ChromBPNet (paper Table 3): ATAC prediction on held-out peaks
Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3.
Evaluation procedure
Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3.
- Model
- ChromBPNet (paper Table 3)
- Benchmark
- ATAC prediction on held-out peaks (AlphaGenome paper)
- Dataset
- ATAC prediction on held-out peaks: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- ChromBPNet (paper Table 3)
- protocol id
- alphagenome-2026-t3-protocol-16
- dataset version
- Not reported
- split
- Intersect ChromBPNet fold-0 test peaks with regions that do not overlap AlphaGenome fold-0 training intervals.
- population
- ChromBPNet test peak regions, fold 0. Only directly matching ENCODE experiment accessions are used.
- inputs
- Not reported
- adaptation
- ChromBPNet (paper Table 3)
- metric implementation
- Not reported
- 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.
- budget
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-a757f4af4277 · 1 evaluation · 3 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ChromBPNet (paper Table 3): ATAC prediction on held-out peaks Model: ChromBPNet (paper Table 3) · Benchmark: ATAC prediction on held-out peaks (AlphaGenome paper) · Dataset: ATAC 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 | ||
| 0.467 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'!J30 Source checking is not independent reproduction. |
| 0.780 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'!J29 Source checking is not independent reproduction. |
| 0.786 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'!J28 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 ChromBPNet (paper Table 3) 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 ChromBPNet (paper Table 3) 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 ChromBPNet (paper Table 3) 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 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. 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 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. 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 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. 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-d62af1dace6614e6
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3.
- version
- ChromBPNet (paper Table 3)
- source evaluation index
- 16
- source table
- 3
- comparison
- protocol id: alphagenome-2026-t3-protocol-16; dataset version: Not reported; split: Intersect ChromBPNet fold-0 test peaks with regions that do not overlap AlphaGenome fold-0 training intervals.; population: ChromBPNet test peak regions, fold 0. Only directly matching ENCODE experiment accessions are used.; inputs: Not reported; adaptation: ChromBPNet (paper Table 3); metric implementation: Not reported; 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.; budget: Not reported
- context
- allowed inputs: Reference DNA; predicted and observed base-resolution profiles on matched assay peaks.; limitations: JSD is lower-is-better. The article calls it both Jensen–Shannon distance and divergence; the precise implementation is not resolved by these descriptions. Matching held-out intervals does not establish external pretraining decontamination.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: ChromBPNet (paper Table 3)
- benchmark: ATAC prediction on held-out peaks (AlphaGenome paper)
- dataset: ATAC prediction on held-out peaks: evaluated data subset
- evaluation: ChromBPNet (paper Table 3): ATAC prediction on held-out peaks, profile jsd
- evaluation: ChromBPNet (paper Table 3): ATAC prediction on held-out peaks, log1p count pearsonr
- evaluation: ChromBPNet (paper Table 3): ATAC prediction on held-out peaks, pearsonr