GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes

The measurement of gene functional similarity plays a critical role in numerous biological applications, such as gene clustering, the construction of gene similarity networks. However, most existing approaches still rely heavily on traditional computational strategies, which are not guaranteed to achieve satisfactory performance. In this study, we propose a novel computational approach called GOGCN to measure gene functional similarity by modeling the Gene Ontology (GO) through Graph Convolutional Network (GCN). GOGCN is a graph-based approach that performs sufficient representation learning for terms and relations in the GO graph. First, GOGCN employs the GCN-based knowledge graph embedding (KGE) model to learn vector representations (i.e., embeddings) for all entities (i.e., terms). Second, GOGCN calculates the semantic similarity between two terms based on their corresponding vector representations. Finally, GOGCN estimates gene functional similarity by making use of the pair-wise strategy. During the representation learning period, GOGCN promotes semantic interaction between terms through GCN, thereby capturing the rich structural information of the GO graph. Further experimental results on various datasets suggest that GOGCN is superior to the other state-of-the-art approaches, which shows its reliability and effectiveness.