Configuration

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 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

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

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: chrombpnet (paper Table 4)	Protocol: SPI1 binding QTL classification (AlphaGenome paper) Dataset subset: SPI1 binding QTL classification: evaluated data subset	0.356 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L36
Configuration: chrombpnet (paper Table 4)	Protocol: European-ancestry LCL caQTL classification (AlphaGenome paper) Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset	0.279 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L22
Configuration: chrombpnet (paper Table 4)	Protocol: Zero-shot CAGI5 MPRA activity-effect prediction (chrombpnet-matched comparison) (AlphaGenome paper) Dataset subset: Zero-shot CAGI5 MPRA activity-effect prediction (chrombpnet-matched comparison): evaluated data subset	0.544 mean_pearsonr_all correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Mean Pearson correlation over the included locus/context comparisons; Table4 rows10 and11 have different AlphaGenome scalars and must remain separate. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L10
Configuration: chrombpnet (paper Table 4)	Protocol: African-ancestry LCL caQTL classification (AlphaGenome paper) Dataset subset: African-ancestry LCL caQTL classification: evaluated data subset	0.415 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L20
Configuration: chrombpnet (paper Table 4)	Protocol: Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper) Dataset subset: Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset	0.658 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L34
Configuration: chrombpnet (paper Table 4)	Protocol: SPI1 binding QTL effect-size prediction (AlphaGenome paper) Dataset subset: SPI1 binding QTL effect-size prediction: evaluated data subset	0.52 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L38
Configuration: chrombpnet (paper Table 4)	Protocol: Microglia caQTL effect-size prediction (AlphaGenome paper) Dataset subset: Microglia caQTL effect-size prediction: evaluated data subset	0.61 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L32
Configuration: chrombpnet (paper Table 4)	Protocol: Yoruba LCL dsQTL classification (AlphaGenome paper) Dataset subset: Yoruba LCL dsQTL classification: evaluated data subset	0.543 auPRC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: auPRC over causal/noncausal labels. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L24
Configuration: chrombpnet (paper Table 4)	Protocol: African-ancestry LCL caQTL effect-size prediction (AlphaGenome paper) Dataset subset: African-ancestry LCL caQTL effect-size prediction: evaluated data subset	0.674 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L26
Configuration: chrombpnet (paper Table 4)	Protocol: Yoruba LCL dsQTL effect-size prediction (AlphaGenome paper) Dataset subset: Yoruba LCL dsQTL effect-size prediction: evaluated data subset	0.772 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L30
Configuration: chrombpnet (paper Table 4)	Protocol: European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper) Dataset subset: European-ancestry LCL caQTL effect-size prediction: evaluated data subset	0.525 pearsonr correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Pearson correlation against reported effect sizes of the causal/significant QTL set. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L28

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

Use this model

How it works, versions and access

Related profile: ChromBPNet. This page retains the exact record and its evaluation context.

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)

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 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

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
Property	Description and evidence
Reported method	chrombpnet 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 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 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 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.
Access	Not extracted or verified for this record.
Code licence	Not extracted or verified for this record.
Weights licence	Not extracted or verified for this record.

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.

18 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 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

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-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.

Related records

Suggest a correction