基于遗传算法的结肠癌基因选择与样本分类

提出了一种基于两轮遗传算法的用于结肠癌微阵列数据基因选择与样本分类的新方法。该方法先根据基因的Bhattacharyya距离指标过滤大部分与分类不相关的基因,而后使用结合了遗传算法和CFS（Correlation-based Feature Selection）的GA/CFS方法选择优秀基因子集,并存档记录这些子集。根据存档子集中基因被选择的频率选择进一步搜索的候选子集,最后以结合了遗传算法和SVM的GA/SVM从候选基因子集中选择分类特征子集。把这种GA/CFS-GA/SVM方法应用到结肠癌微阵列数据,实验结果及与文献的比较表明了该方法效果良好。     

Gene selection using hybrid particle swarm optimization and genetic algorithm

Selecting high discriminative genes from gene expression data has become an important research. Not only can this improve the performance of cancer classification, but it can also cut down the cost of medical diagnoses when a large number of noisy, redundant genes are filtered. In this paper, a hybrid Particle Swarm Optimization (PSO) and Genetic Algorithm (GA) method is used for gene selection, and Support Vector Machine (SVM) is adopted as the classifier. The proposed approach is tested on three benchmark gene expression datasets: Leukemia, Colon and breast cancer data. Experimental results show that the proposed method can reduce the dimensionality of the dataset, and confirm the most informative gene subset and improve classification accuracy.     

基于遗传算法和支持向量机的肿瘤分子分类

提出了一种基于遗传算法(GA)和支持向量机(SVM)的用于肿瘤分子分类和特征基因选择的新方法。该方法针对基因表达数据样本少维数高的特点,先根据基因的散乱度滤掉大量分类无关基因,而后使用相关性分析去除分类冗余基因,得到一个候选基因子集,用遗传算法搜索候选特征基因空间,发现在支持向量机分类器上具有好的分类性能的且含基因个数较少的特征子集。把这种GA/SVM方法应用到结肠癌和急性白血病基因表达谱,能选出多个取得较高分类精度的较小基因子集,实验结果表明了该方法的有效性。     

A two-stage gene selection scheme utilizing MRMR filter and GA wrapper

Gene expression data usually contain a large number of genes, but a small number of samples. Feature selection for gene expression data aims at finding a set of genes that best discriminates biological samples of different types. In this paper, we propose a two-stage selection algorithm for genomic data by combining MRMR (Minimum Redundancy–Maximum Relevance) and GA (Genetic Algorithm). In the first stage, MRMR is used to filter noisy and redundant genes in high-dimensional microarray data. In the second stage, the GA uses the classifier accuracy as a fitness function to select the highly discriminating genes. The proposed method is tested for tumor classification on five open datasets: NCI, Lymphoma, Lung, Leukemia and Colon using Support Vector Machine (SVM) and Naïve Bayes (NB) classifiers. The comparison of the MRMR-GA with MRMR filter and GA wrapper shows that our method is able to find the smallest gene subset that gives the most classification accuracy in leave-one-out cross-validation (LOOCV).     

APPLYING DATA MINING TECHNIQUES FOR CANCER CLASSIFICATION ON GENE EXPRESSION DATA

Cancer classification through gene expression data analysis has recently emerged as an active area of research. This paper applies Genetic Algorithms (GA) for selecting a group of relevant genes from cancer microarray data. Then, the popular classifiers, such as OneR, Naïve Bayes, decision tree, and Support Vector Machine (SVM), are built on the basis of these selected genes. The performance of those classifiers is evaluated by using the publicly available gene expression data sets. Experimental results indicate that the cascade of GA and SVM has the highest rank among different methods. Moreover, the gene selection operation of GA is reproducible.     

