Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
chrombpnet (paper Table 4). A comparator reported by the AlphaGenome authors; protocol pages specify the dataset and adaptation.
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
Release 2026-09-17-d277315f7d76 · 11 evaluations · 11 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| chrombpnet (paper Table 4): SPI1 binding QTL classification Configuration: chrombpnet (paper Table 4)Protocol: SPI1 binding QTL classification (AlphaGenome paper)Dataset subset: SPI1 binding QTL classification: evaluated data subset 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 Configuration: chrombpnet (paper Table 4)Protocol: European-ancestry LCL caQTL classification (AlphaGenome paper)Dataset subset: European-ancestry LCL caQTL classification: evaluated data subset 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) 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 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 Configuration: chrombpnet (paper Table 4)Protocol: African-ancestry LCL caQTL classification (AlphaGenome paper)Dataset subset: African-ancestry LCL caQTL classification: evaluated data subset 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 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 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 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 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 Configuration: chrombpnet (paper Table 4)Protocol: Microglia caQTL effect-size prediction (AlphaGenome paper)Dataset subset: Microglia caQTL effect-size prediction: evaluated data subset 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 Configuration: chrombpnet (paper Table 4)Protocol: Yoruba LCL dsQTL classification (AlphaGenome paper)Dataset subset: Yoruba LCL dsQTL classification: evaluated data subset 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 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 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 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 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 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 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. |
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.
No source-reviewed explanatory claims are recorded here yet.
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-comparator-7f204b96b993dca1Explanatory 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.
| Property | Description and evidence |
|---|---|
| Reported method | chrombpnetSources (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 reviewSources (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. |
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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported method chrombpnet Individual claims | 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Reported method chrombpnet Individual claims | AlphaGenome Nature 2026 supplementary methods '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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Reported method chrombpnet Individual claims | AlphaGenome Nature 2026 supplementary comparison tables '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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims | 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims | AlphaGenome Nature 2026 supplementary methods '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 | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables '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 | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. Individual claims | 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 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_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 '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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| 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 '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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| 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 '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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: alphagenome-2026-comparator-7f204b96b993dca1