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NTv3 650M layer-11 embedding probe (Pearce et al. 2026 Figure 1d)

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The column labelled 'NTv3' in Figure 1b and 1c is not the method the Methods describe. The manuscript repository's plotting code (scripts/figure1/_heatmap_common.py at e5e4a43) renames 'NTv3 cosine dist' to 'NTv3' and drops 'NTv3 subref probe', whereas Methods 'Baseline methods' describe NTv3 650M layer-11 embeddings with L2-regularised logistic regression under 5-fold gene-holdout cross-validation. Figure 1d's NTv3 column is the supervised subref probe. The SNV and deconfounded NTv3 values are recorded as a zero-shot embedding distance.Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Figure 1b and 1c, column 'NTv3' (page 3); Methods 'Baseline methods', NTv3 (page 8); repository scripts/figure1/_heatmap_common.py RENAME_MAP and DROP_METHODS

AlphaMissense's 'Overall' cell in Figure 1b and 1c is its missense AUROC. The plotting code blanks AlphaMissense outside missense and copies the Missense value into the Overall row (scripts/figure1/_heatmap_common.py, am_ov_mask), so it is computed on a different, missense-only population from the other methods' Overall cells.Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Figure 1b and 1c, row 'Overall', column 'AlphaMissense' (page 3); repository scripts/figure1/_heatmap_common.py prepare()

L2-regularised logistic regression on alternate-minus-reference NTv3 650M layer-11 embeddings (1,536-D) over 8,192 bp windows, 5-fold gene-holdout cross-validation.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NTv3 650M layer-11 embedding probe (Pearce et al. 2026 Figure 1d)	Protocol: EVEE ClinVar indel pathogenicity AUROC (Pearce et al. 2026 Figure 1d) Dataset: EVEE ClinVar indel benchmark (73,961 indels)	0.828 AUROC (ClinVar indels, all strata (Overall row); supervised on indels) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The column labelled 'NTv3' in Figure 1b and 1c is not the method the Methods describe. The manuscript repository's plotting code (scripts/figure1/_heatmap_common.py at e5e4a43) renames 'NTv3 cosine dist' to 'NTv3' and drops 'NTv3 subref probe', whereas Methods 'Baseline methods' describe NTv3 650M layer-11 embeddings with L2-regularised logistic regression under 5-fold gene-holdout cross-validation. Figure 1d's NTv3 column is the supervised subref probe. The SNV and deconfounded NTv3 values are recorded as a zero-shot embedding distance.Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Figure 1b and 1c, column 'NTv3' (page 3); Methods 'Baseline methods', NTv3 (page 8); repository scripts/figure1/_heatmap_common.py RENAME_MAP and DROP_METHODS AlphaMissense's 'Overall' cell in Figure 1b and 1c is its missense AUROC. The plotting code blanks AlphaMissense outside missense and copies the Missense value into the Overall row (scripts/figure1/_heatmap_common.py, am_ov_mask), so it is computed on a different, missense-only population from the other methods' Overall cells.Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Figure 1b and 1c, row 'Overall', column 'AlphaMissense' (page 3); repository scripts/figure1/_heatmap_common.py prepare() Methods, coverage and source NTv3 on the EVEE ClinVar indel benchmark (Pearce et al. 2026) gfm-guide-20261014-protocol-evee-clinvar-indel-auroc Aggregation: Not reported Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4; EVEE manuscript repository: figures/figure1/fig1d_indel_heatmap.pdf; EVEE manuscript repository: scripts/figure1/fig1d_indel_heatmap.py · Figure 1d (page 3, raster; matched to repository figures/figure1/fig1d_indel_heatmap.pdf text layer), row 'Overall (n=73,961, 65.1%P)', column 'NTv3'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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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/fig1d_indel_heatmap.py · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f

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Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-config-evee-ntv3-subref-probe

areas: dna-genomes
contexts: research
method types: foundation_model; supervised_machine_learning
source locator: Methods 'Baseline methods' and 'Covariance probe' (page 8); Figure 1 column labels
reported name: NTv3 (repository label 'NTv3 subref probe')
checkpoint: NTv3 650M, layer 11

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configuration of: Nucleotide Transformer v3
system: NTv3 on the EVEE ClinVar indel benchmark (Pearce et al. 2026)

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