基于属性约简和支持向量机集成的乳腺癌诊断决策

针对遗传算法(GA)与支持向量机(SVM)集成相结合的疾病诊断方法存在属性冗余的问题,提出了一种改进的约简和诊断乳腺癌决策方法。该方法将最小化约简属性个数、最大化区分矩阵可区别属性的个数以及最大化约简属性对决策属性的依赖度这三种目标函数相结合作为GA的适应度函数。在约简属性后取多个子集,以便利用SVM集成学习。在UCI数据库中乳腺癌数据集的实验表明,与原始的SVM算法相比,该方法在分类诊断的准确度以及敏感性方面有一定的提高,其中分类准确度至少提高了2%。     

Cascade of genetic algorithm and decision tree for cancer classification on gene expression data

Abstract: Cancer classification, through gene expression data analysis, has produced remarkable results, and has indicated that gene expression assays could significantly aid in the development of efficient cancer diagnosis and classification platforms. However, cancer classification, based on DNA array data, remains a difficult problem. The main challenge is the overwhelming number of genes relative to the number of training samples, which implies that there are a large number of irrelevant genes to be dealt with. Another challenge is from the presence of noise inherent in the data set. It makes accurate classification of data more difficult when the sample size is small. We apply genetic algorithms (GAs) with an initial solution provided by t statistics, called t‐GA, for selecting a group of relevant genes from cancer microarray data. The decision‐tree‐based cancer classifier is built on the basis of these selected genes. The performance of this approach is evaluated by comparing it to other gene selection methods using publicly available gene expression data sets. Experimental results indicate that t‐GA has the best performance among the different gene selection methods. The Z‐score figure also shows that some genes are consistently preferentially chosen by t‐GA in each data set.     

Cancer classification using ensemble of neural networks with multiple significant gene subsets

Molecular level diagnostics based on microarray technologies can offer the methodology of precise, objective, and systematic cancer classification. Genome-wide expression patterns generally consist of thousands of genes. It is desirable to extract some significant genes for accurate diagnosis of cancer because not all genes are associated with a cancer. In this paper, we have used representative gene vectors that are highly discriminatory for cancer classes and extracted multiple significant gene subsets based on those representative vectors respectively. Also, an ensemble of neural networks learned from the multiple significant gene subsets is proposed to classify a sample into one of several cancer classes. The performance of the proposed method is systematically evaluated using three different cancer types: Leukemia, colon, and B-cell lymphoma.     

Ensemble gene selection for cancer classification

Cancer diagnosis is an important emerging clinical application of microarray data. Its accurate prediction to the type or size of tumors relies on adopting powerful and reliable classification models, so as to patients can be provided with better treatment or response to therapy. However, the high dimensionality of microarray data may bring some disadvantages, such as over-fitting, poor performance and low efficiency, to traditional classification models. Thus, one of the challenging tasks in cancer diagnosis is how to identify salient expression genes from thousands of genes in microarray data that can directly contribute to the phenotype or symptom of disease. In this paper, we propose a new ensemble gene selection method (EGS) to choose multiple gene subsets for classification purpose, where the significant degree of gene is measured by conditional mutual information or its normalized form. After different gene subsets have been obtained by setting different starting points of the search procedure, they will be used to train multiple base classifiers and then aggregated into a consensus classifier by the manner of majority voting. The proposed method is compared with five popular gene selection methods on six public microarray datasets and the comparison results show that our method works well.     

A novel approach to feature extraction from classification models based on information gene pairs

Various microarray experiments are now done in many laboratories, resulting in the rapid accumulation of microarray data in public repositories. One of the major challenges of analyzing microarray data is how to extract and select efficient features from it for accurate cancer classification. Here we introduce a new feature extraction and selection method based on information gene pairs that have significant change in different tissue samples. Experimental results on five public microarray data sets demonstrate that the feature subset selected by the proposed method performs well and achieves higher classification accuracy on several classifiers. We perform extensive experimental comparison of the features selected by the proposed method and features selected by other methods using different evaluation methods and classifiers. The results confirm that the proposed method performs as well as other methods on acute lymphoblastic-acute myeloid leukemia, adenocarcinoma and breast cancer data sets using a fewer information genes and leads to significant improvement of classification accuracy on colon and diffuse large B cell lymphoma cancer data sets.     

Optimal gene subset selection using the modified SFFS algorithm for tumor classification

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.     

