CIFM: Cellular Interaction Foundation Model

Overview

CIFM is an AI foundation model that can simulate the activities within living tissues (AI virtual tissue). The signature functions of CIFM are:

• Embedding of celllular microenvironments via embeddings = model.embed(adata) (the 1st Figure below panel D top);
• Inference/simulation of cellular gene expressions within a certain microenvironment via expressions = model.predict_cells_at_locations(adata, target_locs) (the 1st Figure below panel D bottom, and the 2nd Figure below).

More information about the model can be found in the preprint.

Model Checkpoints

• CIFM-100M [huggingface]

Citation

If you use this code for you research, please cite our paper.

@article{you2025building,
  title={Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics},
  author={You, Yuning and Wang, Zitong and Fleisher, Kevin and Liu, Rex and Thomson, Matt},
  journal={bioRxiv},
  pages={2025--01},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}