Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Alternative polyadenylation coverage ratios (AlphaGenome paper)
Can predicted RNA coverage recover relative distal-versus-proximal polyadenylation-site usage?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21At a glance
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 |
|---|---|
| Dataset and biological context | PolyADB-annotated sites near gene boundaries; observed coverage ratios from tissue-pooled GTEx RNA-seq.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| Split | Held-out test sites; the task paragraph does not identify the exact fold/site manifest.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| Allowed inputs and adaptation | RNA-seq predictions and PolyADB site annotations; compare Borzoi coverage-ratio predictions.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| Metrics as reported | spearmanrAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| Aggregation | Spearman correlation of predicted versus observed coverage ratios.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| 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'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 |
| 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. |
How it works
Conceptual summary of the cited procedure; model-specific conditions are given below.
Read the diagram as text
- Held-out annotated polyadenylation sites
- Derive predicted coverage ratios
- Compare with pooled observed ratios
- Quarantine conflicting scalar reports
What is tested
Can predicted RNA coverage recover relative distal-versus-proximal polyadenylation-site usage?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21Procedure
Derive polyadenylation-centric coverage ratios and compare with observed ratios for the distal/proximal sites.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21Tested models and results
Release 2026-09-17-a757f4af4277 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
Strengths and limitations
Limitations and conditions
- QUARANTINED NUMERICAL COMPARISON: Table3 row21 and article Sec9/Extended Data Fig6a report different model/comparator values. Preserve both origins; do not resolve the discrepancy or rank models from this row.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
- This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
- Primary artifact values differ and their evaluation equivalence is unresolved. The affected comparison is withheld from published result tables.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-t3-protocol-12Evidence table
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.
45 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'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 Alternative polyadenylation coverage ratios: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 Alternative polyadenylation coverage ratios: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 Alternative polyadenylation coverage ratios: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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 PolyADB-annotated sites near gene boundaries; observed coverage ratios from tissue-pooled GTEx RNA-seq. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 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-a757f4af4277 · Record review: needs review
- 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-t3-protocol-12
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 12
- source table
- 3
- reference levels
- metric: spearmanr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H21; note: Source reference quantity for relative-performance calculation, not a measured baseline run.