AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: chromatin contact-map prediction
Compare predicted and observed contact maps for each held-out interval and cell type.
Evaluation procedure
Compare predicted and observed contact maps for each held-out interval and cell type.
- Model
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- Benchmark
- chromatin contact-map prediction (AlphaGenome paper)
- Dataset
- chromatin contact-map prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- protocol id
- alphagenome-2026-t3-protocol-23
- dataset version
- Not reported
- split
- Intersection of Orca test chromosomes9/10 with AlphaGenome/Borzoi fold-0 held-out intervals.
- population
- H1-hESC and HFFc6 Micro-C datasets matching Orca’s evaluation.
- inputs
- Not reported
- adaptation
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- metric implementation
- Not reported
- aggregation
- Mean Pearson correlation across held-out interval evaluations; cell types remain explicit before reporting the summary.
- 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 fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: chromatin contact-map prediction Model: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins · Benchmark: chromatin contact-map prediction (AlphaGenome paper) · Dataset: chromatin contact-map prediction: evaluated data subset Compare predicted and observed contact maps for each held-out interval and cell type. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.79 Per-cell type
@4kb pearsonr Unit: correlation · Direction: higher Aggregation: Mean Pearson correlation across held-out interval evaluations; cell types remain explicit before reporting the summary. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K40 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 fold-0 contact-map model, bilinearly resized to Orca 4 kb bins 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 fold-0 contact-map model, bilinearly resized to Orca 4 kb bins 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 fold-0 contact-map model, bilinearly resized to Orca 4 kb bins 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 across held-out interval evaluations; cell types remain explicit before reporting the summary. 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 across held-out interval evaluations; cell types remain explicit before reporting the summary. 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 across held-out interval evaluations; cell types remain explicit before reporting the summary. 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-3b468cd87ca1a89d
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Compare predicted and observed contact maps for each held-out interval and cell type.
- version
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- source evaluation index
- 23
- source table
- 3
- comparison
- protocol id: alphagenome-2026-t3-protocol-23; dataset version: Not reported; split: Intersection of Orca test chromosomes9/10 with AlphaGenome/Borzoi fold-0 held-out intervals.; population: H1-hESC and HFFc6 Micro-C datasets matching Orca’s evaluation.; inputs: Not reported; adaptation: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins; metric implementation: Not reported; aggregation: Mean Pearson correlation across held-out interval evaluations; cell types remain explicit before reporting the summary.; budget: Not reported
- context
- allowed inputs: Reference DNA; contact maps resized from AlphaGenome native bins to Orca’s 4-kb grid using bilinear interpolation.; limitations: Resampling changes the grid and is part of this protocol. Do not treat native AlphaGenome resolution or the cell-difference endpoint as interchangeable with the tabulated 4-kb per-cell evaluation.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- benchmark: chromatin contact-map prediction (AlphaGenome paper)
- dataset: chromatin contact-map prediction: evaluated data subset
- evaluation: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: chromatin contact-map prediction, Per-cell type @4kb pearsonr