基于离散粒子群和支持向量机的特征基因选择算法

基因芯片表达谱信息,为识别疾病相关基因及对癌症等疾病分型、诊断及病理学研究提供一新途径。在基因表达谱数据中选择特征基因可以提高疾病诊断、分类的准确率,并降低分类器的复杂度。本文研究了基于离散粒子群(binary particle swarm optimization,BPSO)和支持向量机(support vector machine,SVM)封装模式的BPSO-SVM特征基因选择方法,首先随机产生若干种群(特征子集),然后用BPSO算法优化随机产生的特征基因,并用SVM分类结果指导搜索,最后选出最佳适应度的特征基因子集以训练SVM。结果表明,基于BPSO-SVM的特征基因选择方法,的确是一种行之有效的特征基因选择方法。     

Feature selection and parameter optimization for support vector machines: A new approach based on genetic algorithm with feature chromosomes

Support vector machines (SVM) are an emerging data classification technique with many diverse applications. The feature subset selection, along with the parameter setting in the SVM training procedure significantly influences the classification accuracy. In this paper, the asymptotic behaviors of support vector machines are fused with genetic algorithm (GA) and the feature chromosomes are generated, which thereby directs the search of genetic algorithm to the straight line of optimal generalization error in the superparameter space. On this basis, a new approach based on genetic algorithm with feature chromosomes, termed GA with feature chromosomes, is proposed to simultaneously optimize the feature subset and the parameters for SVM.To evaluate the proposed approach, the experiment adopts several real world datasets from the UCI database and from the Benchmark database. Compared with the GA without feature chromosomes, the grid search, and other approaches, the proposed approach not only has higher classification accuracy and smaller feature subsets, but also has fewer processing time.     

Simulated annealing for supervised gene selection

Genomic data, and more generally biomedical data, are often characterized by high dimensionality. An input selection procedure can attain the two objectives of highlighting the relevant variables (genes) and possibly improving classification results. In this paper, we propose a wrapper approach to gene selection in classification of gene expression data using simulated annealing along with supervised classification. The proposed approach can perform global combinatorial searches through the space of all possible input subsets, can handle cases with numerical, categorical or mixed inputs, and is able to find (sub-)optimal subsets of inputs giving low classification errors. The method has been tested on publicly available bioinformatics data sets using support vector machines and on a mixed type data set using classification trees. We also propose some heuristics able to speed up the convergence. The experimental results highlight the ability of the method to select minimal sets of relevant features.     

Support vector machines combined with feature selection for breast cancer diagnosis

Breast cancer is the second largest cause of cancer deaths among women. At the same time, it is also among the most curable cancer types if it can be diagnosed early. Research efforts have reported with increasing confirmation that the support vector machines (SVM) have greater accurate diagnosis ability. In this paper, breast cancer diagnosis based on a SVM-based method combined with feature selection has been proposed. Experiments have been conducted on different training-test partitions of the Wisconsin breast cancer dataset (WBCD), which is commonly used among researchers who use machine learning methods for breast cancer diagnosis. The performance of the method is evaluated using classification accuracy, sensitivity, specificity, positive and negative predictive values, receiver operating characteristic (ROC) curves and confusion matrix. The results show that the highest classification accuracy (99.51%) is obtained for the SVM model that contains five features, and this is very promising compared to the previously reported results.     

基于MDA-RS算法的特征基因选取方法*

建立病变组织分类模型的关键在于找出一组能准确区分样本类别的特征基因。糙集理论中的属性依赖度分析方法能对目标数据进行有效分析。基于属性间的依赖关系和属性对决策的影响存在这样的关系,即属性依赖度越大,属性就越重要,对决策划分的影响就越大,提出了一种属性最大依赖度(maximum dependency of attributes based on rough sets,MDA-RS)算法,并将其应用于特征基因选取。首先用启发式K-均值聚类算法对基因进行聚类分析得到类数为k的基因子集;然后用MDA-RS选出每类的     

Applying 1-norm SVM with squared loss to gene selection for cancer classification

