title: A novel weighted support vector machine based on particle swarm optimization for gene selection and tumor classification.
abstract: We develop a detection model based on support vector machines (SVMs) and particle swarm optimization (PSO) for gene selection and tumor classification problems. The proposed model consists of two stages: first, the well-known minimum redundancy-maximum relevance (mRMR) method is applied to preselect genes that have the highest relevance with the target class and are maximally dissimilar to each other. Then, PSO is proposed to form a novel weighted SVM (WSVM) to classify samples. In this WSVM, PSO not only discards redundant genes, but also especially takes into account the degree of importance of each gene and assigns diverse weights to the different genes. We also use PSO to find appropriate kernel parameters since the choice of gene weights influences the optimal kernel parameters and vice versa. Experimental results show that the proposed mRMR-PSO-WSVM model achieves highest classification accuracy on two popular leukemia and colon gene expression datasets obtained from DNA microarrays. Therefore, we can conclude that our proposed method is very promising compared to the previously reported results.
authors.affiliation: Department of Computer Sciences, Faculty of Mathematical Sciences, Tarbiat Modares University, P.O. Box 14115-134, Tehran, Iran. mj.abdi@modares.ac.ir
authors.forename: Mohammad Javad
authors.initials: MJ
authors.lastname: Abdi
authors.forename: Seyed Mohammad
authors.initials: SM
authors.lastname: Hosseini
authors.forename: Mansoor
authors.initials: M
authors.lastname: Rezghi
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007938:Leukemia / Q000175:diagnosis* / Q000235:genetics; D015233:Models, Statistical; D009369:Neoplasms / Q000175:diagnosis / Q000473:pathology*; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D060388:Support Vector Machine