Evaluation

AlphaGenome absolute multimodal scores → RandomForestClassifier: Supervised distance-balanced eQTL causality

Train the source’s random-forest classifier on the same balanced causality dataset and score the held-out chromosome test set.

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Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: AlphaGenome absolute multimodal scores → RandomForestClassifier	Protocol: Supervised distance-balanced eQTL causality (AlphaGenome paper) Dataset subset: Supervised distance-balanced eQTL causality: evaluated data subset	0.8 tissue_weighted_mean_auroc dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AlphaGenome absolute multimodal scores → RandomForestClassifier: Supervised distance-balanced eQTL causality Train the source’s random-forest classifier on the same balanced causality dataset and score the held-out chromosome test set. Aggregation: auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M14

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Evaluation procedure

Train the source’s random-forest classifier on the same balanced causality dataset and score the held-out chromosome test set.

Pipeline: AlphaGenome absolute multimodal scores → RandomForestClassifier
Protocol: Supervised distance-balanced eQTL causality (AlphaGenome paper)
Dataset subset: Supervised distance-balanced eQTL causality: evaluated data subset

origin: Author-reported evaluation
configuration: AlphaGenome absolute multimodal scores → RandomForestClassifier
protocol id: alphagenome-2026-t4-protocol-12
dataset version: Not reported
split: Supervised training chromosomes are 1,4,7,8,10,13,15; validation chromosomes 2,5,11,14,17,20,22,X; test chromosomes 3,6,9,12,16,18,19,21. This is downstream evaluation separation, not a held-out reference-genome claim for the distilled backbone. The task additionally describes five-fold random-forest training excluding test chromosomes, followed by mean test auROC across those fits; exact fold membership is not enumerated.
population: Reprocessed GTEx SuSiE eQTL-catalogue SNVs; positives PIP≥0.9, negatives PIP≤0.01, GENCODEv46 genes, controls downsampled within log-distance-to-TSS bins.
inputs: Not reported
adaptation: AlphaGenome absolute multimodal scores → RandomForestClassifier
metric implementation: Not reported
aggregation: auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds.
budget: Not reported

Metadata review: needs review. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Supervised training chromosomes are 1,4,7,8,10,13,15; validation chromosomes 2,5,11,14,17,20,22,X; test chromosomes 3,6,9,12,16,18,19,21. This is downstream evaluation separation, not a held-out reference-genome claim for the distilled backbone. The task additionally describes five-fold random-forest training excluding test chromosomes, followed by mean test auROC across those fits; exact fold membership is not enumerated.
Adaptation: AlphaGenome absolute multimodal scores → RandomForestClassifier
Scoring implementation: Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Access requirements and official instructions: Supervised distance-balanced eQTL causality (AlphaGenome paper)

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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Evidence table

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63 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation AlphaGenome absolute multimodal scores → RandomForestClassifier Context-only references	alphagenome: Journal full-text XML Original source ↗ 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 Retrieved: 2026-09-16T19:53:03.009088+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
attributes.comparison.adaptation AlphaGenome absolute multimodal scores → RandomForestClassifier Context-only references	AlphaGenome Nature 2026 supplementary methods Original source ↗ 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
attributes.comparison.adaptation AlphaGenome absolute multimodal scores → RandomForestClassifier Context-only references	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 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 Retrieved: 2026-09-17T06:31:06.887921+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
attributes.comparison.aggregation auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds. Context-only references	alphagenome: Journal full-text XML Original source ↗ 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 Retrieved: 2026-09-16T19:53:03.009088+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
attributes.comparison.aggregation auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds. Context-only references	AlphaGenome Nature 2026 supplementary methods Original source ↗ 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
attributes.comparison.aggregation auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds. Context-only references	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 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 Retrieved: 2026-09-17T06:31:06.887921+00:00	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
attributes.comparison.budget Not reported Context-only references	alphagenome: Journal full-text XML Original source ↗ 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 Retrieved: 2026-09-16T19:53:03.009088+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
attributes.comparison.budget Not reported Context-only references	AlphaGenome Nature 2026 supplementary methods Original source ↗ 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
attributes.comparison.budget Not reported Context-only references	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 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 Retrieved: 2026-09-17T06:31:06.887921+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
attributes.comparison.dataset_version Not reported Context-only references	alphagenome: Journal full-text XML Original source ↗ 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 Retrieved: 2026-09-16T19:53:03.009088+00:00	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-29-06401fd5b220 · 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-evaluation-06c0eeb3417ef493

areas: dna-genomes
origin: author_reported
protocol: Train the source’s random-forest classifier on the same balanced causality dataset and score the held-out chromosome test set.
version: AlphaGenome absolute multimodal scores → RandomForestClassifier
source evaluation index: 12
source table: 4
comparison: protocol id: alphagenome-2026-t4-protocol-12; dataset version: Not reported; split: Supervised training chromosomes are 1,4,7,8,10,13,15; validation chromosomes 2,5,11,14,17,20,22,X; test chromosomes 3,6,9,12,16,18,19,21. This is downstream evaluation separation, not a held-out reference-genome claim for the distilled backbone. The task additionally describes five-fold random-forest training excluding test chromosomes, followed by mean test auROC across those fits; exact fold membership is not enumerated.; population: Reprocessed GTEx SuSiE eQTL-catalogue SNVs; positives PIP≥0.9, negatives PIP≤0.01, GENCODEv46 genes, controls downsampled within log-distance-to-TSS bins.; inputs: Not reported; adaptation: AlphaGenome absolute multimodal scores → RandomForestClassifier; metric implementation: Not reported; aggregation: auROC per tissue weighted by the tissue’s variant count; the supervised analysis additionally averages auROC across five fitted folds.; budget: Not reported
context: allowed inputs: Absolute multimodal AlphaGenome variant features, with target-gene selection for gene-specific scores.; limitations: Fine-mapping labels represent putative causality. Distance balancing changes the sampled population and does not establish calibration to genome-wide prevalence. Do not equate the supervised feature pipeline with the RNA-only scorer.
missing metadata: dataset version: unextracted; exact input manifest: unextracted; inference budget: unreported; scoring failures: unreported

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