Biomarkers plays an important role in the prediction and diagnosis of cancers. Therefore, it is urgent to design effective methods to extract biomarkers. The corresponding pathway information of the microarray gene expression data can be obtained from public database, which makes possible to identify biomarkers based on pathway information and has been attracted extensive attention. In the most existing methods, all the member genes in the same pathway are regarded as equally important for inferring pathway activity. However, the contribution of each gene should be different in the process of inferring pathway activity. In this research, an improved multi-objective particle swarm optimization algorithm with penalty boundary intersection decomposition mechanism (IMOPSO-PBI) has been proposed to quantify the relevance of each gene in pathway activity inference. In the proposed algorithm, two optimization objectives namely t-score and z-score respectively has been introduced. In addition, in order to solve the problem that optimal set with poor diversity in the most multi-objective optimization algorithms, an adaptive mechanism for adjusting penalty parameters based on PBI decomposition has been introduced. The performance of the proposed IMOPSO-PBI approach compared with some existing methods on six gene expression datasets has been given. To verify the effectiveness of the proposed IMOPSO-PBI algorithm, experiments were carried out on six gene datasets and the results has been compared with the existing methods. The comparative experiment results show that the proposed IMOPSO-PBI method has a higher classification accuracy and the extracted feature genes are verified possess biological significance.
Keywords: PBI decomposition mechanism; adaptive strategy; multi-objective optimization; particle swarm optimization; pathway activity.