CEll spatial Organization-based graph convolutional network to integrate cell nuclei morphologies and cell-cell spatial interactions in helping clinical dicision, outcome prediction, and model interpretation.
- How to construct graph from cell spatial distribution, how to construct, train, and infer a Ceograph
- How to visualize cellular contribution to Ceograph
- How to visualize morphology and cell-cell interaction contribution to Ceograph
- python 3
- torch==1.0.1.post2
- torch-cluster==1.2.4
- torch-geometric==1.0.3
- torch-scatter==1.1.2
- torch-sparse==0.2.5
- torch-vision==0.1.6.dev0
- scikit-learn==0.20.3
- networkx==2.2
- more detailed environment information can be found in Session Info at the bottom of .ipynb files.