Protocol

Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)

Does supervised combination of sequence-derived modalities better predict CAGI5 reporter-assay effects?

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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

2 evaluations · 2 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Dataset and biological context	CAGI5 training/test sets per locus, using native hg19 sequence and GENCODEv19. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
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. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
Allowed inputs and adaptation	DNase, histone ChIP-seq and target-gene RNA variant-score features across available cell types. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
Metrics as reported	Lasso pearsonr (DNASE + RNA + CHIP) Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
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. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
Uncertainty	Not reported for these summary-table scores. · Not reported in inspected sources Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

How it worksSupervised multimodal CAGI5 MPRA prediction: evaluation procedure

Conceptual summary of the cited procedure; model-specific conditions are given below.

Sources (3)

What is tested

Does supervised combination of sequence-derived modalities better predict CAGI5 reporter-assay effects?

Sources (3)

Procedure

Generate multimodal features using the Borzoi-comparison scoring strategy, standardize from training statistics and fit per-locus LASSO.

Sources (3)

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper)

Lasso pearsonr (DNASE + RNA + CHIP) (correlation) · Higher values are better for this metric.

Does supervised combination of sequence-derived modalities better predict CAGI5 reporter-assay effects?

Evaluation protocol · Supervised multimodal CAGI5 MPRA prediction: evaluated data subset

borzoi-ensemble: multimodal features + LASSO (paper Table 4) · Pipeline · Author-reported evaluation0.615
AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV · Pipeline · Author-reported evaluation0.65

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L12; 'Suppl Table 4 Variant performan'!M12

Values, uncertainty and evidence

Lasso pearsonr (DNASE + RNA + CHIP): original source values
Tested entity	Printed value	Uncertainty	Evidence
borzoi-ensemble: multimodal features + LASSO (paper Table 4) · Pipeline	0.615 correlation	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L12
AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV · Pipeline	0.65 correlation	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M12

Scope and limitations

This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.
Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.
Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
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.

Papers and result coverage

Last literature check: 2026-09-17. Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.

Paper or primary resource	Version	Reference
alphagenome: Journal full-text XML	Retrieved page snapshot; no immutable publisher revision supplied	Read source
AlphaGenome Nature 2026 supplementary comparison tables	Nature version of record, 28 January 2026	Read source DOI: 10.1038/s41586-025-10014-0
AlphaGenome Nature 2026 supplementary methods	Supplement to Nature version of record, 28 January 2026; content hash pinned	Read source

What is still missing

Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.
Subsequent studies use different datasets and are not pooled with this paper.

Search and extraction details

complete comparison extracted

Searches

AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction
AlphaGenome independent evaluation benchmark 2026 variant effects

Evidence locations

'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

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

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.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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
This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · '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

Profile review details

Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.

Stable record: alphagenome-2026-t4-protocol-10

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.

42 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	alphagenome: Journal full-text XML Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ '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 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram steps ["Compute multimodal CAGI5 features","Scale from training data","Fit per-locus cross-validated LASSO","Evaluate test-locus correlations"] Individual claims	alphagenome: Journal full-text XML Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Compute multimodal CAGI5 features","Scale from training data","Fit per-locus cross-validated LASSO","Evaluate test-locus correlations"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ '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 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram steps ["Compute multimodal CAGI5 features","Scale from training data","Fit per-locus cross-validated LASSO","Evaluate test-locus correlations"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram title Supervised multimodal CAGI5 MPRA prediction: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Supervised multimodal CAGI5 MPRA prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ '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 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram title Supervised multimodal CAGI5 MPRA prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Dataset and biological context CAGI5 training/test sets per locus, using native hg19 sequence and GENCODEv19. Individual claims	alphagenome: Journal full-text XML Original source ↗ '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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t4-protocol-10

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 10
source table: 4
reference levels: metric: Lasso pearsonr (DNASE + RNA + CHIP); printed value: 0; numeric value: 0; source locator: Suppl Table 4 Variant performan!J12; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
comparison panels: id: paper-figure-ba4fbf8e64b886af91; title: Supervised multimodal CAGI5 MPRA prediction (AlphaGenome paper); protocol id: alphagenome-2026-t4-protocol-10; dataset id: alphagenome-2026-t4-dataset-10; metric: Lasso pearsonr (DNASE + RNA + CHIP); unit: correlation; direction: higher; result ids: alphagenome-2026-result-4ad8a07799c14c2d; alphagenome-2026-result-e73a0458ca9cd659; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 4 Variant performan'!L12; 'Suppl Table 4 Variant performan'!M12; context: Does supervised combination of sequence-derived modalities better predict CAGI5 reporter-assay effects?; caveats: This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.; Model inputs, training and inference budgets differ or remain partly unextracted. This figure does not establish a controlled architectural advantage.; Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_comparison_extracted; primary sources: evidence-official-56e5abfb5f12f1cd3b20; source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; inspected locators: '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; searched queries: AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction; AlphaGenome independent evaluation benchmark 2026 variant effects; gaps: Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.; Subsequent studies use different datasets and are not pooled with this paper.; claim scope: Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; 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

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