NTv3 cosine distance (Pearce et al. 2026 Figure 1b and 1c)
Zero-shot cosine distance between NTv3 embeddings of variant and reference sequences; the method behind the 'NTv3' column of Figure 1b and 1c according to the manuscript repository's plotting code.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: NTv3 cosine distance (Pearce et al. 2026 Figure 1b and 1c) | Protocol: EVEE deconfounded ClinVar SNV pathogenicity AUROC (Pearce et al. 2026 Figure 1c) Dataset: EVEE deconfounded ClinVar SNV benchmark (158,616 variants) | 0.71 AUROC (Deconfounded ClinVar SNVs, all consequence types (Overall row)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNTv3 on the EVEE deconfounded ClinVar SNV benchmark (Pearce et al. 2026) gfm-guide-20261014-protocol-evee-deconfounded-snv-auroc Aggregation: Not reported Interpretable 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 'NTv3' |
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 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: scripts/figure1/_heatmap_common.py · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f
Technical metadata and extraction receipts
Stable ID: gfm-guide-20261014-config-evee-ntv3-cosine
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- source locator
- Methods 'Baseline methods' and 'Covariance probe' (page 8); Figure 1 column labels
- reported name
- NTv3 (repository label 'NTv3 cosine dist')
- limitations
- Methods describe only a supervised NTv3 650M layer-11 logistic-regression probe; the cosine-distance variant, its model size and layer are named only in the plotting code. See the source's evidence concern.
- missing metadata
- version: reason: unreported; note: Model size and layer for the cosine-distance score are not stated
Related records
- configuration of: Nucleotide Transformer v3
- system: NTv3 on the EVEE deconfounded ClinVar SNV benchmark (Pearce et al. 2026)