Protocol

Zero-shot enhancer–gene linking (AlphaGenome paper)

Can the model identify which candidate regulatory elements affect a target gene?

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17

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	ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
Split	Zero-shot evaluation on the annotated ENCODE-rE2G pairs; do not invent a downstream supervised training split. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
Allowed inputs and adaptation	Reference sequence centred on the target gene, K562 RNA-seq predictions and candidate element coordinates. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
Metrics as reported	auprc Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
Aggregation	auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
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 worksZero-shot enhancer–gene linking: evaluation procedure

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

Sources (3)

What is tested

Can the model identify which candidate regulatory elements affect a target gene?

Sources (3)

Procedure

Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context.

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

Zero-shot enhancer–gene linking (AlphaGenome paper)

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

Can the model identify which candidate regulatory elements affect a target gene?

Evaluation protocol · Zero-shot enhancer–gene linking: evaluated data subset

AlphaGenome distilled all-fold student · Configuration · Author-reported evaluation0.75
borzoi-ensemble (paper Table 4) · Configuration · Author-reported evaluation0.668

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'!M17; 'Suppl Table 4 Variant performan'!L17

Values, uncertainty and evidence

auprc: original source values
Tested entity	Printed value	Uncertainty	Evidence
AlphaGenome distilled all-fold student · Configuration	0.75 dimensionless	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M17
borzoi-ensemble (paper Table 4) · Configuration	0.668 dimensionless	Not reported	Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L17

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: Zero-shot enhancer–gene linking Configuration: AlphaGenome distilled all-fold studentProtocol: Zero-shot enhancer–gene linking (AlphaGenome paper)Dataset subset: Zero-shot enhancer–gene linking: evaluated data subset Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context. Author-reported evaluation · Evaluation metadata: needs review
0.75 auprc Unit: dimensionless · Direction: higher Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M17 Source checking is not independent reproduction.
borzoi-ensemble (paper Table 4): Zero-shot enhancer–gene linking Configuration: borzoi-ensemble (paper Table 4)Protocol: Zero-shot enhancer–gene linking (AlphaGenome paper)Dataset subset: Zero-shot enhancer–gene linking: evaluated data subset Compute expression input-gradient contributions near each candidate element, normalize by gene-context background gradient magnitude and impute zero for elements outside model context. Author-reported evaluation · Evaluation metadata: needs review
0.668 auprc Unit: dimensionless · Direction: higher Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Restricted to this cell context and filtered pair set. Distant elements outside input context are zero-imputed, and the paper notes that distal effects remain underestimated.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17
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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17

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-15

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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Normalize element scores","Evaluate pair-label auPRC"] Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Normalize element scores","Evaluate pair-label auPRC"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 ["Filter annotated element–gene pairs","Compute gene-linked model evidence","Normalize element scores","Evaluate pair-label auPRC"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 Zero-shot enhancer–gene linking: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 Zero-shot enhancer–gene linking: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 Zero-shot enhancer–gene linking: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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 ENCODE-rE2G CRISPRi-validated element–gene pairs in K562, filtered for available annotations and GENCODEv46 gene identities. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17 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-15

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 15
source table: 4
reference levels: metric: auprc; printed value: 0.045; numeric value: 4.4999999999999998E-2; source locator: Suppl Table 4 Variant performan!J17; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
comparison panels: id: paper-figure-ed964b87ed8aa54fc1; title: Zero-shot enhancer–gene linking (AlphaGenome paper); protocol id: alphagenome-2026-t4-protocol-15; dataset id: alphagenome-2026-t4-dataset-15; metric: auprc; unit: dimensionless; direction: higher; result ids: alphagenome-2026-result-ae8a555b252ed026; alphagenome-2026-result-b4dfacaafc9a5084; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 4 Variant performan'!M17; 'Suppl Table 4 Variant performan'!L17; context: Can the model identify which candidate regulatory elements affect a target gene?; 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17; 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'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; methods: p.39, Enhancer-gene linking; paper: Fig.4j; Extended Data Fig.7a–d; tables: Suppl Table 4 Variant performan; evaluation index 15; sheet rows 17; ambiguities: None recorded

Related records

benchmark: borzoi-ensemble (paper Table 4): Zero-shot enhancer–gene linking
benchmark: AlphaGenome distilled all-fold student: Zero-shot enhancer–gene linking
benchmark: Zero-shot enhancer–gene linking: evaluated data subset

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