Datasets:

MulinLab
/

hEvo-benchmarks

---
language:
- en
pretty_name: hEvo benchmarks
tags:
- biology
- genomics
- DNA
- benchmark
gated: true
extra_gated_heading: "Reviewer access request"
extra_gated_description: "This repository is reserved for peer reviewers. Please sign in to Hugging Face and submit an access request with your review purpose. MulinLab will review requests manually."
extra_gated_button_content: "Request reviewer access"
---
<div align="center">
  <img src="https://raw.githubusercontent.com/mulinlab/hEVO/main/header.png" alt="hEvo population-aware DNA foundation model: population diversity, genetic variation, and evolutionary history" width="100%">
</div>

# 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](#task-catalog) · [Request access](#access-and-download) · [Build data](#reproduce-a-task-bundle) · [GitHub workflows](https://github.com/mulinlab/hEVO) · [hEVO-base-o](https://huggingface.co/MulinLab/hEVO-base-o) · [hEVO-large-o](https://huggingface.co/MulinLab/hEVO-large-o)

---

## Contents

- [Dataset overview](#dataset-overview)
- [Task catalog](#task-catalog)
- [Access and download](#access-and-download)
- [Reproduce a task bundle](#reproduce-a-task-bundle)
- [Sources, terms and citation](#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](adaptation/README.md) |
| `ancestry` | Genetic ancestry | [Open guide](ancestry/README.md) |
| `causal_variants` | Fine-mapped GWAS candidate variants | [Open guide](causal_variants/README.md) |
| `clinvar` | ClinVar snapshot dated 2026-06-15 | [Open guide](clinvar/README.md) |
| `clinvar_reclassification` | Retrospective ClinVar reclassification | [Open guide](clinvar_reclassification/README.md) |
| `deepsea` | DeepSEA | [Open guide](deepsea/README.md) |
| `denovo_variants` | DDD de novo variant controls | [Open guide](denovo_variants/README.md) |
| `evolution` | HAR and HAQER classification | [Open guide](evolution/README.md) |
| `haqer_windows` | HAQER grouped windows | [Open guide](haqer_windows/README.md) |
| `genomic_elements` | Genomic elements | [Open guide](genomic_elements/README.md) |
| `mpra` | MPRA emVar | [Open guide](mpra/README.md) |
| `rare_causal_variants` | Rare fine-mapped GWAS candidates | [Open guide](rare_causal_variants/README.md) |
| `rare_variants` | UK Biobank rare variant associations | [Open guide](rare_variants/README.md) |
| `ure_binary` | URE binary classification | [Open guide](ure_binary/README.md) |
| `ure_multiclass` | URE multiclass classification | [Open guide](ure_multiclass/README.md) |

## 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:

```python
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:

```bash
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:

```bash
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](https://github.com/mulinlab/hEVO). For the evaluated checkpoints, see [hEVO-base-o](https://huggingface.co/MulinLab/hEVO-base-o) and [hEVO-large-o](https://huggingface.co/MulinLab/hEVO-large-o).

	---
	language:
	- en
	pretty_name: hEvo benchmarks
	tags:
	- biology
	- genomics
	- DNA
	- benchmark
	gated: true
	extra_gated_heading: "Reviewer access request"
	extra_gated_description: "This repository is reserved for peer reviewers. Please sign in to Hugging Face and submit an access request with your review purpose. MulinLab will review requests manually."
	extra_gated_button_content: "Request reviewer access"
	---
	<div align="center">
	<img src="https://raw.githubusercontent.com/mulinlab/hEVO/main/header.png" alt="hEvo population-aware DNA foundation model: population diversity, genetic variation, and evolutionary history" width="100%">
	</div>

	# 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](#task-catalog) · [Request access](#access-and-download) · [Build data](#reproduce-a-task-bundle) · [GitHub workflows](https://github.com/mulinlab/hEVO) · [hEVO-base-o](https://huggingface.co/MulinLab/hEVO-base-o) · [hEVO-large-o](https://huggingface.co/MulinLab/hEVO-large-o)

	---

	## Contents

	- [Dataset overview](#dataset-overview)
	- [Task catalog](#task-catalog)
	- [Access and download](#access-and-download)
	- [Reproduce a task bundle](#reproduce-a-task-bundle)
	- [Sources, terms and citation](#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](adaptation/README.md) \|
	\| `ancestry` \| Genetic ancestry \| [Open guide](ancestry/README.md) \|
	\| `causal_variants` \| Fine-mapped GWAS candidate variants \| [Open guide](causal_variants/README.md) \|
	\| `clinvar` \| ClinVar snapshot dated 2026-06-15 \| [Open guide](clinvar/README.md) \|
	\| `clinvar_reclassification` \| Retrospective ClinVar reclassification \| [Open guide](clinvar_reclassification/README.md) \|
	\| `deepsea` \| DeepSEA \| [Open guide](deepsea/README.md) \|
	\| `denovo_variants` \| DDD de novo variant controls \| [Open guide](denovo_variants/README.md) \|
	\| `evolution` \| HAR and HAQER classification \| [Open guide](evolution/README.md) \|
	\| `haqer_windows` \| HAQER grouped windows \| [Open guide](haqer_windows/README.md) \|
	\| `genomic_elements` \| Genomic elements \| [Open guide](genomic_elements/README.md) \|
	\| `mpra` \| MPRA emVar \| [Open guide](mpra/README.md) \|
	\| `rare_causal_variants` \| Rare fine-mapped GWAS candidates \| [Open guide](rare_causal_variants/README.md) \|
	\| `rare_variants` \| UK Biobank rare variant associations \| [Open guide](rare_variants/README.md) \|
	\| `ure_binary` \| URE binary classification \| [Open guide](ure_binary/README.md) \|
	\| `ure_multiclass` \| URE multiclass classification \| [Open guide](ure_multiclass/README.md) \|

	## 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:

	```python
	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:

	```bash
	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:

	```bash
	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](https://github.com/mulinlab/hEVO). For the evaluated checkpoints, see [hEVO-base-o](https://huggingface.co/MulinLab/hEVO-base-o) and [hEVO-large-o](https://huggingface.co/MulinLab/hEVO-large-o).