Selection of Cancer Biomarkers from Microarray Gene Expression Data Utilizing the Bi-Objective Optimization Method

Cancer-associated biomarker genes play an indispensable role in the intricate tapestry of cancer development and manifestation. The expression of biomarkers in different types of tumor cells has beneficial implications for shedding light on the development of various cancers, guiding clinical diagnosis, and treatment. Microarray technology enables the expression levels of thousands of genes in samples to be sequenced simultaneously. However, sparse and high-dimensional microarray data present a formidable challenge in identifying biomarker genes. This study presents EREF-NSGA2, a novel method for cancer biomarker selection from microarray data, employing a hybrid gene selection approach. Firstly, the combination of the wrapper and embedded gene selection methods is proposed to filter the microarray data, which efficiently decreases the search space of the algorithm. After that, the improved NSGA-II algorithm is used to search the genes subset obtained from the previous step to reach the optimal subset of cancer biomarker genes. The proposed EREF-NSGA2 is compared with other reported methods on six cancer benchmark gene expression datasets. A detailed biological analysis is performed to analyze the relationship between the selected genes and the cancer data sets they belong to. To summarize, EREF-NSGA2 proves its effectiveness in selecting a feature subset comprising the fewest genes while maintaining the highest classification accuracy.