DNase prediction on held-out peaks: evaluated data subset
ChromBPNet test peak regions, fold 0. Only directly matching ENCODE experiment accessions are used.
Evaluation results
Release 2026-09-17-a757f4af4277 · 2 evaluations · 6 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AlphaGenome fold-0 track model on comparator-matched test peaks: DNase prediction on held-out peaks Model: AlphaGenome fold-0 track model on comparator-matched test peaks · Benchmark: DNase prediction on held-out peaks (AlphaGenome paper) · Dataset: DNase prediction on held-out peaks: evaluated data subset Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.79 log1p_count_pearsonr Unit: correlation · Direction: higher Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K23 Source checking is not independent reproduction. |
| 0.75 pearsonr Unit: correlation · Direction: higher Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K22 Source checking is not independent reproduction. |
| 0.51 profile_jsd Unit: dimensionless · Direction: lower Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K24 Source checking is not independent reproduction. |
| ChromBPNet (paper Table 3): DNase prediction on held-out peaks Model: ChromBPNet (paper Table 3) · Benchmark: DNase prediction on held-out peaks (AlphaGenome paper) · Dataset: DNase prediction on held-out peaks: evaluated data subset Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.660 log1p_count_pearsonr Unit: correlation · Direction: higher Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J23 Source checking is not independent reproduction. |
| 0.527 pearsonr Unit: correlation · Direction: higher Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J22 Source checking is not independent reproduction. |
| 0.561 profile_jsd Unit: dimensionless · Direction: lower Aggregation: Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J24 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.
24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.entity_level evaluation_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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.entity_level evaluation_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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.entity_level evaluation_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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.exact_manifest 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.reported_dataset_counts [] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.reported_dataset_counts [] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| attributes.reported_dataset_counts [] 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 Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| attributes.source_dataset_label ChromBPNet & AlphaGenome intersection 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 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-t3-dataset-13
- areas
- dna-genomes
- entity level
- evaluation_subset
- source dataset label
- ChromBPNet & AlphaGenome intersection
- source subset scope
- Intersect ChromBPNet fold-0 test peaks with regions that do not overlap AlphaGenome fold-0 training intervals.
- exact manifest
- Not reported
- reported dataset counts
- None recorded
- missing metadata
- split manifest: unextracted; per score denominator: unextracted