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benchmark · protocol

Base-resolution RNA-seq prediction (AlphaGenome paper)

Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

2 evaluations · 4 metric rows

At a glance

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
PropertyDescription and evidence
Dataset and biological contextBorzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
SplitHeld-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Allowed inputs and adaptationReference sequence; the additional AlphaGenome RNA-seq head and unscaled Borzoi predictions repeated across each original 32-bp bin.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Metrics as reportedTrack @1bp (log1p scale pearsonr); Track @1bp (normal scale pearsonr)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
AggregationPearson correlation; genome-track methods average individual track correlations for assay groups.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
UncertaintyNot reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
Entity typeprotocol
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

How it works

Base-resolution RNA-seq prediction: evaluation procedure

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

Base-resolution RNA-seq prediction: evaluation procedureMatched held-out RNA tracks. Then: Restore common signal scale. Then: Upsample Borzoi and mask unmappable positions. Then: Compare normal/log1p correlationsMatched held-out RNA tracksRestore common signal scaleUpsample Borzoi and maskunmappable positionsCompare normal/log1pcorrelations
Read the diagram as text
  1. Matched held-out RNA tracks
  2. Restore common signal scale
  3. Upsample Borzoi and mask unmappable positions
  4. Compare normal/log1p correlations
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

What is tested

Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

Procedure

Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

Tested models and results

Release 2026-09-17-a757f4af4277 · 2 evaluations · 4 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
Borzoi (paper Table 3): Base-resolution RNA-seq prediction

Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.

Author-reported evaluation · Evaluation metadata: needs review

0.460 Track @1bp (normal scale pearsonr)

Unit: correlation · Direction: higher

Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10

Source checking is not independent reproduction.

0.750 Track @1bp (log1p scale pearsonr)

Unit: correlation · Direction: higher

Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J11

Source checking is not independent reproduction.

AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: Base-resolution RNA-seq prediction

Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.

Author-reported evaluation · Evaluation metadata: needs review

0.80 Track @1bp (log1p scale pearsonr)

Unit: correlation · Direction: higher

Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K11

Source checking is not independent reproduction.

0.59 Track @1bp (normal scale pearsonr)

Unit: correlation · Direction: higher

Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K10

Source checking is not independent reproduction.

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

  • Upsampled Borzoi output has no new sub-bin information; normal-scale gains partly reflect exon-boundary resolution. The paper restricts inclusion to tracks meeting its data-concordance check.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
  • This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training
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-5

Evidence table

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-a757f4af4277
Property and statementOriginal source and locationReview 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'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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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'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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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'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Format: xlsx

Inspected artifact

Diagram steps

["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"]

Individual claims
alphagenome: Journal full-text XML

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Format: original_artifact

Inspected artifact

Diagram steps

["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"]

Individual claims
AlphaGenome Nature 2026 supplementary methods

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Format: original_pdf

Inspected artifact

Diagram steps

["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"]

Individual claims
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Diagram title

Base-resolution RNA-seq prediction: evaluation procedure

Individual claims
alphagenome: Journal full-text XML

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Inspected artifact

Diagram title

Base-resolution RNA-seq prediction: evaluation procedure

Individual claims
AlphaGenome Nature 2026 supplementary methods

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

Base-resolution RNA-seq prediction: evaluation procedure

Individual claims
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Source artifact SHA-256: 833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154

Hash scope: SHA-256 of exact retrieved original artifact bytes

Format: xlsx

Inspected artifact

Dataset and biological context

Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions.

Individual claims
alphagenome: Journal full-text XML

Original source ↗

'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training

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

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Field: attributes.profile.facts.0.value

Source artifact SHA-256: d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36

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Sources and history

Release 2026-09-17-a757f4af4277 · Record review: needs review

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t3-protocol-5

areas
dna-genomes
entity level
protocol
version
Nature version of record, 28 January 2026
source evaluation index
5
source table
3
reference levels
metric: Track @1bp (normal scale pearsonr); printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H10; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: Track @1bp (log1p scale pearsonr); printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H11; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
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