Gene Selection Of Microarray Data Research Articles

A new multi-objective binary Harris Hawks optimization for gene selection in microarray data

A new multi-objective binary Harris Hawks optimization for gene selection in microarray data

Using data complexity measures and an evolutionary cultural algorithm for gene selection in microarray data

Cancer detection using gene expression data has been a major trend of research for the last decade. Microarray gene expression data is one of the most challenging types of data due to high dimensionality and rarity of available samples. Feature redundancy greatly contributes to the difficulty of prediction task. Therefore, it is essential to apply feature selection to datasets to reduce the number of features selected for the classification task. In this paper, a novel two-staged framework is proposed to confront curse of dimensionality in microarray data using data complexity measures and a customized cultural algorithm, incorporating a static belief space into the genetic algorithm in order to reduce the search space and prioritize important genes. Experimental results indicate highly improved accuracy and reduction in number of selected genes compared to the state-of-the-art methods on Gli85, Colon, DLBCL, SMK and CNS datasets.

Hybridization of Moth flame optimization algorithm and quantum computing for gene selection in microarray data

Ever-increasing data in various fields like Bioinformatics field, which has led to the need to find a way to reduce the data dimensionality. Gene selection problem has a large number of genes (relevant, redundant or noise), which needs an effective method to help us in detecting diseases and cancer. In this problem, computational complexity is reduced by selecting a small number of genes, but it is necessary to choose the relevant genes to keep a high level of accuracy. Therefore, in order to find the optimal gene subset, it is essential to devise an effective exploration approach that can investigate a large number of possible gene subsets. In addition, it is required to use a powerful evaluation method to evaluate the relevance of these gene subsets. In this paper, we present a novel swarm intelligence algorithm for gene selection called quantum moth flame optimization algorithm (QMFOA), which based on hybridization between quantum computation and moth flame optimization (MFO) algorithm. The purpose of QMFOA is to identify a small gene subset that can be used to classify samples with high accuracy. The QMFOA has a simple two-phase approach, the first phase is a pre-processing that uses to address the difficulty of high-dimensional data, which measure the redundancy and the relevance of the gene, in order to obtain the relevant gene set. The second phase is a hybridization among MFOA, quantum computing, and support vector machine with leave-one-out cross-validation, etc., in order to solve the gene selection problem. We use quantum computing to guarantee a good trade-off between the exploration and the exploitation of the search space, while a new update moth operation using Hamming distance and Archimedes spiral allows an efficient exploration of all possible gene-subsets. The main objective of the second phase is to determine the best relevant gene subset of all genes obtained in the first phase. In order to assess the performance of the proposed QMFOA, we test QMFOA on thirteen microarray datasets (six binary-class and seven multi-class) to evaluate and compare the classification accuracy and the number of genes selected by the QMFOA against many recently published algorithms. Experimental results show that QMFOA provides greater classification accuracy and the ability to reduce the number of selected genes compared to the other algorithms.

An efficient gene selection method for microarray data based on LASSO and BPSO

BackgroundThe main goal of successful gene selection for microarray data is to find compact and predictive gene subsets which could improve the accuracy. Though a large pool of available methods exists, selecting the optimal gene subset for accurate classification is still very challenging for the diagnosis and treatment of cancer.ResultsTo obtain the most predictive genes subsets without filtering out critical genes, a gene selection method based on least absolute shrinkage and selection operator (LASSO) and an improved binary particle swarm optimization (BPSO) is proposed in this paper. To avoid overfitting of LASSO, the initial gene pool is divided into clusters based on their structure. LASSO is then employed to select high predictive genes and further calculate the contribution value which indicates the genes’ sensitivity to samples’ classes. With the second-level gene pool established by double filter strategy, the BPSO encoding the contribution information obtained from LASSO is improved to perform gene selection. Moreover, from the perspective of the bit change probability, a new mapping function is defined to guide the updating of the particle to select the more predictive genes in the improved BPSO.ConclusionsWith the compact gene pool obtained by double filter strategies, the improved BPSO could select the optimal gene subsets with high probability. The experimental results on several public microarray data with extreme learning machine verify the effectiveness of the proposed method compared to the relevant methods.

