Graph autoencoders for embedding learning in brain networks and major depressive disorder identification

Fuad Noman, Chee Ming Ting, Hakmook Kang, Raphael C.W. Phan, Hernando Ombao

Research output: Contribution to journalArticleResearchpeer-review


Brain functional connectivity (FC) networks inferred from functional magnetic resonance imaging (fMRI) have shown altered or aberrant brain functional connectome in various neuropsychiatric disorders. Recent application of deep neural networks to connectome-based classification mostly relies on traditional convolutional neural networks (CNNs) using input FCs on a regular Euclidean grid to learn spatial maps of brain networks neglecting the topological information of the brain networks, leading to potentially sub-optimal performance in brain disorder identification. We propose a novel graph deep learning framework that leverages non-Euclidean information inherent in the graph structure for classifying brain networks in major depressive disorder (MDD). We introduce a novel graph autoencoder (GAE) architecture, built upon graph convolutional networks (GCNs), to embed the topological structure and node content of large fMRI networks into low-dimensional representations. For constructing the brain networks, we employ the Ledoit-Wolf (LDW) shrinkage method to efficiently estimate high-dimensional FC metrics from fMRI data. We explore both supervised and unsupervised techniques for graph embedding learning. The resulting embeddings serve as feature inputs for a deep fully-connected neural network (FCNN) to distinguish MDD from healthy controls (HCs). Evaluating our model on resting-state fMRI MDD dataset, we observe that the GAE-FCNN outperforms several state-of-the-art methods for brain connectome classification, achieving the highest accuracy when using LDW-FC edges as node features. The graph embeddings of fMRI FC networks also reveal significant group differences between MDD and HCs. Our framework demonstrates the feasibility of learning graph embeddings from brain networks, providing valuable discriminative information for diagnosing brain disorders.

Original languageEnglish
Pages (from-to)1644-1655
Number of pages12
JournalIEEE Journal of Biomedical and Health Informatics
Issue number3
Publication statusPublished - Mar 2024


  • Bioinformatics
  • Brain connectivity networks
  • Brain modeling
  • Convolutional neural networks
  • Deep learning
  • Functional magnetic resonance imaging
  • graph autoencoder
  • graph convolutional network
  • Image reconstruction
  • major depressive disorder
  • resting-state fMRI
  • Sociology

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