Mutable composite firefly algorithm for gene selection in microarray based cancer classification

Cancer classification is critical due to the strenuous effort required in cancer treatment and the rising cancer mortality rate. Recent trends with high throughput technologies have led to discoveries in terms of biomarkers that successfully contributed to cancerrelated issues. A computational approach for gene selection based on microarray data analysis has been applied in many cancer classification problems. However, the existing hybrid approaches with metaheuristic optimization algorithms in feature selection (specifically in gene selection) are not generalized enough to efficiently classify most cancer microarray data while maintaining a small set of genes. This leads to the classification accuracy and genes subset size problem. Hence, this study proposed to modify the Firefly Algorithm (FA) along with the Correlation-based Feature Selection (CFS) filter for the gene selection task. An improved FA was proposed to overcome FA slow convergence by generating mutable size solutions for the firefly population. In addition, a composite position update strategy was designed for the mutable size solutions. The proposed strategy was to balance FA exploration and exploitation in order to address the local optima problem. The proposed hybrid algorithm known as CFS-Mutable Composite Firefly Algorithm (CFS-MCFA) was evaluated on cancer microarray data for biomarker selection along with the deployment of Support Vector Machine (SVM) as the classifier. Evaluation was performed based on two metrics: classification accuracy and size of feature set. The results showed that the CFS-MCFA-SVM algorithm outperforms benchmark methods in terms of classification accuracy and genes subset size. In particular, 100 percent accuracy was achieved on all four datasets and with only a few biomarkers (between one and four). This result indicates that the proposed algorithm is one of the competitive alternatives in feature selection, which later contributes to the analysis of microarray data

Are screening methods useful in feature selection? An empirical study

Filter or screening methods are often used as a preprocessing step for reducing the number of variables used by a learning algorithm in obtaining a classification or regression model. While there are many such filter methods, there is a need for an objective evaluation of these methods. Such an evaluation is needed to compare them with each other and also to answer whether they are at all useful, or a learning algorithm could do a better job without them. For this purpose, many popular screening methods are partnered in this paper with three regression learners and five classification learners and evaluated on ten real datasets to obtain accuracy criteria such as R-square and area under the ROC curve (AUC). The obtained results are compared through curve plots and comparison tables in order to find out whether screening methods help improve the performance of learning algorithms and how they fare with each other. Our findings revealed that the screening methods were useful in improving the prediction of the best learner on two regression and two classification datasets out of the ten datasets evaluated.Comment: 29 pages, 4 figures, 21 table

Digging into acceptor splice site prediction : an iterative feature selection approach

Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction. We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature. The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets

Feature Analysis for Classification of Physical Actions using surface EMG Data

Based on recent health statistics, there are several thousands of people with limb disability and gait disorders that require a medical assistance. A robot assisted rehabilitation therapy can help them recover and return to a normal life. In this scenario, a successful methodology is to use the EMG signal based information to control the support robotics. For this mechanism to function properly, the EMG signal from the muscles has to be sensed and then the biological motor intention has to be decoded and finally the resulting information has to be communicated to the controller of the robot. An accurate detection of the motor intention requires a pattern recognition based categorical identification. Hence in this paper, we propose an improved classification framework by identification of the relevant features that drive the pattern recognition algorithm. Major contributions include a set of modified spectral moment based features and another relevant inter-channel correlation feature that contribute to an improved classification performance. Next, we conducted a sensitivity analysis of the classification algorithm to different EMG channels. Finally, the classifier performance is compared to that of the other state-of the art algorithm

Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers