Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
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 PredictionsAt 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 · 9 evaluations · 11 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Borzoi (paper Table 3): RNA expression correlation across genes Configuration: Borzoi (paper Table 3)Protocol: RNA expression correlation across genes (AlphaGenome paper)Dataset subset: RNA expression correlation across genes: evaluated data subset Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.765 Gene TPM
(cross-gene pearsonr) Unit: correlation · Direction: higher 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. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J13 Source checking is not independent reproduction. |
| 0.449 Gene TPM normalized
(cross-gene pearsonr) Unit: correlation · Direction: higher 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. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J15 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): histone ChIP-seq track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.669 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J34 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): CAGE track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.713 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J18 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): RNA-seq track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.747 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J12 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): Base-resolution RNA-seq prediction Configuration: Borzoi (paper Table 3)Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper)Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset Compare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.460 Track @1bp
(normal scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J10 Source checking is not independent reproduction. |
| 0.750 Track @1bp
(log1p scale pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J11 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): RNA expression correlation across tracks Configuration: Borzoi (paper Table 3)Protocol: RNA expression correlation across tracks (AlphaGenome paper)Dataset subset: RNA expression correlation across tracks: evaluated data subset Compute per-gene cross-track correlation on normalized, gene-mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.497 Gene TPM normalized
(cross-track pearsonr) Unit: correlation · Direction: higher 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. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J14 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): TF ChIP-seq track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.522 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J37 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): ATAC track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.549 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J31 Source checking is not independent reproduction. |
| Borzoi (paper Table 3): DNase track prediction at 32 bp 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 Align predicted and experimental values on the same 32-bp tracks and test intervals. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.821 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation; group summaries derive from individual track correlations. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J25 Source checking is not independent reproduction. |
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)
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 PredictionsStrengths and limitations
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-12f00a75002435bdSpecifications
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.
| Property | Description and evidence |
|---|---|
| Reported method | BorzoiSources (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 reviewSources (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. |
| 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 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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported method Borzoi Individual claims | 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 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 Borzoi Individual claims | AlphaGenome Nature 2026 supplementary methods '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 | 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 Borzoi Individual claims | AlphaGenome Nature 2026 supplementary comparison tables '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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 '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 | 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · 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
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.
Related records
- model: Borzoi (paper Table 3): TF ChIP-seq track prediction at 32 bp
- model: Borzoi (paper Table 3): histone ChIP-seq track prediction at 32 bp
- model: Borzoi (paper Table 3): RNA expression correlation across tracks
- model: Borzoi (paper Table 3): CAGE track prediction at 32 bp
- model: Borzoi (paper Table 3): Base-resolution RNA-seq prediction
- model: Borzoi (paper Table 3): DNase track prediction at 32 bp
- model: Borzoi (paper Table 3): RNA expression correlation across genes
- model: Borzoi (paper Table 3): ATAC track prediction at 32 bp
- model: Borzoi (paper Table 3): RNA-seq track prediction at 32 bp
- model: Borzoi (paper Table 3): Alternative polyadenylation coverage ratios