A Novel Weighted Support Vector Machine Based on Particle Swarm Optimization for Gene Selection and Tumor Classification

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...

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Bibliographic Details
Published in:Computational and mathematical methods in medicine 2012-01, Vol.2012 (2012), p.1-7
Main Authors: Abdi, Mohammad Javad, Hosseini, Seyed Mohammad, Rezghi, Mansoor
Format: Article
Language:English
Subjects:
Algorithms
Artificial Intelligence
Colonic Neoplasms - diagnosis
Colonic Neoplasms - genetics
Computational Biology - methods
Databases, Genetic
Gene Expression Profiling
Gene Expression Regulation, Leukemic
Gene Expression Regulation, Neoplastic
Humans
Leukemia - diagnosis
Leukemia - genetics
Models, Statistical
Neoplasms - diagnosis
Neoplasms - pathology
Oligonucleotide Array Sequence Analysis
Reproducibility of Results
Support Vector Machine
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Summary: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.
ISSN:1748-670X
1748-6718
DOI:10.1155/2012/320698