An adaptive rule-based classifier for mining big biological data

TitleAn adaptive rule-based classifier for mining big biological data
Publication TypeJournal Article
Year of Publication2016
AuthorsFarid, DMd.
Secondary AuthorsAl-Mamun, MAbdullah
Tertiary AuthorsManderick, B, Nowe, A
JournalExpert Systems with Applications, Elsevier
Volume64
Start Page305-316
Type of ArticleFull length article
KeywordsBrugada syndrome, Classification, Decision tree, Genomic data, Rule-based classifier
Abstract

In this paper, we introduce a new adaptive rule-based classifier for multi-class classification of biological data, where several problems of classifying biological data are addressed: overfitting, noisy instances and class-imbalance data. It is well known that rules are interesting way for representing data in a human interpretable way. The proposed rule-based classifier combines the random subspace and boosting approaches with ensemble of decision trees to construct a set of classification rules without involving global optimisation. The classifier considers random subspace approach to avoid overfitting, boosting approach for classifying noisy instances and ensemble of decision trees to deal with class-imbalance problem. The classifier uses two popular classification techniques: decision tree and k-nearest-neighbor algorithms. Decision trees are used for evolving classification rules from the training data, while k-nearest-neighbor is used for analysing the misclassified instances and removing vagueness between the contradictory rules. It considers a series of k iterations to develop a set of classification rules from the training data and pays more attention to the misclassified instances in the next iteration by giving it a boosting flavour. This paper particularly focuses to come up with an optimal ensemble classifier that will help for improving the prediction accuracy of DNA variant identification and classification task. The performance of proposed classifier is tested with compared to well-approved existing machine learning and data mining algorithms on genomic data (148 Exome data sets) of Brugada syndrome and 10 real benchmark life sciences data sets from the UCI (University of California, Irvine) machine learning repository. The experimental results indicate that the proposed classifier has exemplary classification accuracy on different types of biological data. Overall, the proposed classifier offers good prediction accuracy to new DNA variants classification where noisy and misclassified variants are optimised to increase test performance.

DOI10.1016/j.eswa.2016.08.008