genbio-ai / scFoundation

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 .

The code can be found on the official GitHub .

Usage Examples

This backbone can be adapted for arbitrary downstream tasks with ModelGenerator - please consult the documentation 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}
}