A robust hybrid between genetic algorithm and support vector machine for extracting an optimal feature gene subset

In tissue diagnosis with microarray data, selecting the optimal gene subset is very essential for various merits. Different from existing methods, we propose a novel optimal gene subset selection method based on genetic algorithms (GAs). Special fitness function is applied in this scheme. This GA-based method automatically determines the size of a predictive gene group, as well as the members in such a group. The evaluation experiments are applied to two popular data sets. The results and some discussions are presented too.

Gene selection from microarray gene expression datasets and clustering of samples into different groups are important data mining tasks for disease identification. Selection of more interpretable genes from the gene expression dataset is an essential data-preprocessing task, which helps to study on cancer diseases. Gene selection during sample clustering is inherently a difficult task as there is no obvious criterion to guide the search. Simultaneous gene selection and sample clustering is a two-way data analysis technique which has recently gained attention in research area. The traditional clustering techniques are unable to handle noisy data properly. So, effective clustering algorithms are more desirable which can deal with the relevant and noise free data. Therefore, target genes selection before sample clustering is essential and of course effective if both the tasks are done simultaneously. In this chapter, optimal gene subset is selected and sample clustering is performed simultaneously using Multi-Objective Genetic Algorithm (MOGA). Different versions of MOGA are employed to choose the optimal gene subset, where natural number of optimal clusters of samples is automatically obtained at the end of the process. Non-dominated sorting genetic algorithm (NSGA), Strength pareto evolutionary algorithm (SPEA) and its modified version SPEA2 are applied for the purpose. The methods use nonlinear hybrid uniform cellular automata for generating initial population, tournament selection strategy, two-point crossover operation, and a suitable jumping gene mutation mechanism to maintain diversity in the population. It uses mutual correlation coefficient; internal and external cluster validation indices as objective functions to find out the non-dominated solutions. To measure the cluster validation indices, clustering algorithm is applied on data subset associated to chromosomes in the population to find out different clusters. After the convergence of genetic algorithm, the best solution from the non-dominated solutions is identified that provides the important genes and categorizes the samples into clusters. The experimental results express the correctness of the proposed simultaneous gene selection and sample categorization method. The goodness of optimality of the clusters obtained using different genetic algorithms is expressed by comparing various cluster validation indices.

This paper established evaluation index system of comprehensive utilization of land from the three aspects of economic benefits, ecological benefits and social benefits. Firstly, ridge regression (RR) is used to the indicator index sys- tem for screening, and then genetic algorithm and support vector machine (that is GASVM) is trained to the transformed samples. Moreover, the comprehensive evaluation results between the GASVM and ridge regression and genetic algo- rithm and support vector machine(that is RR-GASVM) is compared, which results by MATLAB show that using RR- GASVM is more accurate and higher efficient for the comprehensive utilization of land evaluation than that of GASVM. The combination of ridge regression and genetic algorithm and support vector machine can improve the decision ability of SVM, so that the decision has higher adaptability, which is the development direction of future research. At last, based on the results of this study, some suggestions are put forward accordingly. The area of Jiangsu, Zhejiang and Shanghai (that is Jiangzhehu) should consolidate the existing achievements and strengthen the innovation of the land management system on the basis of utilizing land comprehensively, realize the intensive, large-scale operation and speed up agricultural mod- ernization development by accelerating rural land circulation, and improve the efficiency of land utilization in order to save the land of urban construction. It is clear that people should insist the principle of paying equal attention to develop- ment and consolidation, and strengthen the cultivated land's ability to resist natural disasters in order to improve the eco- logical environment at the same time that improved the land utilization.

