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Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure

Red Bank Veterinary Hospital, 2051 Briggs Road, Mount Laurel, NJ 08054, USA
Intelligent Systems Program, University of Pittsburgh, 5113 Sennott Square, 210 South Bouquet Street, Pittsburgh, PA 15260, USA
Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Boulevard, Pittsburgh, PA 15206, USA
These authors contributed equally to this work.
Author to whom correspondence should be addressed.
Academic Editor: Pufeng Du
Received: 30 September 2016 / Revised: 14 December 2016 / Accepted: 9 January 2017 / Published: 18 January 2017
(This article belongs to the Special Issue Biomedical Informatics)
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The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilities to summarize the observed data. We extend a Bayesian Rule Learning (BRL-GSS) algorithm, previously shown to be a significantly better predictor than other classical approaches in this domain. It searches a space of Bayesian networks using a decision tree representation of its parameters with global constraints, and infers a set of IF-THEN rules. The number of parameters and therefore the number of rules are combinatorial in the number of predictor variables in the model. We relax these global constraints to learn a more expressive local structure with BRL-LSS. BRL-LSS entails a more parsimonious set of rules because it does not have to generate all combinatorial rules. The search space of local structures is much richer than the space of global structures. We design the BRL-LSS with the same worst-case time-complexity as BRL-GSS while exploring a richer and more complex model space. We measure predictive performance using Area Under the ROC curve (AUC) and Accuracy. We measure model parsimony performance by noting the average number of rules and variables needed to describe the observed data. We evaluate the predictive and parsimony performance of BRL-GSS, BRL-LSS and the state-of-the-art C4.5 decision tree algorithm, across 10-fold cross-validation using ten microarray gene-expression diagnostic datasets. In these experiments, we observe that BRL-LSS is similar to BRL-GSS in terms of predictive performance, while generating a much more parsimonious set of rules to explain the same observed data. BRL-LSS also needs fewer variables than C4.5 to explain the data with similar predictive performance. We also conduct a feasibility study to demonstrate the general applicability of our BRL methods on the newer RNA sequencing gene-expression data. View Full-Text
Keywords: rule based models; gene expression data; Bayesian networks; parsimony rule based models; gene expression data; Bayesian networks; parsimony

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Lustgarten, J.L.; Balasubramanian, J.B.; Visweswaran, S.; Gopalakrishnan, V. Learning Parsimonious Classification Rules from Gene Expression Data Using Bayesian Networks with Local Structure. Data 2017, 2, 5.

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