AlphaGenome splice composite, raw scores (Lu et al. 2025)
AlphaGenome splice variant score from the original AlphaGenome publication: a weighted sum of raw splice site usage, splice site and splice junction scores.
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaGenome splice composite, raw scores (Lu et al. 2025) | Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2) | 0.708 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All splice outputs (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'All splice outputs (raw)', bar label |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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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-config-alphagenome-splice-outputs-raw
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- foundation_model
- reported name
- All splice outputs (raw)
- parameters
- Official AlphaGenome API (deepmind.google.com/science/alphagenome), 1 Mbp input context centred on the variant, organism human, all output modalities enabled (5,930 human genomic annotations across 11 modalities). Splice variant scorer defined in the original AlphaGenome publication: weighted sum of raw scores from splice site usage, splice site and splice junction outputs. Weights not restated in this paper.
- access reuse
- Official AlphaGenome API
- source locator
- Methods 'AlphaGenome' (pages 16 to 17); Supplementary Figure S2
- missing metadata
- model version: reason: unreported; note: API model version and query date not printed.