Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-trainingExplanatory 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 |
|---|---|
| Dataset and biological context | Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Split | Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. This comparison uses Borzoi fold-1.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Allowed inputs and adaptation | Reference sequence; the additional AlphaGenome RNA-seq head and unscaled Borzoi predictions repeated across each original 32-bp bin.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Metrics as reported | Track @1bp (log1p scale pearsonr); Track @1bp (normal scale pearsonr)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Aggregation | Pearson correlation; genome-track methods average individual track correlations for assay groups.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training |
| Entity type | protocol |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Conceptual summary of the cited procedure; model-specific conditions are given below.
Can reference sequence predict the spatial distribution of RNA-seq coverage at nucleotide resolution?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-trainingCompare base-resolution measured coverage with both predictions on normal and log1p scales, keeping these as separate endpoints.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-trainingRelease 2026-09-17-a757f4af4277 · 2 evaluations · 4 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Borzoi (paper Table 3): Base-resolution RNA-seq prediction Model: Borzoi (paper Table 3) · Benchmark: Base-resolution RNA-seq prediction (AlphaGenome paper) · Dataset: 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. |
| 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 · Benchmark: Base-resolution RNA-seq prediction (AlphaGenome paper) · Dataset: 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 | ||
| 0.80 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'!K11 Source checking is not independent reproduction. |
| 0.59 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'!K10 Source checking is not independent reproduction. |
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-t3-protocol-5Trace 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.
42 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram steps ["Matched held-out RNA tracks","Restore common signal scale","Upsample Borzoi and mask unmappable positions","Compare normal/log1p correlations"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Diagram title Base-resolution RNA-seq prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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 |
| Dataset and biological context Borzoi-matched RNA-seq tracks reprocessed at base resolution; retain highly concordant tracks and mask Borzoi unmappable positions. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A10:N10; 'Suppl Table 3 Track performance'!A11:N11; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 5; sheet rows 10, 11; methods: p.19, Training / Pre-training 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-a757f4af4277 · Record review: needs review
Stable ID: alphagenome-2026-t3-protocol-5