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Benchmark

TraitGym

Causal versus matched non-causal noncoding variants for 113 Mendelian and 83 complex traits, scored by AUPRC computed per chromosome and averaged with sample-size weights.

Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.

4 protocols with results

Overview

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Results on linked records

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Methods and evaluation design

Procedure, tasks and evaluated configurations

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

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Baseline status by linked protocol

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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How to read the evidence

Sources and history

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

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-traitgym-benchmark-traitgym

areas
dna-genomes
contexts
research
entity level
suite
version
Hugging Face revision 1fde19555fe8
task
Causal regulatory variant prediction
scope note
Datasets mendelian_traits_matched_9 and complex_traits_matched_9 (nine matched controls per causal variant), subset 'all'. Zero-shot scores and chromosome-held-out logistic regression (linear probing).
source locator
README 'Resources' and 'Running'; dataset paths in this batch
Related records

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