hEvo benchmarks
15 reproducible task bundles for human population genomics
Frozen evaluation inputs or source downloaders, task-specific construction scripts, and documentation for peer review. Model weights are distributed separately.
Task catalog · Request access · Build data · GitHub workflows · hEVO-base-o · hEVO-large-o
Contents
- Dataset overview
- Task catalog
- Access and download
- Reproduce a task bundle
- Sources, terms and citation
Dataset overview
| At a glance | Details |
|---|---|
| Collection | 15 task bundles maintained by MulinLab for peer review |
| Contents | Frozen inputs or upstream downloaders, task-level build.py, and construction documentation |
| Model dependency | Model-independent dataset builders; model weights are hosted separately |
| Build environment | Python 3.10–3.12; validated with Python 3.12 |
| Access | Gated; requests are reviewed manually |
| Data terms | Source-specific; this collection does not claim one license for all included data |
Task catalog
Choose the task folder for its source descriptions, labels, splits, construction parameters, seeds and build command.
| Task | Evaluation content | Task guide |
|---|---|---|
adaptation |
Selected-allele preference | Open guide |
ancestry |
Genetic ancestry | Open guide |
causal_variants |
Fine-mapped GWAS candidate variants | Open guide |
clinvar |
ClinVar snapshot dated 2026-06-15 | Open guide |
clinvar_reclassification |
Retrospective ClinVar reclassification | Open guide |
deepsea |
DeepSEA | Open guide |
denovo_variants |
DDD de novo variant controls | Open guide |
evolution |
HAR and HAQER classification | Open guide |
haqer_windows |
HAQER grouped windows | Open guide |
genomic_elements |
Genomic elements | Open guide |
mpra |
MPRA emVar | Open guide |
rare_causal_variants |
Rare fine-mapped GWAS candidates | Open guide |
rare_variants |
UK Biobank rare variant associations | Open guide |
ure_binary |
URE binary classification | Open guide |
ure_multiclass |
URE multiclass classification | Open guide |
Access and download
Access is gated for peer reviewers and approved manually by MulinLab. Sign in to Hugging Face, request access on this page, and wait for approval. After approval, authenticate locally with hf auth login using your own read token. Download only the task files needed for your analysis.
For example, to fetch the MPRA bundle and shared requirements file:
from huggingface_hub import snapshot_download
snapshot_download(
"MulinLab/hEvo-benchmarks",
repo_type="dataset",
allow_patterns=["mpra/*", "requirements.txt"],
local_dir="hEvo-benchmarks",
)
Individual data tables and source workbooks are also available from the repository Files tab. For one ancestry population or one ClinVar reclassification seed, download the corresponding data/*.tar.zst archive and unpack.py, then run:
python unpack.py ancestry --group afr
python unpack.py clinvar_reclassification --group seed_01
Files are extracted under the selected task's data/ directory. Omit --group to extract all downloaded archives for that task.
Reproduce a task bundle
Use Python 3.10–3.12 (validated with 3.12) and install the construction dependencies:
pip install -r requirements.txt
python <task>/build.py --help
Run the command documented in that task's README. Common path options are resolved against the corresponding script directory. Reference-based tasks require an external indexed hg38 FASTA and its .fai index. Add external tools only where needed: samtools to index a FASTA, curl for ENCODE, and bedtools/pybedtools for recreating the optional evolution negative pool. URE builds use the Python standard library. DeepSEA tensors and HAQER LMDBs are built locally.
Sources, terms and citation
Each task guide documents its source data, publications, labels, splits, output files, construction parameters and random seeds. The terms of the source publications remain applicable; approval to access this collection does not replace them. Check the task guide and cited source before using or redistributing any material. No single collection-wide license is claimed.
For code and complete benchmark workflows, see mulinlab/hEVO. For the evaluated checkpoints, see hEVO-base-o and hEVO-large-o.
- Downloads last month
- 32