A novel gene selection algorithm for cancer classification using microarray datasets

• Main Authors: Russul Alanni, Jingyu Hou, Hasseeb Azzawi, Yong Xiang
• Format: Article
• Language: English
• Published: BMC 2019-01-01
• Series: BMC Medical Genomics
• Subjects: Gene selection; Gene expression programming; Support vector machine; Microarray cancer dataset
• Online Access: http://link.springer.com/article/10.1186/s12920-018-0447-6

Abstract Background Microarray datasets are an important medical diagnostic tool as they represent the states of a cell at the molecular level. Available microarray datasets for classifying cancer types generally have a fairly small sample size compared to the large number of genes involved. This fact is known as a curse of dimensionality, which is a challenging problem. Gene selection is a promising approach that addresses this problem and plays an important role in the development of efficient cancer classification due to the fact that only a small number of genes are related to the classification problem. Gene selection addresses many problems in microarray datasets such as reducing the number of irrelevant and noisy genes, and selecting the most related genes to improve the classification results. Methods An innovative Gene Selection Programming (GSP) method is proposed to select relevant genes for effective and efficient cancer classification. GSP is based on Gene Expression Programming (GEP) method with a new defined population initialization algorithm, a new fitness function definition, and improved mutation and recombination operators. . Support Vector Machine (SVM) with a linear kernel serves as a classifier of the GSP. Results Experimental results on ten microarray cancer datasets demonstrate that Gene Selection Programming (GSP) is effective and efficient in eliminating irrelevant and redundant genes/features from microarray datasets. The comprehensive evaluations and comparisons with other methods show that GSP gives a better compromise in terms of all three evaluation criteria, i.e., classification accuracy, number of selected genes, and computational cost. The gene set selected by GSP has shown its superior performances in cancer classification compared to those selected by the up-to-date representative gene selection methods. Conclusion Gene subset selected by GSP can achieve a higher classification accuracy with less processing time.