Graph embeddings on gene ontology annotations for protein–protein interaction prediction

Background: Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations and disease-drug associations. However, many previous PPI prediction researches do not consider missing and spurious interactions inherent in PPI networks. To address these two issues, we define two corresponding tasks, namely missing PPI prediction and spurious PPI prediction, and propose a method that employs graph embeddings that learn vector representations from constructed Gene Ontology Annotation (GOA) graphs and then use embedded vectors to achieve the two tasks. Our method leverages on information from both term–term relations among GO terms and term-protein annotations between GO terms and proteins, and preserves properties of both local and global structural information of the GO annotation graph. Results: We compare our method with those methods that are based on information content (IC) and one method that is based on word embeddings, with experiments on three PPI datasets from STRING database. Experimental results demonstrate that our method is more effective than those compared methods. Conclusion: Our experimental results demonstrate the effectiveness of using graph embeddings to learn vector representations from undirected GOA graphs for our defined missing and spurious PPI tasks.