Apoptosis is an essential process for controlling tissue homeostasis by regulating a physiological balance between cell proliferation and cell death. The subcellular locations of proteins performing the cell death are determined by mostly independent cellular mechanisms. The regular bioinformatics tools to predict the subcellular locations of such apoptotic proteins do often fail. This work proposes a model for the sorting of proteins that are involved in apoptosis, allowing us to both the prediction of their subcellular locations as well as the molecular properties that contributed to it. We report a novel hybrid Genetic Algorithm (GA)/Support Vector Machine (SVM) approach to predict apoptotic protein sequences using 119 sequence derived properties like frequency of amino acid groups, secondary structure, and physicochemical properties. GA is used for selecting a near-optimal subset of informative features that is most relevant for the classification. Jackknife cross-validation is applied to test the predictive capability of the proposed method on 317 apoptosis proteins. Our method achieved 85.80% accuracy using all 119 features and 89.91% accuracy for 25 features selected by GA. Our models were examined by a test dataset of 98 apoptosis proteins and obtained an overall accuracy of 90.34%. The results show that the proposed approach is promising; it is able to select small subsets of features and still improves the classification accuracy. Our model can contribute to the understanding of programmed cell death and drug discovery. The software and dataset are available at http://www.inb.uni-luebeck.de/tools-demos/apoptosis/GASVM.

A reliable and precise classification of tumors is essential for successful treatment of cancer. Gene selection is an important step for improved diagnostics. The modified SFFS (sequential forward floating selection) algorithm based on weighted Mahalanobis distance, called MSWM, is proposed to identify optimal informative gene subsets taking into account joint discriminatory power for accurate discrimination in this study. Firstly, we make use of the one-dimensional weighted Mahalanobis distance to perform a preliminary selection of genes and then make use of the modified SFFS method and multidimensional weighted Mahalanobis distance to obtain the optimal informative gene subset for tumor classification. Finally, we used the k nearest neighbor and naive Bayes methods to classify tumors based on the optimal gene subset selected using the MSWM method. To validate the efficiency, the proposed MSWM method is applied to classify two different DNA microarray datasets. Our empirical study shows that the MSWM method for tumor classification can obtain better effectiveness of classification than the BWR (the ratio of between-groups to within-groups sum of squares) and IVGA_I (independent variable group analysis I) methods. It suggests that the MSWM gene selection method is ability to obtain correct informative gene subsets taking into account genes’ joint discriminatory power for tumor classification.

Considering the increasingly tense relationship between construction land supply and demand, we study the inherent rules and the spatial evolution in construction land use. In order to solve the problem of parameter optimization effectively, we analysis the fundamental theory of Support Vector Machine and finally accomplish the combination of genetic algorithm and support vector machine. Meanwhile we apply this model to analysis the construction land use and propose a new model, which is based on the support vector machines with genetic algorithm, for construction land evolution. Taking Guandu district in Kunming, Yunnan as a case, we find out that the new model is far superior to recent models in terms of predicting accuracy, algorithm complexity and computational efficiency. And therefore, we believe that this is highly precise, practical and efficient model for forecasting construction land use and evolution.

A hybrid framework composed of two stages for gene selection and classification of DNA microarray data is proposed. At the first stage, five traditional statistical methods are combined for preliminary gene selection (Multiple Fusion Filter). Then, different relevant gene subsets are selected by using an embedded Genetic Algorithm (GA), Tabu Search (TS), and Support Vector Machine (SVM). A gene subset, consisting of the most relevant genes, is obtained from this process, by analyzing the frequency of each gene in the different gene subsets. Finally, the most frequent genes are evaluated by the embedded approach to obtain a final relevant small gene subset with high performance. The proposed method is tested in four DNA microarray datasets. From simulation study, it is observed that the proposed approach works better than other methods reported in the literature.

