AUPRC (maximum over three random seeds; zero-shot) of GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4) on OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)
0.112 AUPRC (maximum over three random seeds; zero-shot)
Methods
- Tested configuration
- GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)
- Protocol
- OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4)
- Dataset
- OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)
- Procedure
- OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4)
- Evaluation
- Don’t replace non-conserved on OMIM (GPN-MSA Supplementary Table 4)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: Only mean and max over seeds are printed
- Evidence
- Author-reported evaluation · source checkedGPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'Don’t replace non-conserved', column 'OMIM' / 'max'
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
- Whole labelled set
- Adaptation
- zero-shot
- Scoring implementation
- Not reported
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 0.112 Individual claims | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 4 (PDF page 23), row 'Don’t replace non-conserved', column 'OMIM' / 'max' Version: bioRxiv v2, posted 2024-04-06 | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-14 author reported Audit detailsExtraction: Parsed the pdftotext 26.08.0 -layout text of the pinned PDF with extract/build_gpnmsa.py; header groups, 'mean max' header, the 17 row labels and the page are asserted. Independent review 2026-10-14: matched. Field: Source artifact SHA-256: Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-gpnmsa-result-ablation-no-replace-nonconserved-omim-max
- printed value
- 0.112
- numeric value
- 0.112
- metric
- auprc
- metric direction
- higher
- unit
- unitless
- metric qualifier
- maximum over three random seeds; zero-shot
- source locator
- Supplementary Table 4 (PDF page 23), row 'Don’t replace non-conserved', column 'OMIM' / 'max'
- missing metadata
- uncertainty: reason: unreported; note: Only mean and max over seeds are printed
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: An independent parser of the pdftotext layer of the pinned PDF read all 17 rows of Supplementary Table 4 and matched all 102 results (value, metric, mean or max, protocol, one configuration or method per row). Six cells also checked by hand.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: 10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4; retrieval url: https://www.biorxiv.org/content/10.1101/2023.10.10.561776v2.full.pdf; note: Extraction: Parsed the pdftotext 26.08.0 -layout text of the pinned PDF with extract/build_gpnmsa.py; header groups, 'mean max' header, the 17 row labels and the page are asserted. Independent review 2026-10-14: matched.