Relevance of EVEE Evo 2 embedding extraction compute (Pearce et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"
- Use case
- Select an execution workflow for large-scale diagnostic genomics
- Assessed by
- EVEE Evo 2 embedding extraction compute (Pearce et al. 2026)
- Relevance
- Proxy evidence
- Endpoint
- Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants
Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure.
1 reviewed evaluation
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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Comparison group evee2026-evo2-embedding-extraction Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Comparison title Evo 2 7B embedding extraction for all ClinVar variants (Pearce et al. 2026) Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
Constraints4 values
| Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Endpoint Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Claimed field links:assessed_by:gfm-guide-20261014-protocol-evee-embedding-extraction-compute Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Headline metric accelerator-time Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
Limitations5 values
| Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
Pinned records5 values
| Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
| Rationale Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure. Context-only references | Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461) Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: 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. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record 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)
Technical metadata and extraction receipts
Stable ID: use-case-mapping-gfm-guide-20261014-evee-embedding-extraction
- field
- links:assessed_by:gfm-guide-20261014-protocol-evee-embedding-extraction-compute
- value
- gfm-guide-20261014-protocol-evee-embedding-extraction-compute
- relevance
- proxy
- endpoint
- Approximate total H100 GPU-hours to extract Evo 2 7B layer-27 embeddings (reference and variant, both strands, 65 kb windows) for 4,252,870 ClinVar variants
- rationale
- Proxy. The only linked figure for running a genomic foundation model over human variants at the scale of a whole variant database, which bears on the accelerator budget for scoring variants with such a model. It is a one-off research embedding harvest rather than a diagnostic workflow, and gives one approximate total with no GPU count, batch size, wall-clock time or per-sample figure.
- constraints
- Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; hardware, inputs, software versions and timing boundaries differ between sources.; Read the value as approximate; it is printed as '∼20,000 H100-hours'.; Do not divide it into a per-variant or per-sample cost without saying the division is yours; the source prints no per-variant timing, and the workload covers both strands and both alleles.
- limitations
- Developer-reported: EVEE's authors built the extraction pipeline, and three of them co-authored Evo 2 (claim gfm-guide-20261014-claim-evee-developer-overlap).; Stated once in Methods (the 'Dataset' paragraph after 'Harvesting'); GPU count, batch size, wall-clock time and software versions are not given.; The workload stores per-position embeddings (bf16, about 34 TB), which a diagnostic scoring pipeline would not need; the figure therefore includes work beyond scoring.; Preprint (bioRxiv v4), not peer reviewed.; The source carries an evidence concern about the NTv3 column of Figures 1b and 1c. It does not touch this figure, but an active judgement needs clean protocol sources, so this judgement stays withheld after review until that concern is resolved.
- revision
- 1
- reason
- Add relevance judgements for the execution and compute protocols of the genomic foundation model guide sources batch (data/omics/gfm-guide-sources-20261014, issue #162), independently reviewed in PR #169.
- citation locators
- source id: gfm-guide-20261014-source-evee-v4; locator: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)
- source locator
- gfm-guide-20261014-source-evee-v4: Methods 'Genomic foundation model', paragraphs 'Harvesting' and 'Dataset' (page 8, line 461)
- comparison group
- evee2026-evo2-embedding-extraction
- comparison title
- Evo 2 7B embedding extraction for all ClinVar variants (Pearce et al. 2026)
- headline metric
- accelerator-time
- reviewed evaluations
- gfm-guide-20261014-eval-evee-embedding-extraction-compute
- review
- method: independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent review-169, independent of the agent that drafted these judgements for issue #162; no human review claimed; reviewed at: 2026-10-14T19:00:00Z; note: Independent relevance review: grade, endpoint, rationale, constraints, limitations and locators checked against the use case and the source text; every value of the listed evaluations checked against the source. No execution, reproduction, qualified human scientific review or clinical validation. See docs/reviews/use-cases/diagnostic-genomics-model-execution-judgements-2026-10-14.md. Checked in a fresh copy of the bioRxiv v4 PDF; bioRxiv stamps each download, so its hash differs from the pinned bytes (hash_scope on the source). Stays withheld while the source carries its evidence concern.
- pins
- record id: gfm-guide-20261014-eval-evee-embedding-extraction-compute; fields: status; links; attributes.origin; attributes.comparison; sha256: 53403c68ad5bea53431fee3eb1b4e81b5cff414530d292e710041a63abd5422a; record id: gfm-guide-20261014-protocol-evee-embedding-extraction-compute; fields: status; name; description; facets; source_ids; links; attributes; sha256: c5c5c758a9673043af191956af05d68bfe66247b928364969f52684a897c9294; record id: gfm-guide-20261014-result-evee-embedding-extraction-h100-hours; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 87e35eacbfca259a686cae9b9fa7b3829ee9358124ea5b57f1d002c6fa0dd6eb; record id: gfm-guide-20261014-source-evee-v4; fields: status; attributes.artifact_sha256; sha256: 7fa901d074087100fbb320434beaf2f77ce2000077cd20e456c03c9285263dd7; record id: use-case-diagnostic-genomics-model-execution; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 1c2a12431556cc6581f5aab019cf91576d2393387b88a8a2bea35ea2a3ee4a70