Evidence claim

Relevance of GFMBench-API TraitGym Mendelian, zs-ar-llr 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-ar-llr
Relevance: Proxy evidence
Endpoint: Zero-shot AUROC and AUPRC of autoregressive log-likelihood ratio for Evo2 (1B, NVIDIA BioNeMo, FP16) on TraitGym Mendelian

GFMBench-API zero-shot autoregressive log-likelihood ratio scores on TraitGym Mendelian as evidence for choosing noncoding variants to edit.

1 reviewed evaluation

Evo2 on GFMBench-API TraitGym Mendelian (zs-ar-llr)

Evidence

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Evidence table

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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 5, 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 5, 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 5, 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 5, 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 5, 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 autoregressive log-likelihood ratio for Evo2 (1B, NVIDIA BioNeMo, FP16) 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 5, 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-ar-llr Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 5, 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 5, 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 AUROC is 0.6041 for Evo2; 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 5, 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
Pinned records 6 values record id lit-genomics-20261011-gfmbench-eval-evo2-zero-shot-traitgym-mendelian-zs-ar-llr fields status links attributes.origin attributes.comparison sha256 1a48088739141e985a151c4864fbd07a448248495d6d071275baa5d2bc5068a1 record id lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-ar-llr fields status name description facets source_ids links attributes sha256 124c92608321024394c2dcceb88a69f9a97885c92ad6f67b795853e89c541122 record id lit-genomics-20261011-gfmbench-result-evo2-zero-shot-traitgym-mendelian-zs-ar-llr-mean-llr-prc fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 bb3d02272ce447f260bf63d3cbbf1de65c46b85c62b8c8be8194077c6c0db053 record id lit-genomics-20261011-gfmbench-result-evo2-zero-shot-traitgym-mendelian-zs-ar-llr-mean-llr-roc fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 08f90ab9e95ecba8c71823a8ffaff9991d903260468d16405270bb2eadcc4a95 record id lit-genomics-20261011-gfmbench-source-larey2026 fields status attributes.artifact_sha256 sha256 a461e55e4db9e70efca0dd40a686ae239e2e254757de72623099c721fd6eb0fc record id use-case-regulatory-variant-gene-follow-up fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 0071547e01ccaec30238aea9e4882dd92e6f51be9c967c7fb88bc61d2788b870 Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 5, 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 5, 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

1 source record and release history

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-ar-llr

field: links:assessed_by:lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-ar-llr
value: lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-ar-llr
relevance: proxy
endpoint: Zero-shot AUROC and AUPRC of autoregressive log-likelihood ratio for Evo2 (1B, NVIDIA BioNeMo, FP16) 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 AUROC is 0.6041 for Evo2; no uncertainty is printed.; Curated Mendelian regulatory variants, not experimental allele effects.
citation locators: source id: lit-genomics-20261011-gfmbench-source-larey2026; locator: Table 5, task 'TraitGym Mendelian'; appendix task description
source locator: lit-genomics-20261011-gfmbench-source-larey2026: Table 5, 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, autoregressive log-likelihood ratio
stratum order: 3
reviewed evaluations: lit-genomics-20261011-gfmbench-eval-evo2-zero-shot-traitgym-mendelian-zs-ar-llr
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.
pins: record id: lit-genomics-20261011-gfmbench-eval-evo2-zero-shot-traitgym-mendelian-zs-ar-llr; fields: status; links; attributes.origin; attributes.comparison; sha256: 1a48088739141e985a151c4864fbd07a448248495d6d071275baa5d2bc5068a1; record id: lit-genomics-20261011-gfmbench-protocol-traitgym-mendelian-zs-ar-llr; fields: status; name; description; facets; source_ids; links; attributes; sha256: 124c92608321024394c2dcceb88a69f9a97885c92ad6f67b795853e89c541122; record id: lit-genomics-20261011-gfmbench-result-evo2-zero-shot-traitgym-mendelian-zs-ar-llr-mean-llr-prc; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: bb3d02272ce447f260bf63d3cbbf1de65c46b85c62b8c8be8194077c6c0db053; record id: lit-genomics-20261011-gfmbench-result-evo2-zero-shot-traitgym-mendelian-zs-ar-llr-mean-llr-roc; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 08f90ab9e95ecba8c71823a8ffaff9991d903260468d16405270bb2eadcc4a95; record id: lit-genomics-20261011-gfmbench-source-larey2026; fields: status; attributes.artifact_sha256; sha256: a461e55e4db9e70efca0dd40a686ae239e2e254757de72623099c721fd6eb0fc; record id: use-case-regulatory-variant-gene-follow-up; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 0071547e01ccaec30238aea9e4882dd92e6f51be9c967c7fb88bc61d2788b870

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subject: Select regulatory variants and genes for functional follow-up

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