Evidence claim

Relevance of GFMBench-API TraitGym Mendelian, zs-embedding to "Select regulatory variants and genes for functional follow-up"

Use case: Select regulatory variants and genes for functional follow-up
Assessed by: GFMBench-API TraitGym Mendelian, zs-embedding
Relevance: Proxy evidence
Endpoint: Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models (DNA-BERT, DNABERT-2, NTv3, Caduceus-Ps, Evo2) on TraitGym Mendelian

GFMBench-API zero-shot embedding distance scores scores on TraitGym Mendelian as evidence for choosing noncoding variants to edit.

5 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

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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.

19 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
Citation locations 1 values source id lit-genomics-20261011-gfmbench-source-larey2026 locator Table 3, task 'TraitGym Mendelian'; appendix task description Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group gfmbench-traitgym Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title GFMBench-API zero-shot scores on TraitGym Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results. Compare only with other rows of the same GFMBench-API table; TraitGym's own paper uses different context lengths and scoring. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models (DNA-BERT, DNABERT-2, NTv3, Caduceus-Ps, Evo2) on TraitGym Mendelian Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-embedding Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric auroc Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 3 values Preprint, not peer reviewed. Mendelian AUROCs reach 0.60-0.63 (Evo2 and DNABERT-2 L2 distance); no uncertainty is printed. Curated Mendelian regulatory variants, not experimental allele effects. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Proxy, not direct: the protocol ranks candidate noncoding variants by zero-shot model scores, which matches the first step of choosing allele edits, but it gives no element-gene link and no effect direction, and it is scored on the GFMBench-API re-implementation of TraitGym rather than on perturbation data. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-lit-genomics-20261011-gfmbench-traitgym-mendelian-zs-embedding

field: links:assessed_by:lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-embedding
value: lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-embedding
relevance: proxy
endpoint: Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models (DNA-BERT, DNABERT-2, NTv3, Caduceus-Ps, Evo2) on TraitGym Mendelian
rationale: Proxy, not direct: the protocol ranks candidate noncoding variants by zero-shot model scores, which matches the first step of choosing allele edits, but it gives no element-gene link and no effect direction, and it is scored on the GFMBench-API re-implementation of TraitGym rather than on perturbation data.
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.; Compare only with other rows of the same GFMBench-API table; TraitGym's own paper uses different context lengths and scoring.
limitations: Preprint, not peer reviewed.; Mendelian AUROCs reach 0.60-0.63 (Evo2 and DNABERT-2 L2 distance); no uncertainty is printed.; Curated Mendelian regulatory variants, not experimental allele effects.
citation locators: source id: lit-genomics-20261011-gfmbench-source-larey2026; locator: Table 3, task 'TraitGym Mendelian'; appendix task description
source locator: lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'TraitGym Mendelian'; appendix task description
headline metric: auroc
reason: Add a relevance judgement for a genomic foundation model benchmark protocol from the 2026-10-11 genomics suite pass, reviewed in docs/reviews/2026-10-11-genomics-gfm-suites.md.
comparison group: gfmbench-traitgym
comparison title: GFMBench-API zero-shot scores on TraitGym
stratum label: TraitGym Mendelian, embedding distance scores
stratum order: 1
reviewed evaluations: lit-genomics-20261011-gfmbench-eval-caduceus-ps-zero-shot-traitgym-mendelian-zs-embedding; lit-genomics-20261011-gfmbench-eval-dna-bert-zero-shot-traitgym-mendelian-zs-embedding; lit-genomics-20261011-gfmbench-eval-dnabert-2-zero-shot-traitgym-mendelian-zs-embedding; lit-genomics-20261011-gfmbench-eval-evo2-zero-shot-traitgym-mendelian-zs-embedding; lit-genomics-20261011-gfmbench-eval-ntv3-zero-shot-traitgym-mendelian-zs-embedding
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the proxy rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-3, independent of the extractor lit-genomics; no human review claimed; reviewed at: 2026-10-11T14:40:00Z; note: Automated review; not human scientific review.
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