AlphaGenome results depend on the scoring method
Evaluation finding of AlphaGenome
Lu et al. report that AlphaGenome is highly sensitive to the method used to extract scores: with the recommended all-output maximum-quantile score it ranks first on non-splice intronic (0.960) and synonymous (0.919) ClinVar SNVs but reaches 0.592 on canonical splice SNVs, where the raw splice site usage score reaches 0.779 and the original publication's splice scorer 0.708 (Supplementary Figure S2).
Descriptive fact transcribed from the pinned source.
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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field evaluation_finding Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
| Source location Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
| Claimed value Lu et al. report that AlphaGenome is highly sensitive to the method used to extract scores: with the recommended all-output maximum-quantile score it ranks first on non-splice intronic (0.960) and synonymous (0.919) ClinVar SNVs but reaches 0.592 on canonical splice SNVs, where the raw splice site usage score reaches 0.779 and the original publication's splice scorer 0.708 (Supplementary Figure S2). Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
| Description Descriptive fact transcribed from the pinned source. Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
| Relationship: subject catalog-model-alphagenome Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
| Name AlphaGenome results depend on the scoring method Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2 Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Original source · bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages)
Technical metadata and extraction receipts
Stable ID: lu-hetero-20261019-claim-alphagenome-scorer-sensitivity
- field
- evaluation_finding
- value
- Lu et al. report that AlphaGenome is highly sensitive to the method used to extract scores: with the recommended all-output maximum-quantile score it ranks first on non-splice intronic (0.960) and synonymous (0.919) ClinVar SNVs but reaches 0.592 on canonical splice SNVs, where the raw splice site usage score reaches 0.779 and the original publication's splice scorer 0.708 (Supplementary Figure S2).
- source locator
- Discussion paragraph 1 (page 10); Methods 'AlphaGenome' (pages 16 to 17); Figure 1; Supplementary Figure S2
- review
- method: source-hash-verification; automated-source-review; scope-review; method note: Statement asserted in the pdftotext -layout text; numbers asserted against the figure transcription.; reviewer: claude; reviewer note: Independent Claude review agent for PR #214, 2026-11-01; did not extract this batch; no human review claimed.; date: 2026-11-01; artifact sha256: 5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2; retrieval url: https://www.biorxiv.org/content/10.1101/2025.09.05.674459v2.full.pdf; note: Checked the claim's statements against the cited pages of a 2026-11-01 retrieval. The 2026-11-01 retrieval is stamped differently from the pinned bytes (different SHA-256); re-running the extractor on it, with only the hash assertion relaxed, reproduced batch.jsonl byte for byte. Verdict in docs/reviews/2026-11-01-alphagenome-atlas-lu-brandes.md.
Related records
- subject: AlphaGenome