protein2vec: Predicting Protein-Protein Interactions Based on LSTM

The semantic similarity of gene ontology (GO) terms is widely used to predict protein-protein interactions (PPIs). The traditional semantic similarity measures are based mainly on manually crafted features, which may ignore some important hidden information of the gene ontology. Moreover, those methods usually obtain the similarity between proteins from similarity between GO terms by some simple statistical rules, such as MAX and BMA (best-match average), oversimplifying the possible complex relationship between the proteins and the GO terms annotated with them. To overcome the two deficiencies, we propose a new method named protein2vec, which characterizes a protein with a vector based on the GO terms annotated to it and combines the information of both the GO and known PPIs. We firstly try to apply the network embedding algorithm on the GO network to generate feature vectors for each GO term. Then, Long Short-Time Memory (LSTM) encodes the feature vectors of the GO terms annotated with a protein into another vector (called protein vector). Finally, two protein vectors are forwarded into a feedforward neural network to predict the interaction between the two corresponding proteins. The experimental results show that protein2vec outperforms almost all commonly used traditional semantic similarity methods.