AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)

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5 evaluations · 5 results. Different protocols are not a single leaderboard.

Sorted by AUPRC relative difference (ablation 'AlphaMissense' (Retrained) 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 'AlphaMissense' (Retrained) relative to the AVI baseline row, ClinVar column)	AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, ncVar column)	AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, SGE column)	AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, TraitGym Complex column)	AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, TraitGym Mendelian column)
AVI ablation 'AlphaMissense' (Retrained, 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	-2.51%	Not reported	Not reported	Not reported	Not reported
AVI ablation 'AlphaMissense' (Retrained, 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	0.18%	Not reported	Not reported	Not reported
AVI ablation 'AlphaMissense' (Retrained, 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	-0.45%	Not reported	Not reported
AVI ablation 'AlphaMissense' (Retrained, 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	0.67%	Not reported
AVI ablation 'AlphaMissense' (Retrained, 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	0.75%

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ClinVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ClinVar 2025-06-15 pathogenic versus benign variants, AVI evaluation set	-2.51% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, ClinVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on ClinVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-clinvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'ClinVar'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.18% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'ncVar'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-0.45% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'SGE'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, TraitGym Complex column, AUPRC (AlphaGenome Atlas Table S2) Dataset subset: TraitGym Complex traits after AVI positional filtering (AlphaGenome Atlas)	0.67% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, TraitGym Complex column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on TraitGym Complex (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-traitgym-complex Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'TraitGym Complex'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, TraitGym Mendelian column, AUPRC (AlphaGenome Atlas Table S2) Dataset subset: TraitGym Mendelian traits after AVI positional filtering (AlphaGenome Atlas)	0.75% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, TraitGym Mendelian column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on TraitGym Mendelian (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-traitgym-mendelian Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'TraitGym Mendelian'

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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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)

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Technical metadata and extraction receipts

Stable ID: ag-atlas-20261019-config-avi-ablation-retrained-no-alphamissense

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: AlphaMissense
parameters: Table S2 section 'Retrained', row 'AlphaMissense'. Ensemble of six retrained models with the same hyperparameters and checkpoint selection as AVI.
source locator: Table S2 and caption (page 70); Methods 'Feature Ablations' (page 27)

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