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---
language:
- en
---
# scFoundation
## Overview
scFoundation is a publicly available single-cell foundation model developed by researchers at BioMap, Tsingua University, and MBZUAI.
Additional details about model design and performance can be found in [Hao et al. 2024](https://www.nature.com/articles/s41592-024-02305-7).
The code can be found on the official [GitHub](https://github.com/biomap-research/scFoundation).
## Usage Examples
This backbone can be adapted for arbitrary downstream tasks with ModelGenerator - please consult the [documentation](https://genbio-ai.github.io/ModelGenerator/) for more details.
### Cell Type Classification
```
mgen fit --model SequenceClassification --model.backbone scfoundation --data CellClassificationDataModule --data.path <hf_or_local_path_to_your_dataset>
mgen test --model SequenceClassification --model.backbone scfoundation --data CellClassificationDataModule --data.path <hf_or_local_path_to_your_dataset>
```
## Limitations
* We only include scFoundation's encoder in ModelGenerator. The decoder is disabled.
## Citation
```
@article{hao2024large,
title={Large-scale foundation model on single-cell transcriptomics},
author={Hao, Minsheng and Gong, Jing and Zeng, Xin and Liu, Chiming and Guo, Yucheng and Cheng, Xingyi and Wang, Taifeng and Ma, Jianzhu and Zhang, Xuegong and Song, Le},
journal={Nature methods},
volume={21},
number={8},
pages={1481--1491},
year={2024},
publisher={Nature Publishing Group US New York}
}
```
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