AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)
Frozen AVI ensemble without AlphaMissense indel imputation and with indel-type features set to zero.
Overview
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Evaluations and results
5 evaluations · 5 results. Different protocols are not a single leaderboard.
Sorted by AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, ClinVar column) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, ClinVar column) | AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, SGE column) | AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, TraitGym Complex column) | AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, TraitGym Mendelian column) |
|---|---|---|---|---|---|---|
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | AVI feature ablation, ClinVar column, AUPRC (AlphaGenome Atlas Table S2), ClinVar 2025-06-15 pathogenic versus benign variants, AVI evaluation set | -0.4% | Not reported | Not reported | Not reported | Not reported |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2), ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas) | Not reported | 0.06% | Not reported | Not reported | Not reported |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2), Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas) | Not reported | Not reported | -5.14% | Not reported | Not reported |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | AVI feature ablation, TraitGym Complex column, AUPRC (AlphaGenome Atlas Table S2), TraitGym Complex traits after AVI positional filtering (AlphaGenome Atlas) | Not reported | Not reported | Not reported | 0% | Not reported |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | AVI feature ablation, TraitGym Mendelian column, AUPRC (AlphaGenome Atlas Table S2), TraitGym Mendelian traits after AVI positional filtering (AlphaGenome Atlas) | Not reported | Not reported | Not reported | Not reported | 0% |
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Evidence
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages)
Technical metadata and extraction receipts
Stable ID: ag-atlas-20261019-config-avi-ablation-zero-alphamissense-indel-and-indel-type
- areas
- dna-genomes
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- + No Indel Type
- parameters
- Table S2 section 'Features Set to Zero', row '+ No Indel Type'. Inference-time zeroing on the frozen AVI ensemble; '+' applies 'No Indel Type' to the row above.
- source locator
- Table S2 and caption (page 70); Methods 'Feature Ablations' (page 27)
Related records
- configuration of: AlphaGenome Variant Impact (AVI)
- system: AVI + No Indel Type (Features Set to Zero) on ClinVar (AlphaGenome Atlas Table S2)
- system: AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2)
- system: AVI + No Indel Type (Features Set to Zero) on SGE (AlphaGenome Atlas Table S2)
- system: AVI + No Indel Type (Features Set to Zero) on TraitGym Complex (AlphaGenome Atlas Table S2)
- system: AVI + No Indel Type (Features Set to Zero) on TraitGym Mendelian (AlphaGenome Atlas Table S2)