AUPRC relative difference (ablation 'Conservation' (Retrained) relative to the AVI baseline row, ncVar column) of AVI ablation 'Conservation' (Retrained, AlphaGenome Atlas Table S2) on ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)
-4.26% AUPRC relative difference (ablation 'Conservation' (Retrained) relative to the AVI baseline row, ncVar column)
Methods
- Tested configuration
- AVI ablation 'Conservation' (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)
- Procedure
- AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2)
- Evaluation
- AVI Conservation (Retrained) on ncVar (AlphaGenome Atlas Table S2)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedAlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Conservation', column 'ncVar'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Not reported
- Adaptation
- Retrained
- Scoring implementation
- Percentage difference in AUPRC relative to the AVI baseline row
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result -4.26% Individual claims | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Table S2 (page 70), section 'Retrained', row 'Conservation', column 'ncVar' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check","automated-source-review"] · 2026-11-01 author reported Audit detailsRe-parsed Table S2 from a pdftotext -raw text layer of a 2026-11-01 retrieval and matched all 70 cells, with numeric value and metric, to the stored values. 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. Field: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Extraction artifact SHA-256: |
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-result-table-s2-retrained-no-conservation-ncvar-auprc-relative-difference
- metric
- auprc-relative-difference
- metric direction
- higher
- unit
- percent
- printed value
- -4.26%
- numeric value
- -4.26
- metric qualifier
- ablation 'Conservation' (Retrained) relative to the AVI baseline row, ncVar column
- source locator
- Table S2 (page 70), section 'Retrained', row 'Conservation', column 'ncVar'
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; automated-source-review; method note: Parsed from pdftotext -layout text of Table S2 with every row label and the column header asserted (extract/build_batch.py).; 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: b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453; retrieval url: https://www.medrxiv.org/content/10.64898/2026.09.16.26363192v1.full.pdf; note: Re-parsed Table S2 from a pdftotext -raw text layer of a 2026-11-01 retrieval and matched all 70 cells, with numeric value and metric, to the stored values. 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.