Graph CNNs for population graphs: classification of the ABIDE dataset

This code provides a python - Tensorflow implementation of graph convolutional networks (GCNs) for semi-supervised disease prediction using population graphs, as described in:

Parisot, S., Ktena, S. I., Ferrante, E., Lee, M., Moreno, R. G., Glocker, B., & Rueckert, D. (2017).
Spectral Graph Convolutions for Population-based Disease Prediction.
MICCAI 2017.

and

*Parisot, S., *Ktena, S. I., Ferrante, E., Lee, M., Moreno, R. G., Glocker, B., & Rueckert, D. (2017).
Disease Prediction using Graph Convolutional Networks: Application to Autism Spectrum Disorder and Alzheimer’s Disease.
Medical Image Analysis, 2018.

We provide an implementation applied to the ABIDE dataset for diagnosis of Autism Spectrum Disorder. We also provide the list of scans from the ADNI dataset used in our experiments. Each element of the list is in the format {SUBJECT_ID}_{ACQUISITION_MONTH}

INSTALLATION

To run the programme, you will need to install the implementation of graph convolutional networks (GCN) by Kipf et al. This project is only compatible with our forked GCN project.

The root folder in fetch_data.py (line 12) and ABIDEParser.py (line 17) has to be updated to the folder were the data will be stored.

Next, to install, organise and pre-process the ABIDE database: python fetch_data.py

USAGE

To run the programme with default parameters:

python main_ABIDE.py 

To get a detailed description of parameters:

python main_ABIDE.py --help 

REQUIREMENTS

tensorflow (>0.12)
networkx
nilearn
scikit-learn
joblib

REFERENCE

Please cite our papers if you use this code in your own work:

@article{parisot2017spectral, 
  title={Spectral Graph Convolutions on Population Graphs for Disease Prediction}, 
  author={Parisot, Sarah and Ktena, Sofia Ira and Ferrante, Enzo and Lee, Matthew and Moreno, Ricardo Guerrerro and Glocker, Ben and Rueckert, Daniel}, 
  journal={MICCAI}, 
  year={2017} 
}

@article{parisot2018disease,
  title={Disease Prediction using Graph Convolutional Networks: Application to Autism Spectrum Disorder and Alzheimer’s Disease},
  author={Parisot, Sarah and Ktena, Sofia Ira and Ferrante, Enzo and Lee, Matthew and Guerrero, Ricardo and Glocker, Ben and Rueckert, Daniel},
  journal={Medical image analysis},
  year={2018},
  publisher={Elsevier}
}