Feature Selection and Extraction Framework for DNA Methylation in Cancer

Abstract

Feature selection methods for cancer classification are aimed to overcome the high dimensionality of the biomedical data which is a challenging task. Most of the feature selection methods based on DNA methylation are time consuming during testing phase to identify the best pertinent features subset that are relevant to accurate prediction. However, the hybridization between feature selection and extraction methods will bring a method that is far fast than only feature selection method. This paper proposes a framework based on both novel feature selection methods that employ statistical variation, standard deviation and entropy, along with extraction methods to predict cancer using three new features, namely, Hypomethylation, Midmethylation and Hypermethylation. These new features represent the average methylation density of the corresponding three regions. The three features are extracted from the selected features based on the analysis of the methylation behavior. The effectiveness of the proposed framework is evaluated by the breast cancer classification accuracy. The results give 98.85% accuracy using only three features out of 485,577 features. This result proves the capability of the proposed approach for breast cancer diagnosis and confirms that feature selection and extraction methods are critical for practical implementation.