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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

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}
}