metadata

license: mit
tags:
  - dna
  - variant-effect-prediction
  - biology
  - genomics
configs:
  - config_name: mendelian_traits
    data_files:
      - split: test
        path: mendelian_traits_matched_9/test.parquet
  - config_name: complex_traits
    data_files:
      - split: test
        path: complex_traits_matched_9/test.parquet
  - config_name: mendelian_traits_full
    data_files:
      - split: test
        path: mendelian_traits_all/test.parquet
  - config_name: complex_traits_full
    data_files:
      - split: test
        path: complex_traits_all/test.parquet

🧬 TraitGym

Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics

🏆 Leaderboard: https://huggingface.co/spaces/songlab/TraitGym-leaderboard

⚡️ Quick start

Load a dataset

from datasets import load_dataset

dataset = load_dataset("songlab/TraitGym", "mendelian_traits", split="test")

Example notebook to run variant effect prediction with a gLM, runs in 5 min on Google Colab: TraitGym.ipynb

🤗 Resources (https://huggingface.co/datasets/songlab/TraitGym)

Datasets: {dataset}/test.parquet
Subsets: {dataset}/subset/{subset}.parquet
Features: {dataset}/features/{features}.parquet
Predictions: {dataset}/preds/{subset}/{model}.parquet
Metrics: {dataset}/{metric}/{subset}/{model}.csv

dataset examples (load_dataset config name):

mendelian_traits_matched_9 (mendelian_traits)
complex_traits_matched_9 (complex_traits)
mendelian_traits_all (mendelian_traits_full)
complex_traits_all (complex_traits_full)

subset examples:

all (default)
3_prime_UTR_variant
disease
BMI

features examples:

GPN-MSA_LLR
GPN-MSA_InnerProducts
Borzoi_L2

model examples:

GPN-MSA_LLR.minus.score
GPN-MSA.LogisticRegression.chrom
CADD+GPN-MSA+Borzoi.LogisticRegression.chrom

metric examples:

AUPRC_by_chrom_weighted_average (main metric)
AUPRC

💻 Code (https://github.com/songlab-cal/TraitGym)

Tries to follow recommended Snakemake structure
GPN-Promoter code is in the main GPN repo

Citation

Link to paper

@article{traitgym,
    author = {Benegas, Gonzalo and Eraslan, Gokcen and Song, Yun S.},
    title = {Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics},
    elocation-id = {2025.02.11.637758},
    year = {2025},
    doi = {10.1101/2025.02.11.637758},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2025/02/12/2025.02.11.637758},
    eprint = {https://www.biorxiv.org/content/early/2025/02/12/2025.02.11.637758.full.pdf},
    journal = {bioRxiv}
}