A study on metaheuristics approaches for gene selection in microarray data: algorithms, applications and open challenges

In the recent decades, researchers have introduced an abundance of feature selection methods many of which are studied and analyzed over the high dimensional datasets typically tiny number of instances and hundreds or thousands of genes. Feature selection methods provide a way of reducing computation cost, improving prediction performance and better understanding of the data structure. However, it is a challenging task due to two reasons such as the considerable solution space and feature interaction. A diversity of feature selection methods is established and applied on high dimensional datasets which includes the metaheuristic algorithms. In this paper, we focus on the basic algorithmic structures of metaheuristic for feature selection that reveals the predominate genes, called biomarkers in microarray gene expression data series with limited resources. In addition, more than hundred articles are carefully screened to prepare the up-to-date comprehensive work on the metaheuristic approach for feature selection and also discussed a range of open issue of recent metaheuristic approaches for feature selection. Furthermore, we have applied some metaheuristic techniques for feature selection on gene expression datasets to demonstrate the applicability of methods. Based on this comprehensive survey, this article suggest some crucial recommendations to researchers for choosing a suitable method from the repository of feature selection methods.

Improving the genetic bee colony optimization algorithm for efficient gene selection in microarray data

Feature selection is a very critical component in the workflow of biomedical data mining applications. In particular, there is a need for feature selection methods that can find complex relationships among genes, yet computationally efficient. Within the scope of microarray data analysis, the genetic bee colony (Gbc) algorithm is one of the best feature selection algorithms, which leverages the combination between genetic and ant colony optimization algorithms to search for the optimal solution. In this paper, we analyse in depth the fundamentals lying behind the Gbc and propose some improvements in both efficiency and accuracy, so that researchers can even take more advantage of this excellent method. By (i) replacing the filtering phase of Gbc with a more efficient technique, (ii) improving the population generation in the artificial colony algorithm used in Gbc, and (iii) improving the exploitation method in Gbc, our experiments in microarray data sets reveal that our new method Gbc+ is not only significantly more accurate, but also around ten times faster on average than the original

Recursive Memetic Algorithm for gene selection in microarray data

Feature selection algorithm contributes a lot in the domain of medical diagnosis. Choosing a small subset of genes that enable a classifier to predict the presence or type of disease accurately is a difficult optimisation problem due to the size of the microarray data. The dual task of achieving higher accuracy and a small number of features makes it a challenging research problem. In our work, we have developed a Recursive Memetic Algorithm (RMA) model for selection of genes. It is a variant of Memetic Algorithm (MA) and performs much better than MA as well as Genetic Algorithm (GA). RMA has been applied on seven microarray datasets namely, AMLGSE2191, Colon, DLBCL, Leukaemia, Prostate, MLL and SRBCT. Encouraging results obtained by the proposed model, reported in this article, are biologically validated with the use of Gene Oncology, KEGG pathways and heat maps.

A recursive PSO scheme for gene selection in microarray data

In DNA microarray datasets, the number of genes are very large, typically in thousands while the number of samples are in hundreds. This raises the issue of generalization in the classification process. Gene selection plays a significant role in improving the accuracy. In this paper, we have proposed a recursive particle swarm optimization approach (PSO) for gene selection. The proposed method refines the feature (gene) space from a very coarse level to a fine-grained one at each recursive step of the algorithm without degrading the accuracy. In addition, we have integrated various filter based ranking methods with the proposed recursive PSO approach. We also propose to use linear support vector machine weight vector to serve as initial gene pool selection. We evaluate our method on five publicly available benchmark microarray datasets. Our approach selects only a small number of genes while yielding substantial improvements in accuracy over state-of-the-art evolutionary methods.

