This repository provides the official PyTorch implementation of the following paper:
Graph Super-Resolution Network for predicting high-resolution connectomes from low-resolution connectomes. Megi Isallari1, Islem Rekik1
1BASIRA Lab, Faculty of Computer and Informatics, Istanbul Technical University, Istanbul, Turkey
Please contact isallari.megi@gmail.com for further inquiries. Thanks.
While a significant number of image super-resolution methods have been proposed for MRI super-resolution, building generative models for super-resolving a low-resolution brain connectome at a higher resolution (i.e., adding new graph nodes/edges) remains unexplored —although this would circumvent the need for costly data collection and manual labelling of anatomical brain regions (i.e. parcellation). To fill this gap, we introduce GSR-Net (Graph Super-Resolution Network), the first super-resolution framework operating on graph-structured data that generates high-resolution brain graphs from low-resolution graphs.
This work has been accepted to “Machine Learning in Medical Imaging” (MLMI) MICCAI 2020 workshop. The key idea of GSR-Net (Graph Super-Resolution Network) can be summarized in three fundamental steps: (i) learning feature embeddings for each brain ROI (node) in the LR connectome, (ii) the design of a graph super-resolution operation that predicts an HR connectome from the LR connectivity matrix and feature embeddings of the LR connectome computed in (i), (iii) learning node feature embeddings for each node in the super-resolved (HR) graph obtained in (ii). We used 5-fold cross-validation to evaluate our framework on 277 subjects from the Southwest University Longitudinal Imaging Multimodal (SLIM) study: http://fcon_1000.projects.nitrc.org/indi/retro/southwestuni_qiu_index.html. In this repository, we release the code for training and testing GSR-Net on the SLIM dataset.
The code has been tested with Google Colaboratory which uses Ubuntu 18.04.3 LTS Bionic, Python 3.6.9 and PyTorch 1.4.0. In case you opt to run the code locally, you need to install the following python packages via pip:
We provide a demo code in demo.py
to run the script of GSR-Net for predicting high-resolution connectomes from low-resolution functional brain connectomes. To set the parameters, you should provide commandline arguments.
If you want to run the code in the hyperparameters described in the paper, you can run it without any commandline arguments:
$ python demo.py
It would be equivalent to:
$ python demo.py –epochs=200 –lr=0.0001 –splits=5 –lmbda=16 –lr_dim=160 –hr_dim=320 –hidden_dim=320 –padding=26
To learn more about how to use the arguments:
$ python demo.py --help
Plugin | README |
---|---|
epochs | number of epochs to train |
lr | learning rate of Adam Optimizer |
splits | number of cross validation folds |
lmbda | self-reconstruction error hyper-parameter |
lr_dim | number of nodes of low-resolution brain graph |
hr_dim | number of nodes of high-resolution brain graph |
hidden_dim | number of hidden GCN layer neurons |
padding | dimensions of padding |
We also note that in our published paper, K was set to 2.
Data preparation
In our paper, we have used the SLIM dataset. In this repository, we simulated a n x l x l tensor X ( low-resolution connectomes for all subjects where l is the number of nodes of the LR connectome) and a n x h x h tensor Y (high-resolution connectomes for all subjects where h is the number of nodes of the HR connectome) It might yield in suboptimal results since data is randomly generated opposed to real brain graph data.
To use a dataset of your own preference, you can edit the data() function at preprocessing.py. In order to train and test the framework, you need to provide:
N
low-resolution brain graph connectomes of dimensionsL*L
for variableX
indemo.py
N
high-resolution brain graph connectomes of dimensionsH*H
for variableY
indemo.py
If you run the demo with the default parameter setting as in the command below,
$ python demo.py –epochs=200 –lr=0.0001 –splits=5 –lmbda=16 –lr_dim=160 –hr_dim=320 –hidden_dim=320 –padding=26
you will get the following outputs:
To install and run GSR-Net, check the following YouTube video: https://youtu.be/GahVu9NeOIg
To learn about how GSR-Net works, check the following YouTube video: https://youtu.be/xwHKRxgMaEM
Graph U-Nets: Gao, H., Ji, S.: Graph u-nets. In Chaudhuri, K., Salakhutdinov, R., eds.: Proceedings of the 36th International Conference on Machine Learning. Volume 97 of Proceedings of Machine Learning Research., Long Beach, California, USA, PMLR (2019) 2083–2092 [https://github.com/HongyangGao/Graph-U-Nets]
SLIM Dataset: Liu, W., Wei, D., Chen, Q., Yang, W., Meng, J., Wu, G., Bi, T., Zhang, Q., Zuo, X.N., Qiu, J.: Longitudinal test-retest neuroimaging data from healthy young adults in southwest china. Scientific Data 4 (2017) [https://www.nature.com/articles/sdata201717]
https://arxiv.org/abs/2009.11080
@inproceedings{Isallari2020,
title={Graph Super-Resolution Network for predicting high-resolution connectomes from low-resolution connectomes},
author={Isallari, Megi and Rekik, Islem},
booktitle={International Workshop on PRedictive Intelligence In MEdicine},
year={2020},
organization={Springer}
}