GCNPMDA: Human microbe-disease association prediction by hierarchical graph convolutional network with layer attention

Abstract

Microorganisms play a crucial role in various physiological processes, including metabolism, immune defense, nutrition absorption, defense against cancer, and protection against pathogen colonization. Changes in microbial communities serve as potential biomarkers for diseases, offering significant insights into disease treatment and diagnosis. However, the association between microorganisms and diseases is still unclear, and more computational methods are needed to predict potential associations. In this paper, we introduce a novel computational model, the Graph Convolutional Network to Predict Microbe-Disease Associations (GCNPMDA), which employs layer attention mechanisms (see Figure 1). GCNPMDA integrates known microbe-disease associations, microbe–microbe similarities, and disease–disease similarities into a heterogeneous network. The model utilizes a Graph Convolutional Network (GCN) to learn embeddings for diseases and microbes. To enhance attribute information, microbe–microbe similarities are computed using Cosine similarity, Jaccard similarity, Gaussian kernel, and functional information, while disease–disease similarities are computed using Cosine similarity, Jaccard similarity, Gaussian kernel, and symptom information. Additionally, attention mechanisms are applied to combine embeddings from multiple graph convolution layers. The model’s predictive effectiveness is evaluated on Human Microbe-Disease Association Database (HMDAD). Leave-one-out cross-validation (LOOCV) was conducted. The Area Under ROC Curve (AUC) of LOOCV is 0.98. The 5-fold cross-validation (5-fold CV) on HMDAD yields average AUC of 0.98 ± 0.009. Furthermore, we carried out a case study of type 2 diabetes (T2D), inflammatory bowel disease (IBD), and rheumatoid arthritis. Based on existing literature evidence, it was confirmed that 6, 7, and 7 of the top-10 inferred microbes have established associations with T2D, IBD, and rheumatoid arthritis, respectively. GCNPMDA demonstrates potential efficacy in identifying disease-related microbes, offering a promising tool to uncover the intricate relationship between microorganisms and their human hosts.