Evaluation

AlphaMissense on the EVEE deconfounded ClinVar SNV benchmark (Pearce et al. 2026)

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()

Published result; transcribed, not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense hg38, 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)	0.972 AUROC (Deconfounded ClinVar SNVs, missense only (value plotted in the Overall row)) 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 AlphaMissense 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 'AlphaMissense'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

EVEE deconfounded ClinVar SNV pathogenicity AUROC (Pearce et al. 2026 Figure 1c)

Configuration: AlphaMissense hg38, 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)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-14
dataset version: ClinVar release 2026-03-21
split: Deconfounded subset; gene-holdout cross-validation for supervised probes
population: 158,616 ClinVar SNVs, 27.8% pathogenic
inputs: Variant and reference sequence or pre-computed score
adaptation: Not reported
metric implementation: Not reported
aggregation: One AUROC over all consequence types
budget: Not reported
protocol id: gfm-guide-20261014-protocol-evee-deconfounded-snv-auroc

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

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

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Evidence table

Inspect claims, sources and review details

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54 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Not reported Context-only references	EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `3dd79f2055d965fa486ae6c33193c646bb21db51f1491694111b9c96d148eec6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	EVEE manuscript repository: scripts/figure1/_heatmap_common.py Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `1d477d2e1eb4213591015b26baca654e5ca1ca19ee9a1fd39e5f106fc8e56e2e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ 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 'AlphaMissense' 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) Retrieved: 2026-10-14T12:02:25Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8` 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. Inspected artifact
Comparison: aggregation One AUROC over all consequence types Context-only references	EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `3dd79f2055d965fa486ae6c33193c646bb21db51f1491694111b9c96d148eec6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation One AUROC over all consequence types Context-only references	EVEE manuscript repository: scripts/figure1/_heatmap_common.py Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `1d477d2e1eb4213591015b26baca654e5ca1ca19ee9a1fd39e5f106fc8e56e2e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation One AUROC over all consequence types Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ 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 'AlphaMissense' 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) Retrieved: 2026-10-14T12:02:25Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8` 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. Inspected artifact
Comparison: budget Not reported Context-only references	EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `3dd79f2055d965fa486ae6c33193c646bb21db51f1491694111b9c96d148eec6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	EVEE manuscript repository: scripts/figure1/_heatmap_common.py Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `1d477d2e1eb4213591015b26baca654e5ca1ca19ee9a1fd39e5f106fc8e56e2e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ 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 'AlphaMissense' 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) Retrieved: 2026-10-14T12:02:25Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8` 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. Inspected artifact
Comparison: dataset version ClinVar release 2026-03-21 Context-only references	EVEE manuscript repository: figures/figure1/fig1c_deconf_heatmap.pdf Original source ↗ 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 'AlphaMissense' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `3dd79f2055d965fa486ae6c33193c646bb21db51f1491694111b9c96d148eec6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

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

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Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-eval-evee-deconfounded-alphamissense

areas: dna-genomes
contexts: research
origin: independent_paper
protocol: gfm-guide-20261014-protocol-evee-deconfounded-snv-auroc
version: Primary source as retrieved 2026-10-14
comparison: dataset version: ClinVar release 2026-03-21; split: Deconfounded subset; gene-holdout cross-validation for supervised probes; population: 158,616 ClinVar SNVs, 27.8% pathogenic; inputs: Variant and reference sequence or pre-computed score; adaptation: Not reported; metric implementation: Not reported; aggregation: One AUROC over all consequence types; budget: Not reported; protocol id: gfm-guide-20261014-protocol-evee-deconfounded-snv-auroc
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 'AlphaMissense'
missing metadata: comparison.adaptation: reason: unreported; comparison.budget: reason: unreported; comparison.metric implementation: reason: unreported

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