Protocol

PRO-cap prediction on held-out peaks (AlphaGenome paper)

Can reference sequence predict local PRO-cap profile shape and total signal at held-out peaks?

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17

2 evaluations · 4 results

Overview

Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.

Evaluation procedure diagram

How it worksPRO-cap prediction on held-out peaks: evaluation procedure

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

Sources (3)

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

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Evaluation scope and datasetMetric and reported setup

PRO-cap prediction on held-out peaks (AlphaGenome paper)

pearsonr log total count (correlation) · Higher values are better.

PRO-cap prediction on held-out peaks (AlphaGenome paper) · PRO-cap prediction on held-out peaks: evaluated data subset

Evidence origin: Author-reported evaluation.

AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K16; 'Suppl Table 3 Track performance'!J16

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Superseded and quarantined score conflicts are excluded; comparator-specific subsets remain separate.

Comparison details and limitations

Can reference sequence predict local PRO-cap profile shape and total signal at held-out peaks?

This is the AlphaGenome paper’s comparison. Source-checked scores are not independent reproductions.

Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Find a tested model or method

Showing 2 of 2 matching rows.

Zoom to observed range

Tested configuration

-1-0.500.51

Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

What is tested

Can reference sequence predict local PRO-cap profile shape and total signal at held-out peaks?

Sources (3)

Procedure

Evaluate signal correlation, log-total-count correlation and profile JSD as separate metrics; retain only endpoints actually listed for this evaluation in Table3.

Sources (3)

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

No reviewed evaluations with results linked in this release.

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

JSD is lower-is-better. The article calls it both Jensen–Shannon distance and divergence; the precise implementation is not resolved by these descriptions. Matching held-out intervals does not establish external pretraining decontamination.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17

Profile review details

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

Stable record: alphagenome-2026-t3-protocol-9

Specifications

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	ProCapNet test peak regions, fold 5. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17
Split	Intersect ProCapNet fold-5 test peaks with regions that do not overlap AlphaGenome fold-0 training intervals. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17
Allowed inputs and adaptation	Reference DNA; predicted and observed base-resolution profiles on matched assay peaks. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17
Metrics as reported	jsd; pearsonr log total count Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17
Aggregation	Table3 reports task summary scalars; Extended Data Fig.3 shows per-cell-line comparisons. The inspected caption does not fully specify pooling across peaks/cell lines. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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.

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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

Historical gaps recorded on 2026-09-17

The catalogue now holds 4 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.

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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17

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 2026-09-29-06401fd5b220
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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 Peer-model test peaks Remove AlphaGenome training overlap Align assay predictions and observations Evaluate count and shape metrics Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 Peer-model test peaks Remove AlphaGenome training overlap Align assay predictions and observations Evaluate count and shape metrics Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 Peer-model test peaks Remove AlphaGenome training overlap Align assay predictions and observations Evaluate count and shape metrics Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 PRO-cap prediction on held-out peaks: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 PRO-cap prediction on held-out peaks: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 PRO-cap prediction on held-out peaks: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 ProCapNet test peak regions, fold 5. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

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

Download this release

Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t3-protocol-9

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 9
source table: 3
reference levels: metric: pearsonr log total count; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H16; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: jsd; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H17; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
comparison panels: id: paper-figure-7a042a3de250e599e1; title: PRO-cap prediction on held-out peaks (AlphaGenome paper); protocol id: alphagenome-2026-t3-protocol-9; dataset id: alphagenome-2026-t3-dataset-9; metric: pearsonr log total count; unit: correlation; direction: higher; result ids: alphagenome-2026-result-140530d4dbf2ebe8; alphagenome-2026-result-271e782e0fb76363; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 3 Track performance'!K16; 'Suppl Table 3 Track performance'!J16; context: Can reference sequence predict local PRO-cap profile shape and total signal at held-out peaks?; 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; id: paper-figure-d33ecf02bfb6ecda55; title: PRO-cap prediction on held-out peaks (AlphaGenome paper); protocol id: alphagenome-2026-t3-protocol-9; dataset id: alphagenome-2026-t3-dataset-9; metric: jsd; unit: dimensionless; direction: lower; result ids: alphagenome-2026-result-714a93b907108acb; alphagenome-2026-result-71c6b395ccee17cb; source ids: source-alphagenome-nature2026-tables; source locator: 'Suppl Table 3 Track performance'!K17; 'Suppl Table 3 Track performance'!J17; context: Can reference sequence predict local PRO-cap profile shape and total signal at held-out peaks?; 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 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 3 Track performance'!A16:N16; 'Suppl Table 3 Track performance'!A17:N17; Supplementary Methods p.21, continuous-track evaluation; Table8 ProCapNet port; Main paper Extended Data Fig.3f,g caption; paper: Extended Data Fig.3f,g caption; methods: p.21, Benchmarking Against Existing Methods; tables: Suppl Table 3 Track performance; evaluation index 9; sheet rows 16, 17; ambiguities: None recorded

Related records

Suggest a correction