A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder

• Published in: BMC bioinformatics Vol. 24; no. 1; pp. 1 - 17
• Main Authors: Shao, Lizhen, Fu, Cong, Chen, Xunying
• Format: Journal Article
• Language: English
• Published: London BioMed Central 27.09.2023; BioMed Central Ltd; BMC
• Subjects: Accuracy; Algorithms; Artificial neural networks; ASD; Attention mechanism; Autism; Bioinformatics; Biomarkers; Biomedical and Life Sciences; Brain; Brain mapping; Classification; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Data exchange; Datasets; Deep learning; Discriminant analysis; Feature selection; FMRI; Fourier transforms; Functional magnetic resonance imaging; Genotype & phenotype; Graph neural networks; Graphs; Heterogeneous graph convolution network; Information processing; Life Sciences; Machine learning; Magnetic resonance imaging; Medical imaging; Methods; Microarrays; Multilayer perceptrons; Neural networks; Neuroimaging; Phenotypes; Structured data; Support vector machines; Attention mechanism; ASD; FMRI; Heterogeneous graph convolution network
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05495-7

Background Autism spectrum disorder (ASD) is a serious developmental disorder of the brain. Recently, various deep learning methods based on functional magnetic resonance imaging (fMRI) data have been developed for the classification of ASD. Among them, graph neural networks, which generalize deep neural network models to graph structured data, have shown great advantages. However, in graph neural methods, because the graphs constructed are homogeneous, the phenotype information of the subjects cannot be fully utilized. This affects the improvement of the classification performance. Methods To fully utilize the phenotype information, this paper proposes a heterogeneous graph convolutional attention network (HCAN) model to classify ASD. By combining an attention mechanism and a heterogeneous graph convolutional network, important aggregated features can be extracted in the HCAN. The model consists of a multilayer HCAN feature extractor and a multilayer perceptron (MLP) classifier. First, a heterogeneous population graph was constructed based on the fMRI and phenotypic data. Then, a multilayer HCAN is used to mine graph-based features from the heterogeneous graph. Finally, the extracted features are fed into an MLP for the final classification. Results The proposed method is assessed on the autism brain imaging data exchange (ABIDE) repository. In total, 871 subjects in the ABIDE I dataset are used for the classification task. The best classification accuracy of 82.9% is achieved. Compared to the other methods using exactly the same subjects in the literature, the proposed method achieves superior performance to the best reported result. Conclusions The proposed method can effectively integrate heterogeneous graph convolutional networks with a semantic attention mechanism so that the phenotype features of the subjects can be fully utilized. Moreover, it shows great potential in the diagnosis of brain functional disorders with fMRI data.