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Borzoi (paper Table 3)

Borzoi (paper Table 3). A comparator reported by the AlphaGenome authors; protocol pages specify the dataset and adaptation.

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions

9 evaluations · 11 results

Overview

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

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

Evaluations and results

9 evaluations · 11 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Borzoi (paper Table 3)	Protocol: RNA expression correlation across genes (AlphaGenome paper) Dataset subset: RNA expression correlation across genes: evaluated data subset	0.765 Gene TPM (cross-gene pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): RNA expression correlation across genes Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J13
Configuration: Borzoi (paper Table 3)	Protocol: RNA expression correlation across genes (AlphaGenome paper) Dataset subset: RNA expression correlation across genes: evaluated data subset	0.449 Gene TPM normalized (cross-gene pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): RNA expression correlation across genes Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J15
Configuration: Borzoi (paper Table 3)	Protocol: histone ChIP-seq track prediction at 32 bp (AlphaGenome paper) Dataset subset: histone ChIP-seq track prediction at 32 bp: evaluated data subset	0.669 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): histone ChIP-seq track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J34
Configuration: Borzoi (paper Table 3)	Protocol: CAGE track prediction at 32 bp (AlphaGenome paper) Dataset subset: CAGE track prediction at 32 bp: evaluated data subset	0.713 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): CAGE track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J18
Configuration: Borzoi (paper Table 3)	Protocol: RNA-seq track prediction at 32 bp (AlphaGenome paper) Dataset subset: RNA-seq track prediction at 32 bp: evaluated data subset	0.747 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): RNA-seq track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J12
Configuration: Borzoi (paper Table 3)	Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper) Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset	0.46 Track @1bp (normal scale pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10
Configuration: Borzoi (paper Table 3)	Protocol: RNA expression correlation across tracks (AlphaGenome paper) Dataset subset: RNA expression correlation across tracks: evaluated data subset	0.497 Gene TPM normalized (cross-track pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): RNA expression correlation across tracks Compute per-gene cross-track correlation on normalized, gene-mean-centred expression. Aggregation: Pearson correlation across tracks. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J14
Configuration: Borzoi (paper Table 3)	Protocol: TF ChIP-seq track prediction at 32 bp (AlphaGenome paper) Dataset subset: TF ChIP-seq track prediction at 32 bp: evaluated data subset	0.522 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): TF ChIP-seq track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J37
Configuration: Borzoi (paper Table 3)	Protocol: ATAC track prediction at 32 bp (AlphaGenome paper) Dataset subset: ATAC track prediction at 32 bp: evaluated data subset	0.549 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): ATAC track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J31
Configuration: Borzoi (paper Table 3)	Protocol: DNase track prediction at 32 bp (AlphaGenome paper) Dataset subset: DNase track prediction at 32 bp: evaluated data subset	0.821 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Borzoi (paper Table 3): DNase track prediction at 32 bp Align predicted and experimental values on the same 32-bp tracks and test intervals. Aggregation: Pearson correlation; group summaries derive from individual track correlations. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J25
Configuration: Borzoi (paper Table 3)	Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper) Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset	0.75 Track @1bp (log1p scale pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J11

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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How it works

How this comparator was evaluated

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

Sources (3)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

A table label does not establish identity with any other catalogue configuration bearing the same name.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions

Profile review details

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

Stable record: alphagenome-2026-comparator-12f00a75002435bd

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.

Inputs, outputs and configuration
Property	Description and evidence
Reported method	Borzoi Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions
Exact checkpoint	Not established by the summary table; inspect the protocol and original implementation. · Needs further source review Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions
Model type	Not extracted or verified for this record.
Inputs	Not extracted or verified for this record.
Outputs	Not extracted or verified for this record.
Parameters	Not extracted or verified for this record.
Training data	Not extracted or verified for this record.
Context limits	Not extracted or verified for this record.
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Evidence

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

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.

15 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Reported method Borzoi Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Reported method Borzoi Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Reported method Borzoi Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	unextracted automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	unextracted automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	unextracted automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.limitations.0.text` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.limitations.0.text` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.limitations.0.text` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
How this comparator was evaluated The source table identifies Borzoi. Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: needs review

3 source records and release history

AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-comparator-12f00a75002435bd

areas: dna-genomes
entity level: method
configuration type: reported_configuration
version: Borzoi (paper Table 3)
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

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