Protocol

Polyadenylation-QTL causality (AlphaGenome paper)

Can RNA-coverage changes distinguish fine-mapped paQTLs from matched negative variants?

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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9

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	Borzoi tissue-pooled fine-mapped 3-prime QTL dataset, with negative controls matched for cleavage-site distance and expression. 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
Split	Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds. 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
Allowed inputs and adaptation	REF/ALT RNA predictions and annotated polyadenylation sites; pooled track score. 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
Metrics as reported	PAS_10000_average_auprc 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
Aggregation	Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000. 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
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 worksPolyadenylation-QTL causality: evaluation procedure

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

Sources (3)

What is tested

Can RNA-coverage changes distinguish fine-mapped paQTLs from matched negative variants?

Sources (3)

Procedure

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)

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

Polyadenylation-QTL causality (AlphaGenome paper)

PAS_10000_average_auprc (dimensionless) · Higher values are better for this metric.

Can RNA-coverage changes distinguish fine-mapped paQTLs from matched negative variants?

Evaluation protocol · Polyadenylation-QTL causality: evaluated data subset

AlphaGenome distilled all-fold student · Configuration · Author-reported evaluation0.63
borzoi-ensemble (paper Table 4) · Configuration · Author-reported evaluation0.620662

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'!M9; 'Suppl Table 4 Variant performan'!L9

Values, uncertainty and evidence

PAS_10000_average_auprc: original source values
Tested entity	Printed value	Uncertainty	Evidence
AlphaGenome distilled all-fold student · Configuration	0.63 dimensionless	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M9
borzoi-ensemble (paper Table 4) · Configuration	0.620662 dimensionless	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L9

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
AlphaGenome distilled all-fold student: Polyadenylation-QTL causality Configuration: AlphaGenome distilled all-fold studentProtocol: Polyadenylation-QTL causality (AlphaGenome paper)Dataset subset: Polyadenylation-QTL causality: evaluated data subset 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. Author-reported evaluation · Evaluation metadata: needs review
0.63 PAS_10000_average_auprc Unit: dimensionless · Direction: higher Aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M9 Source checking is not independent reproduction.
borzoi-ensemble (paper Table 4): Polyadenylation-QTL causality Configuration: borzoi-ensemble (paper Table 4)Protocol: Polyadenylation-QTL causality (AlphaGenome paper)Dataset subset: Polyadenylation-QTL causality: evaluated data subset 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. Author-reported evaluation · Evaluation metadata: needs review
0.620662 PAS_10000_average_auprc Unit: dimensionless · Direction: higher Aggregation: Average auPRC over100 random positive-to-negative matching permutations; Table4 endpoint is PAS_10000.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L9 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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

The100 permutations quantify sensitivity to negative matching, not100 independent experiments. Variants beyond the threshold and incomplete PAS context are not equivalent populations. This paQTL variant endpoint is separate from the quarantined Table3 coverage-ratio conflict.
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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9
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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9

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-8

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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 ["Held-out paQTLs and matched negatives","Compute PAS-usage change","Repeat negative matching","Average matching-specific auPRC"] 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 ["Held-out paQTLs and matched negatives","Compute PAS-usage change","Repeat negative matching","Average matching-specific auPRC"] 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 ["Held-out paQTLs and matched negatives","Compute PAS-usage change","Repeat negative matching","Average matching-specific auPRC"] 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 Polyadenylation-QTL causality: evaluation procedure 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 Polyadenylation-QTL causality: evaluation procedure 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 Polyadenylation-QTL causality: evaluation procedure 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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 Borzoi tissue-pooled fine-mapped 3-prime QTL dataset, with negative controls matched for cleavage-site distance and expression. 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; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9 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-8

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 8
source table: 4
reference levels: metric: PAS_10000_average_auprc; printed value: 0.5; numeric value: 0.5; source locator: Suppl Table 4 Variant performan!J9; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
comparison panels: id: paper-figure-972cb575af05ac931a; title: Polyadenylation-QTL causality (AlphaGenome paper); protocol id: alphagenome-2026-t4-protocol-8; dataset id: alphagenome-2026-t4-dataset-8; metric: PAS_10000_average_auprc; unit: dimensionless; direction: higher; result ids: alphagenome-2026-result-1e88bdedfa8823be; alphagenome-2026-result-88b308c542d9a9bb; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 4 Variant performan'!M9; 'Suppl Table 4 Variant performan'!L9; context: Can RNA-coverage changes distinguish fine-mapped paQTLs from matched negative variants?; 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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9; 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'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants; methods: p.36, Polyadenylation variants; paper: Fig.4k; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 8; sheet rows 9; ambiguities: None recorded

Related records

benchmark: borzoi-ensemble (paper Table 4): Polyadenylation-QTL causality
benchmark: AlphaGenome distilled all-fold student: Polyadenylation-QTL causality
benchmark: Polyadenylation-QTL causality: evaluated data subset

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