Evidence claim

Developer overlap: EVEE authors and Evo 2

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()

Developer overlap of EVEE

EVEE is reported by its developers: 11 of its 23 authors, including the first and last authors, are Goodfire employees (Competing interests); 11 are at Mayo Clinic. Three EVEE authors, N. Nguyen, D. Balsam and N. K. Wang, also appear by name and initials in the author list of the Evo 2 preprint (bioRxiv 10.1101/2025.02.18.638918), so the Evo 2 based configurations are treated as author_reported. The match is by name only; affiliations were not compared.

Descriptive fact transcribed from the pinned source.

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.

12 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
Claimed field developer_overlap Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' 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 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` 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
Claimed field developer_overlap Context-only references	bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv API details record, version 1 posted 2025-02-21 Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `8b50005d8a5e8f37d9e504dec246994bf21a326cfb17dcdd086683db616d2254` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' 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 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` 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
Source location EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Context-only references	bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv API details record, version 1 posted 2025-02-21 Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `8b50005d8a5e8f37d9e504dec246994bf21a326cfb17dcdd086683db616d2254` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value EVEE is reported by its developers: 11 of its 23 authors, including the first and last authors, are Goodfire employees (Competing interests); 11 are at Mayo Clinic. Three EVEE authors, N. Nguyen, D. Balsam and N. K. Wang, also appear by name and initials in the author list of the Evo 2 preprint (bioRxiv 10.1101/2025.02.18.638918), so the Evo 2 based configurations are treated as author_reported. The match is by name only; affiliations were not compared. Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' 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 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.value` 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
Claimed value EVEE is reported by its developers: 11 of its 23 authors, including the first and last authors, are Goodfire employees (Competing interests); 11 are at Mayo Clinic. Three EVEE authors, N. Nguyen, D. Balsam and N. K. Wang, also appear by name and initials in the author list of the Evo 2 preprint (bioRxiv 10.1101/2025.02.18.638918), so the Evo 2 based configurations are treated as author_reported. The match is by name only; affiliations were not compared. Context-only references	bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv API details record, version 1 posted 2025-02-21 Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `8b50005d8a5e8f37d9e504dec246994bf21a326cfb17dcdd086683db616d2254` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Descriptive fact transcribed from the pinned source. Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' 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 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` 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
Description Descriptive fact transcribed from the pinned source. Context-only references	bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv API details record, version 1 posted 2025-02-21 Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8b50005d8a5e8f37d9e504dec246994bf21a326cfb17dcdd086683db616d2254` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject gfm-guide-20261014-method-evee Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' 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 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `links:subject:gfm-guide-20261014-method-evee` 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
Relationship: subject gfm-guide-20261014-method-evee Context-only references	bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) Original source ↗ EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv API details record, version 1 posted 2025-02-21 Retrieved: 2026-10-14T12:48:26Z	not individually reviewed No individual claim review recorded Audit details Field: `links:subject:gfm-guide-20261014-method-evee` Source artifact SHA-256: `8b50005d8a5e8f37d9e504dec246994bf21a326cfb17dcdd086683db616d2254` 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

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)
bioRxiv API metadata for the Evo 2 preprint (10.1101/2025.02.18.638918) · Original source · bioRxiv API details record, version 1 posted 2025-02-21

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Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-claim-evee-developer-overlap

field: developer_overlap
value: EVEE is reported by its developers: 11 of its 23 authors, including the first and last authors, are Goodfire employees (Competing interests); 11 are at Mayo Clinic. Three EVEE authors, N. Nguyen, D. Balsam and N. K. Wang, also appear by name and initials in the author list of the Evo 2 preprint (bioRxiv 10.1101/2025.02.18.638918), so the Evo 2 based configurations are treated as author_reported. The match is by name only; affiliations were not compared.
source locator: EVEE v4 title page author list and 'Competing interests' (page 15); bioRxiv API details for 10.1101/2025.02.18.638918, field 'authors'
review: method: source-hash-verification; ai-assisted-source-review; method note: Each source sentence the claim rests on asserted verbatim in the reviewer's own text extraction (review/check_gfm_guide.py); the claim text was then read against them.; 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: Review corrected 'mostly Goodfire employees' to the count on the title page and in Competing interests (11 of 23).

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