A hierarchical multi-label classification method based on neural networks for gene function prediction

Abstract

Gene function prediction is used to assign biological or biochemical functions to genes, which continues to be a challenging problem in modern biology. Genes may exhibit many functions simultaneously, and these functions are organized into a hierarchy, such as a directed acyclic graph (DAG) for Gene Ontology (GO). Because of these characteristics, gene function prediction can be seen as a typical hierarchical multi-label classification (HMC) task. A novel HMC method based on neural networks is proposed in this article for predicting gene function based on GO. The proposed method belongs to a local approach by transferring the HMC task to a set of subtasks. There are three strategies implemented in this method to improve its performance. First, to tackle the imbalanced data set problem when building the training data set for each class, negative instances selecting policy and SMOTE approach are used to preprocess each imbalanced training data set. Second, a particular multi-layer perceptron (MLP) is designed for each node in GO. Third, a post processing method based on the Bayesian network is used to guarantee that the results are consistent with the hierarchy constraint. The experimental results indicate that the proposed HMC-MLPN method is a promising method for gene function prediction based on a comparison with two other state-of-the-art methods.