Combining graph and sequence information to learn protein representations

Computational methods that infer the function of proteins are key to understanding life at the molecular level. In recent years, representation learning has emerged as a powerful paradigm to discover new patterns among entities as varied as images, words, speech, molecules. In typical representation learning, there is only one source of data or one level of abstraction at which the learned representation occurs. However, proteins can be described by their primary, secondary, tertiary, and quaternary structure or even as nodes in protein-protein interaction networks. Given that protein function is an emergent property of all these levels of interactions in this work, we learn joint representations from both amino acid sequence and multilayer networks representing tissue-specific protein-protein interactions. Using these representations, we train machine learning models that outperform existing methods on the task of tissue-specific protein function prediction on 10 out of 13 tissues. Furthermore, we outperform existing methods by 19% on average.