Gene selection methods available have high computational complexity. This paper applies an 1-norm support vector machine with the squared loss (1-norm SVMSL) to implement fast gene selection for cancer classification. The 1-norm SVMSL, a variant of the 1-norm support vector machine (1-norm SVM) has been proposed. Basically, the 1-norm SVMSL can perform gene selection and classification at the same. However, to improve classification performance, we only use the 1-norm SVMSL as a gene selector, and adopt a subsequent classifier to classify the selected genes. We perform extensive experiments on four DNA microarray data sets. Experimental results indicate that the 1-norm SVMSL has a very fast gene selection speed compared with other methods. For example, the 1-norm SVMSL is almost an order of magnitude faster than the 1-norm SVM, and at least four orders of magnitude faster than SVM-RFE (recursive feature elimination), a state-of-the-art method.     

Simultaneous cancer classification and gene selection with Bayesian nearest neighbor method: An integrated approach

Since most cancer treatments come with a certain degree of toxicity it is very essential to identify a cancer type correctly and then administer the relevant therapy. With the arrival of powerful tools such as gene expression microarrays the cancer classification basis is slowly changing from morphological properties to molecular signatures. Several recent studies have demonstrated a marked improvement in prediction accuracy of tumor types based on gene expression microarray measurements over clinical markers. The main challenge in working with gene expression microarrays is that there is a huge number of genes to work with. Out of them only a small fraction are actually relevant for differentiating between different types of cancer. A Bayesian nearest neighbor model equipped with an integrated variable selection technique is proposed to overcome this challenge. This classification and gene selection model is able to classify different cancer types accurately and simultaneously identify the relevant or important genes. The proposed model is completely automatic in the sense that it adaptively picks up the neighborhood size and the important covariates. The method is successfully applied to three simulated data sets and four well known real data sets. To demonstrate the competitiveness of the method a comparative study is also done with several other “off the shelf” popular classification methods. For all the simulated data sets and real life data sets, the proposed method produced highly competitive if not better results. While the standard approach is two step model building for gene selection and then tumor prediction, this novel adaptive gene selection technique automatically selects the relevant genes along with tumor class prediction in one go. The biological relevance of the selected genes are also discussed to validate the claim.     

基于主成份分析的肿瘤分类检测算法研究

基于基因表达谱的肿瘤诊断方法有望成为临床医学上一种快速而有效的诊断方法，但由于基因表达数据存在维数过高、样本量很小以及噪音大等特点，使得提取与肿瘤有关的信息基因成为一件有挑战性的工作。因此，在分析了目前肿瘤分类检测所采用方法的基础上，本文提出了一种结合基因特征记分和主成份分析的混合特征抽取方法。实验表明明，这种方法能够有效地提取分类特征信息，并在保持较高的肿瘤识别准确率的前提下大幅度地降低基因表达数据的维数，使得分类器性能得到很大提高。实验采用了两种与肿瘤有关的基因表达数据集来验证这种混合特征抽取方法的有效性，采用支持向量机的分类实验结果表明，所提出的混合方法不仅交叉验证识别准确率高而且分类结果能够可
可视化。对于结肠癌组织样本集，其交叉验证识别准确率高这95．16％；而对于急性白血病组织样本集，其交叉验证识别准确率高这100％。     

Improving the SVM gender classification accuracy using clustering and incremental learning

Gender recognition has been playing a very important role in various applications such as human–computer interaction, surveillance, and security. Nonlinear support vector machines (SVMs) were investigated for the identification of gender using the Face Recognition Technology (FERET) image face database. It was shown that SVM classifiers outperform the traditional pattern classifiers (linear, quadratic, Fisher linear discriminant, and nearest neighbour). In this context, this paper aims to improve the SVM classification accuracy in the gender classification system and propose new models for a better performance. We have evaluated different SVM learning algorithms; the SVM‐radial basis function with a 5% outlier fraction outperformed other SVM classifiers. We have examined the effectiveness of different feature selection methods. AdaBoost performs better than the other feature selection methods in selecting the most discriminating features. We have proposed two classification methods that focus on training subsets of images among the training images. Method 1 combines the outcome of different classifiers based on different image subsets, whereas method 2 is based on clustering the training data and building a classifier for each cluster. Experimental results showed that both methods have increased the classification accuracy.