| --- |
| 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} |
| } |
| ``` |
