Analysis of high-dimensional genomic data employing a novel bio-inspired algorithm

• Published in: Applied soft computing Vol. 77; pp. 520 - 532
• Main Authors: Baliarsingh, Santos Kumar, Vipsita, Swati, Muhammad, Khan, Dash, Bodhisattva, Bakshi, Sambit
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.04.2019
• Subjects: Classification; Fisher score; Kernel extreme learning machine (KELM); Microarray; Salp swarm optimization algorithm (SSA); Fisher score; Kernel extreme learning machine (KELM); Microarray; Salp swarm optimization algorithm (SSA); Classification
• ISSN: 1568-4946; 1872-9681
• DOI: 10.1016/j.asoc.2019.01.007

Over the last decade, there has been a rapid growth in the generation and analysis of the genomics data. Though the existing data analysis methods are capable of handling a particular problem, they cannot guarantee to solve all problems with different nature. Therefore, there always lie a scope of a new algorithm to solve a problem which cannot be efficiently solved by the existing algorithms. In the present work, a novel hybrid approach is proposed based on the improved version of a recently developed bio-inspired optimization technique, namely, salp swarm algorithm (SSA) for microarray classification. Initially, the Fisher score filter is employed to pre-select a subset of relevant genes from the original high-dimensional microarray dataset. Later, a weighted-chaotic SSA (WCSSA) is proposed for the simultaneous optimal gene selection and parameter optimization of the kernel extreme learning machine (KELM) classifier. The proposed scheme is experimented on both binary-class and multi-class microarray datasets. An extensive comparison is performed against original SSA-KELM, particle swarm optimized-KELM (PSO-KELM), and genetic algorithm-KELM (GA-KELM). Lastly, the proposed method is also compared against the results of sixteen existing techniques to emphasize its capacity and competitiveness to successfully reduce the number of original genes by more than 98%. The experimental results show that the genes selected by the proposed method yield higher classification accuracy compared to the alternative techniques. The performance of the proposed scheme demonstrates its effectiveness in terms of number of selected genes (NSG), accuracy, sensitivity, specificity, Matthews correlation coefficient (MCC), and F-measure. The proposed WCSSA-KELM method is validated using a ten-fold cross-validation technique. •We propose a method for simultaneous gene selection and parameter optimization.•A novel chaotic-weighted salp swarm algorithm is presented.•The proposed method is compared with original SSA-KELM, PSO-KELM, and GA-KELM.•Results show higher classification accuracy compared to the alternative techniques.•Validation is done on seven binary-class and multi-class microarray datasets.