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README.md
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# CI-FM: Cellular Interaction Foundation Model
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This is the pytorch implementation of the CI-FM model -- an AI model that can simulate the cellular activities within a living tissue (AI virtual tissue). The signature functions of CI-FM are:
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- **Embedding** of celllular microenvironments via ```embeddings = model.embed(adata)``` (Figure below panel D top);
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- **Inference** of cellular gene expressions at a certain microenvironment via ```expressions = model.predict_cells_at_locations(adata, rand_loc)``` (Figure below panel D bottom).
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The detailed usage of the model can be found in the [tutorial](https://huggingface.co/ynyou/CIFM/blob/main/test.ipynb).
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More information about the model can be found in the [preprint]().
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# CI-FM: Cellular Interaction Foundation Model
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## Overview
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This is the pytorch implementation of the CI-FM model -- an AI model that can simulate the cellular activities within a living tissue (AI virtual tissue). The signature functions of CI-FM are:
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- **Embedding** of celllular microenvironments via ```embeddings = model.embed(adata)``` (Figure below panel D top);
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- **Inference** of cellular gene expressions at a certain microenvironment via ```expressions = model.predict_cells_at_locations(adata, rand_loc)``` (Figure below panel D bottom).
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The detailed usage of the model can be found in the [tutorial](https://huggingface.co/ynyou/CIFM/blob/main/test.ipynb).
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Before running the tutorial, please set up an environment following the instructions.
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More information about the model can be found in the [preprint]().
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