RNA expression correlation across genes: evaluated data subset
Borzoi-matched RNA-seq coverage aggregated over GENCODE v46 exons with strand matching; retain genes with at least half their exons in a test interval.
Evaluation results
Release 2026-09-17-a757f4af4277 · 2 evaluations · 4 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Borzoi (paper Table 3): RNA expression correlation across genes Model: Borzoi (paper Table 3) · Benchmark: RNA expression correlation across genes (AlphaGenome paper) · Dataset: RNA expression correlation across genes: evaluated data subset Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.765 Gene TPM
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J13 Source checking is not independent reproduction. |
| 0.449 Gene TPM normalized
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J15 Source checking is not independent reproduction. |
| AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across genes Model: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head · Benchmark: RNA expression correlation across genes (AlphaGenome paper) · Dataset: RNA expression correlation across genes: evaluated data subset Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.52 Gene TPM normalized
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K15 Source checking is not independent reproduction. |
| 0.80 Gene TPM
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K13 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 Borzoi RNA-seq tracks at base resolution 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-7
- areas
- dna-genomes
- entity level
- evaluation_subset
- source dataset label
- Borzoi RNA-seq tracks at base resolution
- source subset scope
- 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. Borzoi fold-1 RNA comparison.
- exact manifest
- Not reported
- reported dataset counts
- None recorded
- missing metadata
- split manifest: unextracted; per score denominator: unextracted