Convolutional Neural Networks in Combination with Support Vector Machines for Complex Sequential Data Classification

Abstract

Trying to extract features from complex sequential data for classification and prediction problems is an extremely difficult task. Deep Machine Learning techniques, such as Convolutional Neural Networks (CNNs), have been exclusively designed to face this class of problems. Support Vector Machines (SVMs) are a powerful technique for general classification problems, regression, and outlier detection. In this paper we present the development and implementation of an innovative by design combination of CNNs with SVMs as a solution to the Protein Secondary Structure Prediction problem, with a novel two dimensional (2D) input representation method, where Multiple Sequence Alignment profile vectors are placed one under another. This 2D input is used to train the CNNs achieving preliminary results of 80.40% per residue accuracy (Q3), which are expected to increase with the use of larger training datasets and more sophisticated ensemble methods.