Dimension reduction and classifier-based feature selection for oversampled gene expression data and cancer classification

• Main Authors: Petinrin, Olutomilayo Olayemi, Saeed, Faisal, Salim, Naomie, Muhammad Toseef, Muhammad Toseef, Liu, Zhe, Muyide, Ibukun Omotayo
• Format: Article
• Language: English
• Published: MDPI 2023
• Subjects: Q Science (General); QA75 Electronic computers. Computer science
• Online Access: http://eprints.utm.my/106539/1/NaomieSalim2023_DimensionReductionandClassifierBasedFeature.pdf; http://eprints.utm.my/106539/; http://dx.doi.org/10.3390/pr11071940

Gene expression data are usually known for having a large number of features. Usually, some of these features are irrelevant and redundant. However, in some cases, all features, despite being numerous, show high importance and contribute to the data analysis. In a similar fashion, gene expression data sometimes have limited instances with a high rate of imbalance among the classes. This can limit the exposure of a classification model to instances of different categories, thereby influencing the performance of the model. In this study, we proposed a cancer detection approach that utilized data preprocessing techniques such as oversampling, feature selection, and classification models. The study used SVMSMOTE for the oversampling of the six examined datasets. Further, we examined different techniques for feature selection using dimension reduction methods and classifier-based feature ranking and selection. We trained six machine learning algorithms, using repeated 5-fold cross-validation on different microarray datasets. The performance of the algorithms differed based on the data and feature reduction technique used.