---
language:
- en
license: mit
tags:
- genomics
- population-genetics
- transformers
- axial-attention
- self-supervised
- natural-selection
- haplotype
---

# Popformer

An axial attention transformer for haplotype matrices, pre-trained with self-supervised masked haplotype reconstruction.

**Paper:** [Popformer: Learning general signatures of positive selection with a self-supervised transformer](https://www.biorxiv.org/content/10.64898/2026.03.06.710163v1)

## Model Description

Popformer is pre-trained on masked haplotype reconstruction and evaluated on:
- Natural selection detection
- Genotype imputation
- Population classification

## Usage

See the [repository README](https://github.com/zongleon/popformer) for full preprocessing and inference examples, including VCF/HDF5 input and genome-wide selection scans.

## Citation
```bibtex
@article{popformer2026,
  title   = {Popformer: Learning general signatures of positive selection with a self-supervised transformer},
  url     = {https://www.biorxiv.org/content/10.64898/2026.03.06.710163v1}
}
```