Borzoi (paper Table 3): Base-resolution RNA-seq prediction
Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.
Evaluation procedure
Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.
- Model
- Borzoi (paper Table 3)
- Benchmark
- Base-resolution RNA-seq prediction (AlphaGenome paper)
- Dataset
- Base-resolution RNA-seq prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- Borzoi (paper Table 3)
- protocol id
- alphagenome-2026-t3-protocol-5
- 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
- Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions.
- inputs
- Not reported
- adaptation
- Borzoi (paper Table 3)
- metric implementation
- Not reported
- aggregation
- Pearson correlation; genome-track methods average individual track correlations for assay groups.
- budget
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-a757f4af4277 · 1 evaluation · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Borzoi (paper Table 3): Base-resolution RNA-seq prediction Model: Borzoi (paper Table 3) · Benchmark: Base-resolution RNA-seq prediction (AlphaGenome paper) · Dataset: Base-resolution RNA-seq prediction: evaluated data subset Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.460 Track @1bp
(normal scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10 Source checking is not independent reproduction. |
| 0.750 Track @1bp
(log1p scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J11 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 Borzoi (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 Borzoi (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 Borzoi (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 Pearson correlation; genome-track methods average individual track correlations for assay groups. 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; genome-track methods average individual track correlations for assay groups. 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; genome-track methods average individual track correlations for assay groups. 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-97bd57832bf82219
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.
- version
- Borzoi (paper Table 3)
- source evaluation index
- 5
- source table
- 3
- comparison
- protocol id: alphagenome-2026-t3-protocol-5; 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: Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions.; inputs: Not reported; adaptation: Borzoi (paper Table 3); metric implementation: Not reported; aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.; budget: Not reported
- context
- allowed inputs: Reference sequence; the additional AlphaGenome RNA-seq head and unscaled Borzoi predictions repeated across each original 32-bp bin.; limitations: Upsampled Borzoi output has no new sub-bin information; normal-scale gains partly reflect exon-boundary resolution. The paper restricts inclusion to tracks meeting its data-concordance check.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: Borzoi (paper Table 3)
- benchmark: Base-resolution RNA-seq prediction (AlphaGenome paper)
- dataset: Base-resolution RNA-seq prediction: evaluated data subset
- evaluation: Borzoi (paper Table 3): Base-resolution RNA-seq prediction, Track @1bp (normal scale pearsonr)
- evaluation: Borzoi (paper Table 3): Base-resolution RNA-seq prediction, Track @1bp (log1p scale pearsonr)