borzoi-ensemble: multimodal features + LASSO (paper Table 4): Supervised multimodal CAGI5 MPRA prediction
Generate multimodal features using the Borzoi-comparison scoring strategy, standardize from training statistics and fit per-locus LASSO.
Evaluation procedure
Generate multimodal features using the Borzoi-comparison scoring strategy, standardize from training statistics and fit per-locus LASSO.
- Model
- borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- Benchmark
- Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)
- Dataset
- Supervised multimodal CAGI5 MPRA prediction: evaluated data subset
- origin
- Author-reported evaluation
- configuration
- borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- protocol id
- alphagenome-2026-t4-protocol-10
- dataset version
- Not reported
- split
- Fit feature scaling on challenge training data only; tune a separate LassoCV per locus with10-fold cross-validation, then evaluate the challenge test set.
- population
- CAGI5 training/test sets per locus, using native hg19 sequence and GENCODEv19.
- inputs
- Not reported
- adaptation
- borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- metric implementation
- Not reported
- aggregation
- Mean Pearson correlation across included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons.
- 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 |
|---|---|---|
| borzoi-ensemble: multimodal features + LASSO (paper Table 4): Supervised multimodal CAGI5 MPRA prediction Model: borzoi-ensemble: multimodal features + LASSO (paper Table 4) · Benchmark: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper) · Dataset: Supervised multimodal CAGI5 MPRA prediction: evaluated data subset Generate multimodal features using the Borzoi-comparison scoring strategy, standardize from training statistics and fit per-locus LASSO. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.615 Lasso pearsonr (DNASE + RNA + CHIP) Unit: correlation · Direction: higher Aggregation: Mean Pearson correlation across included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L12 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-ensemble: multimodal features + LASSO (paper Table 4) 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-ensemble: multimodal features + LASSO (paper Table 4) 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-ensemble: multimodal features + LASSO (paper Table 4) 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 included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons. 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 included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons. 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 included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons. 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-10258803d6641706
- areas
- dna-genomes
- origin
- author_reported
- protocol
- Generate multimodal features using the Borzoi-comparison scoring strategy, standardize from training statistics and fit per-locus LASSO.
- version
- borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- source evaluation index
- 10
- source table
- 4
- comparison
- protocol id: alphagenome-2026-t4-protocol-10; dataset version: Not reported; split: Fit feature scaling on challenge training data only; tune a separate LassoCV per locus with10-fold cross-validation, then evaluate the challenge test set.; population: CAGI5 training/test sets per locus, using native hg19 sequence and GENCODEv19.; inputs: Not reported; adaptation: borzoi-ensemble: multimodal features + LASSO (paper Table 4); metric implementation: Not reported; aggregation: Mean Pearson correlation across included locus/context tests. The figure-average protocol excludes MYC for LASSO non-convergence and TERT-GBM for matched comparisons.; budget: Not reported
- context
- allowed inputs: DNase, histone ChIP-seq and target-gene RNA variant-score features across available cell types.; limitations: This is supervised pipeline performance, not a zero-shot base-model result. The F9 exclusion described for DNase-only LASSO must not be automatically applied to this multimodal row.
- missing metadata
- dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported
Related records
- model: borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- benchmark: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)
- dataset: Supervised multimodal CAGI5 MPRA prediction: evaluated data subset
- evaluation: borzoi-ensemble: multimodal features + LASSO (paper Table 4): Supervised multimodal CAGI5 MPRA prediction, Lasso pearsonr (DNASE + RNA + CHIP)