7459f008ef6b0d7188277c4328f8b3e3 pmc_29562690.pdf 7231097243aca6a74e34dacfcb216992fbb8f2ca pmc_29562690.pdf eacb14505eb34043183b1637dbfe738e62401360d33206c4ad9b3c4e26191ca8 pmc_29562690.pdf Title: Representation Learning for Class C G Protein-Coupled Receptors Classification Subject: G protein-coupled receptors (GPCRs) are integral cell membrane proteins of relevance for pharmacology. The complete tertiary structure including both extracellular and transmembrane domains has not been determined for any member of class C GPCRs. An alternative way to work on GPCR structural models is the investigation of their functionality through the analysis of their primary structure. For this, sequence representation is a key factor for the GPCRs' classification context, where usually, feature engineering is carried out. In this paper, we propose the use of representation learning to acquire the features that best represent the class C GPCR sequences and at the same time to obtain a model for classification automatically. Deep learning methods in conjunction with amino acid physicochemical property indices are then used for this purpose. Experimental results assessed by the classification accuracy, Matthews' correlation coefficient and the balanced error rate show that using a hydrophobicity index and a restricted Boltzmann machine (RBM) can achieve performance results (accuracy of 92.9%) similar to those reported in the literature. As a second proposal, we combine two or more physicochemical property indices instead of only one as the input for a deep architecture in order to add information from the sequences. Experimental results show that using three hydrophobicity-related index combinations helps to improve the classification performance (accuracy of 94.1%) of an RBM better than those reported in the literature for class C GPCRs without using feature selection methods. Keywords: representation learning; G protein-coupled receptors; deep learning; pattern classification Author: Raúl Cruz-Barbosa, Erik G. 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