ABSTRACT
Classifying microarray datasets, which usually contains many noise genes that degrade the performance of classifiers and decrease classification accuracy rate, is a competitive research topic. Feature selection (FS) is one of the most practical ways for finding the most optimal subset of genes that increases classification's accuracy for diagnostic and prognostic prediction of tumor cancer from the microarray datasets. This means that we always need to develop more efficient FS methods, that select only optimal or close-to-optimal subset of features to improve classification performance. In this paper, we propose a hybrid FS method for microarray data processing, that combines an ensemble filter with an Improved Intelligent Water Drop (IIWD) algorithm as a wrapper by adding one of three local search (LS) algorithms: Tabu search (TS), Novel LS algorithm (NLSA), or Hill Climbing (HC) in each iteration from IWD, and using a correlation coefficient filter as a heuristic undesirability (HUD) for next node selection in the original IWD algorithm. The effects of adding three different LS algorithms to the proposed IIWD algorithm have been evaluated through comparing the performance of the proposed ensemble filter-IIWD-based wrapper without adding any LS algorithms named (PHFS-IWD) FS method versus its performance when adding a specific LS algorithm from (TS, NLSA or HC) in FS methods named, (PHFS-IWDTS, PHFS-IWDNLSA, and PHFS-IWDHC), respectively. Naïve Bayes(NB) classifier with five microarray datasets have been deployed for evaluating and comparing the proposed hybrid FS methods. Results show that using LS algorithms in each iteration from the IWD algorithm improves F-score value with an average equal to 5% compared with PHFS-IWD. Also, PHFS-IWDNLSA improves the F-score value with an average of 4.15% over PHFS-IWDTS, and 5.67% over PHFS-IWDHC while PHFS-IWDTS outperformed PHFS-IWDHC with an average of increment equal to 1.6%. On the other hand, the proposed hybrid-based FS methods improve accuracy with an average equal to 8.92% in three out of five datasets and decrease the number of genes with a percentage of 58.5% in all five datasets compared with six of the most recent state-of-the-art FS methods.
Subject(s)
Algorithms , Neoplasms , Humans , Bayes Theorem , Microarray Analysis , Neoplasms/diagnosis , Neoplasms/geneticsABSTRACT
This systematic review provides researchers interested in feature selection (FS) for processing microarray data with comprehensive information about the main research directions for gene expression classification conducted during the recent seven years. A set of 132 researches published by three different publishers is reviewed. The studied papers are categorized into nine directions based on their objectives. The FS directions that received various levels of attention were then summarized. The review revealed that 'propose hybrid FS methods' represented the most interesting research direction with a percentage of 34.9%, while the other directions have lower percentages that ranged from 13.6% down to 3%. This guides researchers to select the most competitive research direction. Papers in each category are thoroughly reviewed based on six perspectives, mainly: method(s), classifier(s), dataset(s), dataset dimension(s) range, performance metric(s), and result(s) achieved.