Multi-task Learning for Classifying Proteins Using Dual Hierarchies

Several biological databases organize information in taxonomies/hierarchies. These databases differ in terms of curation process, input data, coverage and annotation errors. SCOP and CATH are examples of two databases that classify proteins hierarchically into structurally related groups based on experimentally determined structures. Given the large number of protein sequences with unavailable structure, there is a need to develop prediction methods to classify protein sequences into structural classes. We have developed a novel classification approach that utilizes the underlying relationships across multiple hierarchical source databases within a multi-task learning (MTL) framework. MTL is used to simultaneously learn multiple related tasks, and has been shown to improve generalization performance. Specifically, we have developed and evaluated an MTL approach for predicting the structural class, as defined by two hierarchical databases, CATH and SCOP, using protein sequence information only. We define one task per node of the hierarchies and formulate the MTL problem as a combination of these binary classification tasks. Our experimental evaluation demonstrates that the MTL approach that integrates both the hierarchies outperforms the base-line approach that trains independent models per task, as well as a MTL approach that integrates tasks across a single hierarchical database. We also performed extensive experiments that evaluate different regularization penalties and incorporate different task relationships that achieve superior classification performance.