Alpha-plane based automatic general type-2 fuzzy clustering based on simulated annealing meta-heuristic algorithm for analyzing gene expression data

• Published in: Computers in biology and medicine Vol. 64; pp. 347 - 359
• Main Authors: Doostparast Torshizi, Abolfazl, Fazel Zarandi, Mohammad Hossein
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01.09.2015; Elsevier Limited
• Subjects: Algorithms; Animals; Arabidopsis; Cluster Analysis; Clustering; Computational Biology - methods; Databases, Genetic; Fuzzy Logic; Fuzzy sets; Gene expression data; Gene Expression Profiling - methods; General type-2 fuzzy sets; Humans; Internal Medicine; Methods; Optimization; Other; Rats; Simulated annealing; α-plane representation; General type-2 fuzzy sets; Gene expression data; α-plane representation; Clustering; Simulated annealing
• ISSN: 0010-4825; 1879-0534; 1879-0534
• DOI: 10.1016/j.compbiomed.2014.06.017

This paper considers microarray gene expression data clustering using a novel two stage meta-heuristic algorithm based on the concept of α-planes in general type-2 fuzzy sets. The main aim of this research is to present a powerful data clustering approach capable of dealing with highly uncertain environments. In this regard, first, a new objective function using α-planes for general type-2 fuzzy c-means clustering algorithm is represented. Then, based on the philosophy of the meta-heuristic optimization framework ‘Simulated Annealing’, a two stage optimization algorithm is proposed. The first stage of the proposed approach is devoted to the annealing process accompanied by its proposed perturbation mechanisms. After termination of the first stage, its output is inserted to the second stage where it is checked with other possible local optima through a heuristic algorithm. The output of this stage is then re-entered to the first stage until no better solution is obtained. The proposed approach has been evaluated using several synthesized datasets and three microarray gene expression datasets. Extensive experiments demonstrate the capabilities of the proposed approach compared with some of the state-of-the-art techniques in the literature. •Presenting a new two-stage meta-heuristic clustering algorithm based on general type-2 fuzzy sets.•Incorporating a new similarity-based objective function using alpha-plane representation of general type-2 fuzzy sets.•Implementing the proposed approach on real microarray gene expression datasets.