borzoi-ensemble (paper Table 4)

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limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Evaluations and results

14 evaluations · 14 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Zero-shot distance-balanced eQTL causality (AlphaGenome paper) Dataset subset: Zero-shot distance-balanced eQTL causality: evaluated data subset	0.702 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 borzoi-ensemble (paper Table 4): Zero-shot distance-balanced eQTL causality Evaluate the gene-specific RNA variant score directly on the distance-balanced labels. Aggregation: auROC per tissue weighted by the tissue’s variant count; the table’s “gene_balanced” identifier must not override the methods’ explicit distance-balancing description. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L13
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Yoruba LCL dsQTL effect-size prediction (AlphaGenome paper) Dataset subset: Yoruba LCL dsQTL effect-size prediction: evaluated data subset	0.792 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Yoruba LCL dsQTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L29
Configuration: borzoi-ensemble (paper Table 4)	Protocol: African-ancestry LCL caQTL classification (AlphaGenome paper) Dataset subset: African-ancestry LCL caQTL classification: evaluated data subset	0.462 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): African-ancestry LCL caQTL classification Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L19
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Polyadenylation-QTL causality (AlphaGenome paper) Dataset subset: Polyadenylation-QTL causality: evaluated data subset	0.621 PAS_10000_average_auprc dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Polyadenylation-QTL causality Summarize predicted RNA coverage near PASs, derive the largest allelic change in proximal-versus-distal usage, average tracks and classify positive versus matched negative variants. Unscored variants receive zero as specified by the paper. Aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L9
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Microglia caQTL effect-size prediction (AlphaGenome paper) Dataset subset: Microglia caQTL effect-size prediction: evaluated data subset	0.616 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Microglia caQTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L31
Configuration: borzoi-ensemble (paper Table 4)	Protocol: European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper) Dataset subset: European-ancestry LCL caQTL effect-size prediction: evaluated data subset	0.511 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): European-ancestry LCL caQTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L27
Configuration: borzoi-ensemble (paper Table 4)	Protocol: European-ancestry LCL caQTL classification (AlphaGenome paper) Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset	0.312 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): European-ancestry LCL caQTL classification Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L21
Configuration: borzoi-ensemble (paper Table 4)	Protocol: African-ancestry LCL caQTL effect-size prediction (AlphaGenome paper) Dataset subset: African-ancestry LCL caQTL effect-size prediction: evaluated data subset	0.649 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): African-ancestry LCL caQTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L25
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Zero-shot enhancer–gene linking (AlphaGenome paper) Dataset subset: Zero-shot enhancer–gene linking: evaluated data subset	0.668 auprc dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Zero-shot enhancer–gene linking Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context. Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L17
Configuration: borzoi-ensemble (paper Table 4)	Protocol: SPI1 binding QTL effect-size prediction (AlphaGenome paper) Dataset subset: SPI1 binding QTL effect-size prediction: evaluated data subset	0.535 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): SPI1 binding QTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L37
Configuration: borzoi-ensemble (paper Table 4)	Protocol: SPI1 binding QTL classification (AlphaGenome paper) Dataset subset: SPI1 binding QTL classification: evaluated data subset	0.468 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): SPI1 binding QTL classification Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L35
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) (AlphaGenome paper) Dataset subset: Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison): evaluated data subset	0.55 mean_pearsonr_all correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Zero-shot CAGI5 MPRA activity-effect prediction (borzoi-ensemble-matched comparison) Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context. Aggregation: Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L11
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Yoruba LCL dsQTL classification (AlphaGenome paper) Dataset subset: Yoruba LCL dsQTL classification: evaluated data subset	0.606 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Yoruba LCL dsQTL classification Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L23
Configuration: borzoi-ensemble (paper Table 4)	Protocol: Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper) Dataset subset: Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset	0.63 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source borzoi-ensemble (paper Table 4): Coronary smooth-muscle caQTL effect-size prediction Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L33

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The source table identifies borzoi-ensemble. Summarize predicted RNA coverage near PASs, derive the largest allelic change in proximal-versus-distal usage, average tracks and classify positive versus matched negative variants. Unscored variants receive zero as specified by the paper.

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants

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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.

Inputs, outputs and configuration
Property	Description and evidence
Reported method	borzoi-ensemble Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants
Exact checkpoint	Not established by the summary table; inspect the protocol and original implementation. · Needs further source review Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants
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Inputs	Not extracted or verified for this record.
Outputs	Not extracted or verified for this record.
Parameters	Not extracted or verified for this record.
Training data	Not extracted or verified for this record.
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Evidence

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15 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
Reported method borzoi-ensemble Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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
Reported method borzoi-ensemble Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.facts.0.value` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Reported method borzoi-ensemble Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.facts.0.value` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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	unextracted 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.1.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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	unextracted 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.1.value` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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	unextracted 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.1.value` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.limitations.0.text` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.limitations.0.text` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.limitations.0.text` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
How this comparator was evaluated The source table identifies borzoi-ensemble. Summarize predicted RNA coverage near PASs, derive the largest allelic change in proximal-versus-distal usage, average tracks and classify positive versus matched negative variants. Unscored variants receive zero as specified by the paper. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants 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.sections.0.body` 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-comparator-8505839e4f17fac1

areas: dna-genomes
entity level: method
configuration type: reported_configuration
version: borzoi-ensemble (paper Table 4)
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

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