Create README.md

README.md

@@ -0,0 +1,40 @@
+---
+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}
+}
+```