AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2)
Score the ncVar evaluation set with the full AVI model and with each ablated AVI model, reporting the full model's AUPRC and each ablation's percentage difference from it.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
14 recorded evaluations, 14 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
14 evaluations · 14 results. Different protocols are not a single leaderboard.
Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) · Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)
Sorted by AUPRC (AVI baseline row, ncVar 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 | AUPRC (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, ncVar column) | AUPRC relative difference (ablation '+ No Indel Type' (Features Set to Zero) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'All except AlphaGenome' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'AlphaGenome' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Cactus' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Consequence' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Conservation' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Indel Type' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'No AlphaMissense Indel Features' (Features Set to Zero) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'PhastCons' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Protein' (Retrained) relative to the AVI baseline row, ncVar column) | AUPRC relative difference (ablation 'Splicing Removed Only' (Retrained) relative to the AVI baseline row, ncVar column) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AVI six-model ensemble (AlphaGenome Atlas v1)Evaluation | 0.936 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'All except AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | -3.82% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | -17.6% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | 0.18% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'Cactus' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | -0.91% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'Consequence' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.1% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'Conservation' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | -4.26% | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'Indel Type' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | -0.44% | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'PhastCons' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.04% | Not reported | Not reported |
| AVI ablation 'Protein' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.1% | Not reported |
| AVI ablation 'Splicing Removed Only' (Retrained, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | -15% |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | Not reported | 0.06% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AVI ablation 'No AlphaMissense Indel Features' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0% | Not reported | Not reported | Not reported |
| AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)Evaluation | Not reported | Not reported | 0.06% | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 14 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AVI AVI Model (Baseline) on ncVar (AlphaGenome Atlas Table S2)
- AVI All except AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI AlphaMissense (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Cactus (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Consequence (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Conservation (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Indel Type (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI PhastCons (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Protein (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI Splicing Removed Only (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 14
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-11-02-a7f03c9e55a5. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
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Evidence table
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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-protocol-table-s2-ncvar
- areas
- dna-genomes
- contexts
- research
- metric
- auprc
- metric direction
- higher
- source locator
- Table S2 and caption (page 70); Methods 'Feature Ablations' (page 27)
- limitations
- Table S2 does not say which variants (SNVs, indels, test or validation split) each column uses; its AVI values differ from Fig. 2 and fig. S7 for ClinVar and SGE.; The caption says the best result per column is bolded; bolding is not captured in the text layer and is not recorded.; No uncertainty is printed.
- task link exemption
- No task or benchmark in the store covers ncVar noncoding pathogenic variants; left unlinked on purpose so the discrepancy rules treat its scope as unknown rather than guess (#208). Reviewed 2026-11-01.
Related records
- uses data: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)
- assessment: AVI AVI Model (Baseline) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI All except AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI AlphaMissense (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Cactus (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Consequence (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Conservation (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Indel Type (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI PhastCons (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Protein (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI Splicing Removed Only (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI No AlphaMissense Indel Features (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2)
- assessment: AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2)