Dependency network methods for hierarchical multi-label classification of gene functions

Hierarchical Multi-label Classification (HMC) is a challenging real-world problem that naturally emerges in several areas. This work proposes two new algorithms using a Probabilistic Graphical Model based on Dependency Networks (DN) to solve the HMC problem of classifying gene functions into pre-established class hierarchies. DNs are especially attractive for their capability of using traditional, “out-of-the-shelf”, classification algorithms to model the relationship among classes and for their ability to cope with cyclic dependencies, resulting in greater flexibility with respect to Bayesian Networks. We tested our two algorithms: the first is a stand-alone Hierarchical Dependency Network (HDN) algorithm, and the second is a hybrid between the HDN and the Predictive Clustering Tree (PCT) algorithm, a well-known classifier for HMC. Based on our experiments, the hybrid classifier, using SVMs as base classifiers, obtained higher predictive accuracy than both the standard PCT algorithm and the HDN algorithm, considering 22 bioinformatics datasets and two out of three predictive accuracy measures specific for hierarchical classification (AU(PRC) and AUPRC w).