AUROC (Deconfounded ClinVar SNVs, all consequence types (Overall row)) of GPN-MSA hg38 scores, pre-computed (Pearce et al. 2026) on EVEE deconfounded ClinVar SNV benchmark (158,616 variants)
0.952 AUROC (Deconfounded ClinVar SNVs, all consequence types (Overall row))
Methods
- Tested configuration
- GPN-MSA hg38 scores, pre-computed (Pearce et al. 2026)
- Protocol
- EVEE deconfounded ClinVar SNV pathogenicity AUROC (Pearce et al. 2026 Figure 1c)
- Dataset
- EVEE deconfounded ClinVar SNV benchmark (158,616 variants)
- Procedure
- EVEE deconfounded ClinVar SNV pathogenicity AUROC (Pearce et al. 2026 Figure 1c)
- Evaluation
- GPN-MSA on the EVEE deconfounded ClinVar SNV benchmark (Pearce et al. 2026)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedInterpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4; EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf; EVEE manuscript repository: scripts/figure1/_heatmap_common.py · Figure 1c (page 3, raster; matched to repository figures/figure1/fig1c_deconf_heatmap.pdf text layer), row 'Overall (n=158,616, 27.8%P)', column 'GPN-MSA'
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
- Deconfounded subset; gene-holdout cross-validation for supervised probes
- Adaptation
- Not reported
- 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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.952 Individual claims | EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf Figure 1c (page 3, raster; matched to repository figures/figure1/fig1c_deconf_heatmap.pdf text layer), row 'Overall (n=158,616, 27.8%P)', column 'GPN-MSA' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f | source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-14 independent paper Audit detailsValue matches. Transcribed, not reproduced. Baseline run by the EVEE authors, who did not develop it; independent_paper accepted. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.952 Individual claims | EVEE manuscript repository: scripts/figure1/_heatmap_common.py Figure 1c (page 3, raster; matched to repository figures/figure1/fig1c_deconf_heatmap.pdf text layer), row 'Overall (n=158,616, 27.8%P)', column 'GPN-MSA' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f | source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-14 independent paper Audit detailsValue matches. Transcribed, not reproduced. Baseline run by the EVEE authors, who did not develop it; independent_paper accepted. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.952 Individual claims | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Figure 1c (page 3, raster; matched to repository figures/figure1/fig1c_deconf_heatmap.pdf text layer), row 'Overall (n=158,616, 27.8%P)', column 'GPN-MSA' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | source checked ["source-hash-verification","pdf-text-parse","rendered-source-visual-check","independent-cell-check"] · 2026-10-14 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsValue matches. Transcribed, not reproduced. Baseline run by the EVEE authors, who did not develop it; independent_paper accepted. Field: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF (2026-10-14T12:02:25Z). bioRxiv stamps the PDF on each download (XMP ModifyDate, MetadataDate, DocumentID and InstanceID, the Info ModDate and the trailer /ID), so later retrievals differ. The extractor's copy was not retained, so the pinned bytes could not be re-verified. The independent reviewer's retrieval on 2026-10-14 (5,466,701 bytes, 26 pages, ModDate D:20261014063735-07'00') had SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; its Figure 1c and 1d match the repository vector PDFs cell for cell in the Overall rows, and the quoted Methods and Competing interests sentences are present. Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Original source · bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11)
- EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f
- EVEE manuscript repository: scripts/figure1/_heatmap_common.py · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f
Technical metadata and extraction receipts
Stable ID: gfm-guide-20261014-result-evee-deconfounded-gpn-msa
- metric
- auroc
- metric direction
- higher
- unit
- unitless
- printed value
- 0.952
- numeric value
- 0.952
- source locator
- Figure 1c (page 3, raster; matched to repository figures/figure1/fig1c_deconf_heatmap.pdf text layer), row 'Overall (n=158,616, 27.8%P)', column 'GPN-MSA'
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; pdf-text-parse; rendered-source-visual-check; independent-cell-check; method note: Overall row parsed by the reviewer's own script (review/check_gfm_guide.py) from the repository vector PDF of Figure 1c (SHA-256 matches the pinned record), column order taken from the pinned plotting code and checked against a 300 dpi render of page 3 of a fresh copy of the paper (SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; bioRxiv stamps each download, see the source's hash_scope).; reviewer: claude; reviewer note: Independent Claude (Opus 5.5) review agent for PR #150; did not extract this batch; no human review claimed; date: 2026-10-14; artifact sha256: 1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8; retrieval url: https://www.biorxiv.org/content/biorxiv/early/2026/07/11/2026.04.10.717844.full.pdf; note: Value matches. Transcribed, not reproduced. Baseline run by the EVEE authors, who did not develop it; independent_paper accepted.
- metric qualifier
- Deconfounded ClinVar SNVs, all consequence types (Overall row)