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}
}