Evidence claim

Relevance of TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average to "Select regulatory variants and genes for functional follow-up"

Use case: Select regulatory variants and genes for functional follow-up
Assessed by: TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average
Relevance: Proxy evidence
Endpoint: AUPRC (per-chromosome weighted average, with bootstrap SE) of linear-probing scores from gLMs, sequence-to-function models, CADD and conservation for Mendelian traits causal versus matched noncoding variants

TraitGym Mendelian traits linear-probing AUPRC as evidence for choosing causal noncoding variants to follow up.

18 reviewed evaluations

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.

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-traitgym-source-hf-metrics locator mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Comparison group traitgym-official Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Comparison title TraitGym official metrics Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) 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 within the same dataset and mode; the baseline AUPRC is 0.1. Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Endpoint AUPRC (per-chromosome weighted average, with bootstrap SE) of linear-probing scores from gLMs, sequence-to-function models, CADD and conservation for Mendelian traits causal versus matched noncoding variants Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Claimed field links:assessed_by:lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Headline metric auprc Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Limitations 5 values Benchmark authors developed GPN-MSA and GPN-Promoter (author_reported). Mendelian positives are curated regulatory pathogenic variants, enriched for conserved promoter and UTR sites, which favours conservation scores and CADD. Labels are not experimental allele effects. Official metrics files on a mutable Hugging Face dataset, pinned by revision. Linear-probing scores are fitted on TraitGym labels with leave-one-chromosome-out training, so they are not comparable with zero-shot scores. Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
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97657a89d336f833ab667954f2b46c4944b1c5959b57be5540a69b828a667902 record id lit-genomics-20261011-traitgym-source-hf-metrics fields status attributes.artifact_sha256 sha256 865b9568f1a674d20cfecf890361ad3606fcb35a0932b64fbe70ff045e727a59 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	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact
Rationale Proxy, not direct: the inputs match fine-mapped or curated candidate variants at a locus, but the output only ranks variants; it gives no element-gene link and no effect direction, which the use case needs to design perturbations. Context-only references	TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) Original source ↗ lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/ Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ Retrieved: 2026-10-11T01:40:33Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e` Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · Original source · Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-lit-genomics-20261011-traitgym-mendelian-traits-matched-9-linear-probing

field: links:assessed_by:lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing
value: lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-linear-probing
relevance: proxy
endpoint: AUPRC (per-chromosome weighted average, with bootstrap SE) of linear-probing scores from gLMs, sequence-to-function models, CADD and conservation for Mendelian traits causal versus matched noncoding variants
rationale: Proxy, not direct: the inputs match fine-mapped or curated candidate variants at a locus, but the output only ranks variants; it gives no element-gene link and no effect direction, which the use case needs to design perturbations.
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 within the same dataset and mode; the baseline AUPRC is 0.1.
limitations: Benchmark authors developed GPN-MSA and GPN-Promoter (author_reported).; Mendelian positives are curated regulatory pathogenic variants, enriched for conserved promoter and UTR sites, which favours conservation scores and CADD.; Labels are not experimental allele effects.; Official metrics files on a mutable Hugging Face dataset, pinned by revision.; Linear-probing scores are fitted on TraitGym labels with leave-one-chromosome-out training, so they are not comparable with zero-shot scores.
citation locators: source id: lit-genomics-20261011-traitgym-source-hf-metrics; locator: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/
source locator: lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/
headline metric: auprc
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: traitgym-official
comparison title: TraitGym official metrics
stratum label: Mendelian traits, linear-probing
stratum order: 2
reviewed evaluations: lit-genomics-20261011-traitgym-eval-aido-dna-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-borzoi-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-cadd-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-cadd-plus-borzoi-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-cadd-plus-gpn-msa-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-cadd-plus-gpn-msa-plus-borzoi-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-caduceus-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-enformer-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-evo2-1b-base-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-evo2-40b-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-evo2-7b-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-gpn-final-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-gpn-msa-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-gpn-msa-plus-borzoi-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-hyenadna-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-nucleotidetransformer-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-sei-logisticregression-chrom-mendelian-traits-matched-9; lit-genomics-20261011-traitgym-eval-specieslm-logisticregression-chrom-mendelian-traits-matched-9
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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