Chapter 14 - Review on hybrid feature selection and classification of microarray gene expression data

Identification of gene transcript signatures predictive for estrogen receptor and lymph node status using a stepwise forward selection artificial neural network modelling approach

In order to obtain the higher classification accuracy in specific categories for the different feature subset, a hierarchical classification algorithm based on Feature Selection is proposed, and is used for synthetic aperture radar (SAR) image classification, and feature selection is achieved by Genetic algorithm. The algorithm has two main characteristics: one is hierarchical classification which consists of many two-class classifier, and the two-class classifier is trained by the optimal feature subset which is selected according to different categories; the second is the classifier of support vector machine SVM (Support Vector Machine); the two is Genetic algorithm which can search out the optimal feature subset and parameters of support vector machine that is most suitable for the category, by unified coding the feature set and the parameters of SVM to constitute the Chromosome. The experiment on the first polarimetric SAR data show that the algorithm can obtain higher classification accuracy rate.

State forecast of machine using support vector machines has good generalization ability in situation of rare samples. Appropriate parameter selection is very crucial to the learning results and generalization ability of support vector machines. In addition, embedding dimension influences the phase space reconstitution of nonlinear systems, as well as the precision of machine state forecasting. In this paper, an approach to optimize the parameters of SVM and the embedding dimension based on genetic algorithms was proposed. The proposed model is applied to the tendency forecasting of the vibration of shovel electric drive system. The results show that it can avoid blindness of manually selection of parameters and meanwhile improves the prediction performance greatly.

Hybrid algorithm for the classification of prostate cancer patients of the MCC-Spain study based on support vector machines and genetic algorithms

In order to solve the shortcoming of support vector regression algorithm, sports economic activities income forecasting based on genetic support vector regression algorithm is presented in this paper. As the kernel parameter, insensitive loss parameter and penalty parameter have a great influence on the forecasting performance of support vector regression algorithm, genetic algorithm is used to perform the parameters optimization of support vector regression algorithm simultaneously in this study. The experimental results show that the sports economic activities income forecasting results of genetic support vector regression model trained by the four-dimension training samples are more excellent than those of genetic support vector regression model trained by the three-dimension training samples, and the sports economic activities income forecasting ability of genetic support vector regression model trained by the four- dimension training samples is better than that of support vector regression model trained by the four-dimension training samples. Thus, genetic support vector regression algorithm has a good application prospect in sports economic activities income forecasting.

The reliable operation of brain-computer interfaces (BCIs) based on spontaneous electroencephalogram (EEG) signals requires an accurate classification and recognition of multichannel EEG. The design of EEG representations and classifiers for BCI are open research questions whose difficulty stems from the need to extract complex spatial and temporal patterns from noisy multidimensional time series obtained from EEG measurements. This paper proposes a Genetic algorithm (GA) and Support Vector Machine (SVM) hybrid approach to accomplish this EEG classification task for potential BCI applications. An Oddball stimulus program and evoked event-related coherence program were designed to evaluate our method. The present study systematically evaluates the performance of the one channel pair event-related coherence feature set for EEG signal classification of auditory task. A GA approach for feature selection is presented which used to reduce the dimension of event-related coherence feature parameters. With the base classifiers of SVM, classification experiments are carried out upon real EEG recordings. Experimental results suggest the feasibilities of the new feature set, and we also derive some valuable conclusions on the performance of the EEG signal classification methods. The high recognition rates and the method's procedural and computational simplicity make it a particularly promising method for achieving real-time BCI system based on evoked potential event-related coherence in the future.

In text classification, feature selection is essential to improve the classification effectiveness. This paper provides an empirical study of a feature selection method based on genetic algorithms for different text representation methods. This feature selection algorithm can accomplish two goals: in one hand is the search of a feature subset such that the performance of classifier is best; in other hands is find a feature subset with the smallest dimensionality which achieves higher accuracy in classification. To evaluate the performance of this approach, three from the best classifiers have been selected: Naive Bayes (NB), Nearest Neighbors (KNN) and Support Vector Machines (SVMs). Our objective is to determine whether the genetic algorithms based feature selection will improve the performances in text classification with smaller size using F-measure. Experimentations were carried out on two benchmark document collections 20Newsgroups, and Reuters-21578. And the results were very interesting.