Efficient technique of microarray missing data imputation using clustering and weighted nearest neighbour

Abstract

AbstractFor most bioinformatics statistical methods, particularly for gene expression data classification, prognosis, and prediction, a complete dataset is required. The gene sample value can be missing due to hardware failure, software failure, or manual mistakes. The missing data in gene expression research dramatically affects the analysis of the collected data. Consequently, this has become a critical problem that requires an efficient imputation algorithm to resolve the issue. This paper proposed a technique considering the local similarity structure that predicts the missing data using clustering and top K nearest neighbor approaches for imputing the missing value. A similarity-based spectral clustering approach is used that is combined with the K-means. The spectral clustering parameters, cluster size, and weighting factors are optimized, and after that, missing values are predicted. For imputing each cluster’s missing value, the top K nearest neighbor approach utilizes the concept of weighted distance. The evaluation is carried out on numerous datasets from a variety of biological areas, with experimentally inserted missing values varying from 5 to 25%. Experimental results prove that the proposed imputation technique makes accurate predictions as compared to other imputation procedures. In this paper, for performing the imputation experiments, microarray gene expression datasets consisting of information of different cancers and tumors are considered. The main contribution of this research states that local similarity-based techniques can be used for imputation even when the dataset has varying dimensionality and characteristics.