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, Stephen J. Price

Research output: Chapter or section in a book/report/conference proceedingChapter in a published conference proceeding

2 Citations (SciVal)
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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
Title of host publicationInternational MICCAI Brain Lesion Workshop
Subtitle of host publicationBrainLes 2021
PublisherSpringer Science and Business Media Deutschland GmbH
Number of pages12
ISBN (Electronic)978-3-031-08999-2
ISBN (Print)978-3-031-08998-5
Publication statusPublished - 22 Jul 2022

Publication series

NameLecture Notes in Computer Science
PublisherSpringer, Cham.
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Bibliographical note

Accepted by Brain Lesion Workshop


  • eess.IV
  • cs.CV
  • q-bio.NC


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