Evaluation

NTv3 on the EVEE ClinVar indel 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.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
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'

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

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

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

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

EVEE ClinVar indel pathogenicity AUROC (Pearce et al. 2026 Figure 1d)

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)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-14
dataset version: ClinVar release 2026-03-21
split: Not reported
population: 73,961 ClinVar indels, 65.1% pathogenic
inputs: Variant and reference sequence or pre-computed score
adaptation: supervised on indels
metric implementation: Not reported
aggregation: One AUROC over all indels
budget: Not reported
protocol id: gfm-guide-20261014-protocol-evee-clinvar-indel-auroc

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

Reproduction

Split: Not reported
Adaptation: supervised on indels
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.

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 supervised on indels Context-only references	EVEE manuscript repository: figures/figure1/fig1d_indel_heatmap.pdf Original source ↗ 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' 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.adaptation` Source artifact SHA-256: `b1ec938f98392f1b169798f0d9232337d0635ee909e103745151c0c572578136` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation supervised on indels Context-only references	EVEE manuscript repository: scripts/figure1/fig1d_indel_heatmap.py Original source ↗ 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' 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.adaptation` Source artifact SHA-256: `5c03755c6807fef579e234676d86b9e6a20d675e0d520e656e8a60615331e34d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation supervised on indels Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ 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' 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.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 indels Context-only references	EVEE manuscript repository: figures/figure1/fig1d_indel_heatmap.pdf Original source ↗ 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' 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: `b1ec938f98392f1b169798f0d9232337d0635ee909e103745151c0c572578136` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation One AUROC over all indels Context-only references	EVEE manuscript repository: scripts/figure1/fig1d_indel_heatmap.py Original source ↗ 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' 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: `5c03755c6807fef579e234676d86b9e6a20d675e0d520e656e8a60615331e34d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation One AUROC over all indels Context-only references	Interpretable variant effect prediction from genomic foundation model representations (EVEE), bioRxiv v4 Original source ↗ 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' 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/fig1d_indel_heatmap.pdf Original source ↗ 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' 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: `b1ec938f98392f1b169798f0d9232337d0635ee909e103745151c0c572578136` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	EVEE manuscript repository: scripts/figure1/fig1d_indel_heatmap.py Original source ↗ 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' 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: `5c03755c6807fef579e234676d86b9e6a20d675e0d520e656e8a60615331e34d` 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 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' 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/fig1d_indel_heatmap.pdf Original source ↗ 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' 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: `b1ec938f98392f1b169798f0d9232337d0635ee909e103745151c0c572578136` 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/fig1d_indel_heatmap.pdf · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f
EVEE manuscript repository: scripts/figure1/fig1d_indel_heatmap.py · Original source · goodfire-ai/evee-manuscript commit e5e4a43d60bb217819144c09ab509ed44f49cd5f

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-eval-evee-indel-ntv3-subref-probe

areas: dna-genomes
contexts: research
origin: independent_paper
protocol: gfm-guide-20261014-protocol-evee-clinvar-indel-auroc
version: Primary source as retrieved 2026-10-14
comparison: dataset version: ClinVar release 2026-03-21; split: Not reported; population: 73,961 ClinVar indels, 65.1% pathogenic; inputs: Variant and reference sequence or pre-computed score; adaptation: supervised on indels; metric implementation: Not reported; aggregation: One AUROC over all indels; budget: Not reported; protocol id: gfm-guide-20261014-protocol-evee-clinvar-indel-auroc
source locator: 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'
missing metadata: comparison.budget: reason: unreported; comparison.metric implementation: reason: unreported; comparison.split: reason: unreported

Related records

system: NTv3 650M layer-11 embedding probe (Pearce et al. 2026 Figure 1d)
assessment: EVEE ClinVar indel pathogenicity AUROC (Pearce et al. 2026 Figure 1d)
data: EVEE ClinVar indel benchmark (73,961 indels)
evaluation: NTv3 AUROC, EVEE ClinVar indels

Suggest a correction