Modified Cuckoo Search-Support Vector Machine (MCS-SVM) Gene Selection and Classification for Autism Spectrum Disorder (ASD) Gene Expression

Abstract

Autism Spectrum Disorder (ASD) is a neuro developmental disorder characterized by weakened social skills, impaired verbal and non-verbal interaction, and repeated behavior. ASD has increased in the past few years and the root cause of the symptom cannot yet be determined. In ASD with gene expression is analyzed by classification methods. For the selection of genes in ASD, statistical philtres and a wrapper-based Geometric Binary Particle Swarm Optimization-Support Vector Machine (GBPSO-SVM) algorithm have recently been implemented. However GBPSO has provides lesser accuracy, if the dataset samples are large and it cannot directly apply to multiple output systems. To overcome this issue, Modified Cuckoo Search-Support Vector Machine (MCS-SVM) based wrapper feature selection algorithm is proposed which improves the accuracy of the classifier in ASD. This work consists of three major steps, (i) preprocessing, (ii) gene selection, and (iii) classification. Firstly, preprocessing is performed by mean or median ratios close to unity was removed from original gene dataset; based on this samples are reduced from 54,613 to 9454. Secondly, gene selection is performed by using statistical filters and wrapper algorithm. Statistical filters methods like Wilcox on Rank Sum test (WRS), Class Correlation (COR) function and Two-sample T-test (TT) were applied in parallel to a ten-fold cross validation range of the most discriminatory genes. In the wrapper algorithm, Modified Cuckoo Search (MCS) is also proposed to gene selection. This step decreases the number of genes of the dataset by removing genes. Finally, SVM classifier combined forms of gene subsets for grading. The autism microarray dataset used in the analysis was downloaded from the benchmark public repository Gene Expression Omnibus (GEO) (National Center for Biotechnology Information (NCBI)). The classification methods are measured in terms of the metrics like precision, recall, f-measure and accuracy. Proposed MCS-SVM classifier achieves highest accuracy when compared Linear Regression (LR), and GBPSO-SVM classifiers.