A Hybrid Discrete Imperialist Competition Algorithm for Gene Selection for Microarray Data

A Hybrid Discrete Imperialist Competition Algorithm for Gene Selection for Microarray Data

Artificial Neural Network Classification of High Dimensional Data with Novel Optimization Approach of Dimension Reduction

Classification of high dimensional data is a very crucial task in bioinformatics. Cancer classification of the microarray is a typical application of machine learning due to the large numbers of genes. Feature (genes) selection and classification with computational intelligent techniques play an important role in diagnosis and prediction of disease in the microarray. Artificial neural networks (ANN) is an artificial intelligence technique for classifying, image processing and predicting the data. This paper evaluates the performance of ANN classifier using six different hybrid feature selection techniques, for gene selection of microarray data. These hybrid techniques use Independent component analysis (ICA), as an extraction technique, popular filter techniques and bio-inspired algorithm for optimization of the ICA feature vector. Five binary gene expression microarray datasets are used to compare the performance of these techniques and determine how these techniques improve the performance of ANN classifier. These techniques can be extremely useful in feature selection because they achieve the highest classification accuracy along with the lowest average number of selected genes. Furthermore, to check the significant difference between these different algorithms a statistical hypothesis test was employed with a certain level of confidence. The experimental result shows that a combination of ICA with genetic bee colony algorithm shows superior performance as it heuristically removes non-contributing features to improve the performance of classifiers.

A hybrid gene selection approach for microarray data classification using cellular learning automata and ant colony optimization

This paper proposes an approach for gene selection in microarray data. The proposed approach consists of a primary filter approach using Fisher criterion which reduces the initial genes and hence the search space and time complexity. Then, a wrapper approach which is based on cellular learning automata (CLA) optimized with ant colony method (ACO) is used to find the set of features which improve the classification accuracy. CLA is applied due to its capability to learn and model complicated relationships. The selected features from the last phase are evaluated using ROC curve and the most effective while smallest feature subset is determined. The classifiers which are evaluated in the proposed framework are K-nearest neighbor; support vector machine and naïve Bayes. The proposed approach is evaluated on 4 microarray datasets. The evaluations confirm that the proposed approach can find the smallest subset of genes while approaching the maximum accuracy.

A Granular Self-Organizing Map for Clustering and Gene Selection in Microarray Data.

A new granular self-organizing map (GSOM) is developed by integrating the concept of a fuzzy rough set with the SOM. While training the GSOM, the weights of a winning neuron and the neighborhood neurons are updated through a modified learning procedure. The neighborhood is newly defined using the fuzzy rough sets. The clusters (granules) evolved by the GSOM are presented to a decision table as its decision classes. Based on the decision table, a method of gene selection is developed. The effectiveness of the GSOM is shown in both clustering samples and developing an unsupervised fuzzy rough feature selection (UFRFS) method for gene selection in microarray data. While the superior results of the GSOM, as compared with the related clustering methods, are provided in terms of β -index, DB-index, Dunn-index, and fuzzy rough entropy, the genes selected by the UFRFS are not only better in terms of classification accuracy and a feature evaluation index, but also statistically more significant than the related unsupervised methods. The C-codes of the GSOM and UFRFS are available online at http://avatharamg.webs.com/software-code.

A novel strategy for gene selection of microarray data based on gene-to-class sensitivity information.

To obtain predictive genes with lower redundancy and better interpretability, a hybrid gene selection method encoding prior information is proposed in this paper. To begin with, the prior information referred to as gene-to-class sensitivity (GCS) of all genes from microarray data is exploited by a single hidden layered feedforward neural network (SLFN). Then, to select more representative and lower redundant genes, all genes are grouped into some clusters by K-means method, and some low sensitive genes are filtered out according to their GCS values. Finally, a modified binary particle swarm optimization (BPSO) encoding the GCS information is proposed to perform further gene selection from the remainder genes. For considering the GCS information, the proposed method selects those genes highly correlated to sample classes. Thus, the low redundant gene subsets obtained by the proposed method also contribute to improve classification accuracy on microarray data. The experiments results on some open microarray data verify the effectiveness and efficiency of the proposed approach.

Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification

BackgroundMicroarray technology is widely used in cancer diagnosis. Successfully identifying gene biomarkers will significantly help to classify different cancer types and improve the prediction accuracy. The regularization approach is one of the effective methods for gene selection in microarray data, which generally contain a large number of genes and have a small number of samples. In recent years, various approaches have been developed for gene selection of microarray data. Generally, they are divided into three categories: filter, wrapper and embedded methods. Regularization methods are an important embedded technique and perform both continuous shrinkage and automatic gene selection simultaneously. Recently, there is growing interest in applying the regularization techniques in gene selection. The popular regularization technique is Lasso (L1), and many L1 type regularization terms have been proposed in the recent years. Theoretically, the Lq type regularization with the lower value of q would lead to better solutions with more sparsity. Moreover, the L1/2 regularization can be taken as a representative of Lq (0 <q < 1) regularizations and has been demonstrated many attractive properties.ResultsIn this work, we investigate a sparse logistic regression with the L1/2 penalty for gene selection in cancer classification problems, and propose a coordinate descent algorithm with a new univariate half thresholding operator to solve the L1/2 penalized logistic regression. Experimental results on artificial and microarray data demonstrate the effectiveness of our proposed approach compared with other regularization methods. Especially, for 4 publicly available gene expression datasets, the L1/2 regularization method achieved its success using only about 2 to 14 predictors (genes), compared to about 6 to 38 genes for ordinary L1 and elastic net regularization approaches.ConclusionsFrom our evaluations, it is clear that the sparse logistic regression with the L1/2 penalty achieves higher classification accuracy than those of ordinary L1 and elastic net regularization approaches, while fewer but informative genes are selected. This is an important consideration for screening and diagnostic applications, where the goal is often to develop an accurate test using as few features as possible in order to control cost. Therefore, the sparse logistic regression with the L1/2 penalty is effective technique for gene selection in real classification problems.

A Novel Hybrid Method for Gene Selection of Microarray Data

A Novel Hybrid Method for Gene Selection of Microarray Data

A Novel Hybrid Method for Gene Selection of Microarray Data

A Novel Hybrid Method for Gene Selection of Microarray Data

On sparse Fisher discriminant method for microarray data analysis.

One of the applications of the discriminant analysis on microarray data is to classify patient and normal samples based on gene expression values. The analysis is especially important in medical trials and diagnosis of cancer subtypes. The main contribution of this paper is to propose a simple Fisher-type discriminant method on gene selection in microarray data. In the new algorithm, we calculate a weight for each gene and use the weight values as an indicator to identify the subsets of relevant genes that categorize patient and normal samples. A l(2) - l(1) norm minimization method is implemented to the discriminant process to automatically compute the weights of all genes in the samples. The experiments on two microarray data sets have shown that the new algorithm can generate classification results as good as other classification methods, and effectively determine relevant genes for classification purpose. In this study, we demonstrate the gene selection's ability and the computational effectiveness of the proposed algorithm. Experimental results are given to illustrate the usefulness of the proposed model.

Quality assessment of gene selection in microarray data

In microarray data, gene selection can make data analysis efficient and biological interpretations of the selected genes can be very useful. However, microarray data have typically several thousands of genes but only tens of samples, referred to as a small sample-size problem. In this paper, we discuss some problems on gene selection that can occur owing to a small sample size: whether gene selection relying on the extremely small number of samples is reliable and meaningful. Experimental comparisons of well-known three gene selection methods show that classification performances can be very sensitive to training samples and preprocessing steps. We also measure consistency in gene ranking under the changes of training samples or different selection criteria.