported
- aggregation
- Pearson correlation; group summaries derive from individual track correlations.
- 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 Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: DNase track prediction at 32 bp Model: AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head · Benchmark: DNase track prediction at 32 bp (AlphaGenome paper) · Dataset: DNase track prediction at 32 bp: evaluated data subset Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.86 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K25 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 Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head 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 Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head 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 Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head 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 Pearson correlation; group summaries derive from individual track correlations. 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 Pearson correlation; group summaries derive from individual track correlations. 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 Pearson correlation; group summaries derive from individual track correlations. 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-b9e4d4e1df2b70f7
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Align predicted and experimental values on the same 32-bp tracks and test intervals.
- version
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- source evaluation index
- 14
- source table
- 3
- comparison
- protocol id: alphagenome-2026-t3-protocol-14; dataset version: Not reported; split: Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.; population: Original Borzoi TFRecords, retaining their scaling and 32-bp target bins.; inputs: Not reported; adaptation: AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head; metric implementation: Not reported; aggregation: Pearson correlation; group summaries derive from individual track correlations.; budget: Not reported
- context
- allowed inputs: Reference DNA and the dedicated Borzoi-matched AlphaGenome output head; compare published Borzoi fold-1 predictions.; limitations: This is a fine-tuned comparison head, not the generic distilled variant model. Scaling and resolution differ from the separate base-resolution RNA endpoint.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- benchmark: DNase track prediction at 32 bp (AlphaGenome paper)
- dataset: DNase track prediction at 32 bp: evaluated data subset
- evaluation: AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: DNase track prediction at 32 bp, pearsonr