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chrombpnet (paper Table 4)

chrombpnet (paper Table 4). 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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

11 evaluations · 11 metric rows

At a glance

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

Release 2026-09-17-d277315f7d76 · 11 evaluations · 11 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
chrombpnet (paper Table 4): SPI1 binding QTL classification

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.356366 auPRC

Unit: dimensionless · Direction: higher

Aggregation: auPRC over causal/noncausal labels.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L36

Source checking is not independent reproduction.

chrombpnet (paper Table 4): European-ancestry LCL caQTL classification

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.27872 auPRC

Unit: dimensionless · Direction: higher

Aggregation: auPRC over causal/noncausal labels.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L22

Source checking is not independent reproduction.

chrombpnet (paper Table 4): Zero-shot CAGI5 MPRA activity-effect prediction (chrombpnet-matched comparison)

Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.

Author-reported evaluation · Evaluation metadata: needs review

0.544 mean_pearsonr_all

Unit: correlation · Direction: higher

Aggregation: Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L10

Source checking is not independent reproduction.

chrombpnet (paper Table 4): African-ancestry LCL caQTL classification

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.414834 auPRC

Unit: dimensionless · Direction: higher

Aggregation: auPRC over causal/noncausal labels.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L20

Source checking is not independent reproduction.

chrombpnet (paper Table 4): Coronary smooth-muscle caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.658407 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L34

Source checking is not independent reproduction.

chrombpnet (paper Table 4): SPI1 binding QTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.520421 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L38

Source checking is not independent reproduction.

chrombpnet (paper Table 4): Microglia caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.609557 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L32

Source checking is not independent reproduction.

chrombpnet (paper Table 4): Yoruba LCL dsQTL classification

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.54317 auPRC

Unit: dimensionless · Direction: higher

Aggregation: auPRC over causal/noncausal labels.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L24

Source checking is not independent reproduction.

chrombpnet (paper Table 4): African-ancestry LCL caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.673739 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L26

Source checking is not independent reproduction.

chrombpnet (paper Table 4): Yoruba LCL dsQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.772194 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L30

Source checking is not independent reproduction.

chrombpnet (paper Table 4): European-ancestry LCL caQTL effect-size prediction

Use the source’s local log-fold-change scorer, select the task-specific cell/assay tracks and compare against the source-provided QTL labels or measured effects.

Author-reported evaluation · Evaluation metadata: needs review

0.524861 pearsonr

Unit: correlation · Direction: higher

Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set.

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L28

Source checking is not independent reproduction.

How it works

How this comparator was evaluated

The source table identifies chrombpnet. Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.

Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Profile review details

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

Stable record: alphagenome-2026-comparator-7f204b96b993dca1

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
PropertyDescription and evidence
Reported methodchrombpnet
Sources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption
Exact checkpointNot 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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption
Model typeNot extracted or verified for this record.
InputsNot extracted or verified for this record.
OutputsNot extracted or verified for this record.
ParametersNot extracted or verified for this record.
Training dataNot extracted or verified for this record.
Context limitsNot extracted or verified for this record.
AccessNot extracted or verified for this record.
Code licenceNot extracted or verified for this record.
Weights licenceNot extracted or verified for this record.

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 2026-09-17-d277315f7d76
Property and statementOriginal source and locationReview and provenance
Reported method

chrombpnet

Individual claims
alphagenome: Journal full-text XML

Original source ↗

'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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

chrombpnet

Individual claims
AlphaGenome Nature 2026 supplementary methods

Original source ↗

'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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

chrombpnet

Individual claims
AlphaGenome Nature 2026 supplementary comparison tables

Original source ↗

'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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 chrombpnet. Compute locus/context Pearson correlations between predicted and observed effects. The Borzoi strategy uses its reported scoring windows and modified matching; the ChromBPNet comparison excludes the unavailable TERT-GBM context.

Individual claims
alphagenome: Journal full-text XML

Original source ↗

'Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption

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

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: alphagenome-2026-comparator-7f204b96b993dca1

areas
dna-genomes
entity level
method
configuration type
reported_configuration
version
chrombpnet (paper Table 4)
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 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption; 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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