update

README.md

@@ -13,8 +13,7 @@ tags:
 # CI-FM: Cellular Interaction Foundation Model
 
 ## Overview
-
-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:
+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:
 - **Embedding** of celllular microenvironments via ```embeddings = model.embed(adata)``` (Figure below panel D top);
 - **Inference** of cellular gene expressions at a certain microenvironment via ```expressions = model.predict_cells_at_locations(adata, rand_loc)``` (Figure below panel D bottom).
 
@@ -24,3 +23,19 @@ Before running the tutorial, please set up an environment following the [instruc
 More information about the model can be found in the [preprint]().
 
 ![](./figures/cifm.png)
+
+## Environment
+The environment can be set up via:
+```
+pip install torch==2.1.0 --index-url https://download.pytorch.org/whl/cu118
+pip install torch-scatter torch-sparse torch-cluster torch-geometric -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
+pip install scanpy e3nn
+pip install lightning==2.1.0
+pip install numpy==1.26.4
+```
+
+## Citation
+If you use this code for you research, please cite our paper.
+```
+    TBD
+```