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README.md
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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 biological 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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# 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 biological activities within a living tissue (AI virtual tissue), which has 138M parameters (current version) and is trained on around 23M cells of spatial genomics. 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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