Predicting isocitrate dehydrogenase mutation status in glioma using structural brain networks and graph neural networks

Yiran Wei, Yonghao Li, Xi Chen, Carola-Bibiane Schönlieb, Chao Li (Lead / Corresponding author), Stephen J. Price

Research output: Working paper/PreprintPreprint

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Glioma is a common malignant brain tumor with distinct survival among patients. The isocitrate dehydrogenase (IDH) gene mutation provides critical diagnostic and prognostic value for glioma. It is of crucial significance to non-invasively predict IDH mutation based on pre-treatment MRI. Machine learning/deep learning models show reasonable performance in predicting IDH mutation using MRI. However, most models neglect the systematic brain alterations caused by tumor invasion, where widespread infiltration along white matter tracts is a hallmark of glioma. Structural brain network provides an effective tool to characterize brain organisation, which could be captured by the graph neural networks (GNN) to more accurately predict IDH mutation. Here we propose a method to predict IDH mutation using GNN, based on the structural brain network of patients. Specifically, we firstly construct a network template of healthy subjects, consisting of atlases of edges (white matter tracts) and nodes (cortical/subcortical brain regions) to provide regions of interest (ROIs). Next, we employ autoencoders to extract the latent multi-modal MRI features from the ROIs of edges and nodes in patients, to train a GNN architecture for predicting IDH mutation. The results show that the proposed method outperforms the baseline models using the 3D-CNN and 3D-DenseNet. In addition, model interpretation suggests its ability to identify the tracts infiltrated by tumor, corresponding to clinical prior knowledge. In conclusion, integrating brain networks with GNN offers a new avenue to study brain lesions using computational neuroscience and computer vision approaches.
Original languageEnglish
Number of pages11
Publication statusPublished - 4 Sept 2021


  • glioma
  • MRI
  • isocitrate dehydrogenase
  • structural brain network
  • graph neural network


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  • Predicting Isocitrate Dehydrogenase Mutation Status in Glioma Using Structural Brain Networks and Graph Neural Networks

    Wei, Y., Li, Y., Chen, X., Schönlieb, C. B., Li, C. (Lead / Corresponding author) & Price, S. J., 2022, Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: 7th International Workshop, BrainLes 2021, Held in Conjunction with MICCAI 2021, Virtual Event, September 27, 2021, Revised Selected Papers, Part I. Crimi, A. & Bakas, S. (eds.). 1 ed. Switzerland: Springer , Vol. 1. p. 140-150 11 p. (Lecture Notes in Computer Science; vol. 12962).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
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