Supervised multimodal CAGI5 MPRA prediction: evaluated data subset
CAGI5 training/test sets per locus, using native hg19 sequence and GENCODEv19.
Subset and evaluation context
This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.
Evaluation results
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. 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 Pipeline: borzoi-ensemble: multimodal features + LASSO (paper Table 4)Protocol: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)Dataset subset: 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. |
| AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV: Supervised multimodal CAGI5 MPRA prediction Pipeline: AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCVProtocol: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)Dataset subset: 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 | ||
| 0.65 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'!M12 Source checking is not independent reproduction. |
Evidence table
Inspect claims, sources and review details
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 CAGI5 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-d277315f7d76 · Record review: needs review
3 source records and release history
- 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-t4-dataset-10
- areas
- dna-genomes
- entity level
- evaluation_subset
- source dataset label
- CAGI5
- source subset scope
- Fit feature scaling on challenge training data only; tune a separate LassoCV per locus with10-fold cross-validation, then evaluate the challenge test set.
- exact manifest
- Not reported
- reported dataset counts
- None recorded
- missing metadata
- split manifest: unextracted; per score denominator: unextracted
- legacy kinds
- dataset
- entity classification
- review date: 2026-09-17; rationale: The record explicitly identifies the source-filtered and split-specific evaluated data population. Preserve it as a dataset subset, including comparator-specific selection, without inferring an unrecorded parent accession or equating differently filtered populations.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 4 Variant performan'!A12:P12; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption; methods: p.40, Benchmarking on the CAGI5 MPRA challenge; paper: Extended Data Fig.8c; Fig.5j; tables: Suppl Table 4 Variant performan; evaluation index 10; sheet rows 12; ambiguities: None recorded
Related records
- benchmark: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)
- dataset: borzoi-ensemble: multimodal features + LASSO (paper Table 4): Supervised multimodal CAGI5 MPRA prediction
- dataset: AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV: Supervised multimodal CAGI5 MPRA prediction