Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head
AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head. This is the configuration evaluated in the Nature paper, not an identification of the current hosted API revision.
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 PredictionsOverview
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
3 evaluations · 5 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head | Protocol: RNA expression correlation across tracks (AlphaGenome paper) Dataset subset: RNA expression correlation across tracks: evaluated data subset | 0.57 Gene TPM normalized
(cross-track pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCompute per-gene cross-track correlation on normalized, gene-mean-centred expression. Aggregation: Pearson correlation across tracks. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K14 |
| Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head | Protocol: RNA expression correlation across genes (AlphaGenome paper) Dataset subset: RNA expression correlation across genes: evaluated data subset | 0.52 Gene TPM normalized
(cross-gene pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCompute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K15 |
| Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head | Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper) Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset | 0.8 Track @1bp
(log1p scale pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCompare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K11 |
| Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head | Protocol: Base-resolution RNA-seq prediction (AlphaGenome paper) Dataset subset: Base-resolution RNA-seq prediction: evaluated data subset | 0.59 Track @1bp
(normal scale pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCompare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints. Aggregation: Pearson correlation; genome-track methods average individual track correlations for assay groups. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K10 |
| Configuration: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head | Protocol: RNA expression correlation across genes (AlphaGenome paper) Dataset subset: RNA expression correlation across genes: evaluated data subset | 0.8 Gene TPM
(cross-gene pearsonr) correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCompute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. AlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K13 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
Related profile: AlphaGenome. This page retains the exact record and its evaluation context.
How it works
Evaluated configuration
AlphaGenome trained on Borzoi fold-1, then fine-tuned with an additional RNA-seq head on Borzoi-matched tracks reprocessed at 1 bp and without Borzoi scaling. 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, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
- The publication result does not establish equivalence to another checkpoint or hosted service.
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-model-c4a6184e7c007e87Specifications
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 |
|---|---|
| Evaluated system | AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq headSources (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 |
| Checkpoint artifact | Not established for these paper scores; no released checkpoint is inferred. · 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 |
| Evaluation scope | Paper-evaluated AlphaGenome configurationSources (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
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluated system AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head 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 |
| Evaluated system AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head 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 |
| Evaluated system AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head 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 |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. 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 |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. 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 |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. 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 |
| Evaluation scope Paper-evaluated AlphaGenome configuration 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 |
| Evaluation scope Paper-evaluated AlphaGenome configuration 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 |
| Evaluation scope Paper-evaluated AlphaGenome configuration 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 |
| Limitation The publication result does not establish equivalence to another checkpoint or hosted service. 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
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
Technical metadata and extraction receipts
Stable ID: alphagenome-2026-model-c4a6184e7c007e87
- areas
- dna-genomes
- entity level
- method
- configuration type
- paper_evaluation
- version
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head
- 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
- family: AlphaGenome
- model: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across genes
- model: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: Base-resolution RNA-seq prediction
- model: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across tracks
- subject: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: family