Result

Accelerator time (Evo 2 7B embedding extraction for 4,252,870 ClinVar variants) of EVEE covariance probe on Evo 2 7B layer 27 (Pearce et al. 2026) on EVEE full ClinVar variant set (4,252,870 variants)

∼20,000 Accelerator time (Evo 2 7B embedding extraction for 4,252,870 ClinVar variants)

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

Tested configuration: EVEE covariance probe on Evo 2 7B layer 27 (Pearce et al. 2026)
Protocol: EVEE Evo 2 embedding extraction compute (Pearce et al. 2026)
Dataset: EVEE full ClinVar variant set (4,252,870 variants)
Procedure: EVEE Evo 2 embedding extraction compute (Pearce et al. 2026)
Evaluation: EVEE Evo 2 7B embedding extraction compute (Pearce et al. 2026)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Author-reported evaluation · source checkedInterpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 · Methods 'Harvesting', page 8, line 461: 'Extraction used ∼20,000 H100-hours'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: All variants
Adaptation: Inference only
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

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.

1 evidence row 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
Reported result ∼20,000 Individual claims	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ Methods 'Harvesting', page 8, line 461: 'Extraction used ∼20,000 H100-hours' Version: bioRxiv v4, posted 2026-07-11 (v1 posted 2026-04-11) Retrieved: 2026-10-14T12:02:25Z	source checked ["pdf-text-parse","independent-cell-check"] · 2026-10-14 author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Value matches. Approximate figure; GPU count and wall clock not stated. Transcribed, not reproduced. Field: `attributes.printed_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 Extraction artifact SHA-256: `1d65b07059c50e8e3f88b8fde950f011630886097bf2784a6653282c6424eef8` Extraction artifact

How to read the evidence

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)

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Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-result-evee-embedding-extraction-h100-hours

metric: accelerator-time
metric direction: lower
unit: hour
printed value: ∼20,000
numeric value: 20000
source locator: Methods 'Harvesting', page 8, line 461: 'Extraction used ∼20,000 H100-hours'
missing metadata: uncertainty: reason: unreported
review: method: pdf-text-parse; independent-cell-check; method note: Sentence 'Extraction used ∼20,000 H100-hours' located in the reviewer's text extraction of a fresh copy of the paper (SHA-256 9e2176440dfae6740b9e799796297cdd70b9bd59edb5c0a1e7fcdb5d6978710a; per-download stamp, see hash_scope).; 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: Value matches. Approximate figure; GPU count and wall clock not stated. Transcribed, not reproduced.
metric qualifier: Evo 2 7B embedding extraction for 4,252,870 ClinVar variants
unit detail: H100 GPU-hours
approximate: true

Related records

evaluation: EVEE Evo 2 7B embedding extraction compute (Pearce et al. 2026)

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