TripletProt: Deep Representation Learning of Proteins based on Siamese Networks

We introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. We evaluate TripletProt comprehensively in protein functional annotation tasks including sub-cellular localization (14 categories) and gene ontology prediction (more than 2000 classes), which are both challenging multi-class multi-label classification machine learning problems. We compare the performance of TripletProt with the state-of-the-art approaches including recurrent language model-based approach (i.e., UniRep), as well as protein-protein interaction (PPI) network and sequence-based method (i.e., DeepGO). Our TripletProt showed an overall improvement of F1 score in the above mentioned comprehensive functional annotation tasks, solely relying on the PPI network. TripletProt and in general Siamese Network offer great potentials for the protein informatics tasks and can be widely applied to similar tasks.