Hybrid feature selection algorithm using symmetrical uncertainty and a harmony search algorithm

Microarray technology can be used as an efficient diagnostic system to recognise diseases such as tumours or to discriminate between different types of cancers in normal tissues. This technology has received increasing attention from the bioinformatics community because of its potential in designing powerful decision-making tools for cancer diagnosis. However, the presence of thousands or tens of thousands of genes affects the predictive accuracy of this technology from the perspective of classification. Thus, a key issue in microarray data is identifying or selecting the smallest possible set of genes from the input data that can achieve good predictive accuracy for classification. In this work, we propose a two-stage selection algorithm for gene selection problems in microarray data-sets called the symmetrical uncertainty filter and harmony search algorithm wrapper (SU-HSA). Experimental results show that the SU-HSA is better than HSA in isolation for all data-sets in terms of the accuracy and achieves a lower number of genes on 6 out of 10 instances. Furthermore, the comparison with state-of-the-art methods shows that our proposed approach is able to obtain 5 (out of 10) new best results in terms of the number of selected genes and competitive results in terms of the classification accuracy.     

基于GA/SVM的微阵列数据特征的选择与分类

微阵列数据样本小、维度高的特点给数据分析造成了困难，而主基因的挑选又十分的重要。该文采用遗传算法挑选主基因，其中，用k最邻居距离作为模式识别方法，用支持向量机构造了诊断系统，用不同核函数进行预测分类性能测试。在经典的白血病数据集上，对34个样本的测试集的分类准确率为100%。     

A multi-objective strategy in genetic algorithms for gene selection of gene expression data

A microarray machine offers the capacity to measure the expression levels of thousands of genes simultaneously. It is used to collect information from tissue and cell samples regarding gene expression differences that could be useful for cancer classification. However, the urgent problems in the use of gene expression data are the availability of a huge number of genes relative to the small number of available samples, and the fact that many of the genes are not relevant to the classification. It has been shown that selecting a small subset of genes can lead to improved accuracy in the classification. Hence, this paper proposes a solution to the problems by using a multiobjective strategy in a genetic algorithm. This approach was tried on two benchmark gene expression data sets. It obtained encouraging results on those data sets as compared with an approach that used a single-objective strategy in a genetic algorithm. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

A novel ACO–GA hybrid algorithm for feature selection in protein function prediction

Protein function prediction is an important problem in functional genomics. Typically, protein sequences are represented by feature vectors. A major problem of protein datasets that increase the complexity of classification models is their large number of features. Feature selection (FS) techniques are used to deal with this high dimensional space of features. In this paper, we propose a novel feature selection algorithm that combines genetic algorithms (GA) and ant colony optimization (ACO) for faster and better search capability. The hybrid algorithm makes use of advantages of both ACO and GA methods. Proposed algorithm is easily implemented and because of use of a simple classifier in that, its computational complexity is very low. The performance of proposed algorithm is compared to the performance of two prominent population-based algorithms, ACO and genetic algorithms. Experimentation is carried out using two challenging biological datasets, involving the hierarchical functional classification of GPCRs and enzymes. The criteria used for comparison are maximizing predictive accuracy, and finding the smallest subset of features. The results of experiments indicate the superiority of proposed algorithm.     

Identification of cancerous gene groups from microarray data by employing adaptive genetic and support vector machine technique

Nowadays, microarray gene expression data plays a vital role in tumor classification. However, due to the accessibility of a limited number of tissues compared to large number of genes in genomic data, various existing methods have failed to identify a small subset of discriminative genes. To overcome this limitation, in this paper, we developed a new hybrid technique for gene selection, called ensemble multipopulation adaptive genetic algorithm (EMPAGA) that can overlook the irrelevant genes and classify cancer accurately. The proposed hybrid gene selection algorithm comprises of two phase. In the first phase, an ensemble gene selection (EGS) method used to filter the noisy and redundant genes in high-dimensional datasets by combining multilayer and F-score approaches. Then, an adaptive genetic algorithm based on multipopulation strategy with support vector machine and naïve Bayes (NB) classifiers as a fitness function is applied for gene selection to select the extremely sensible genes from the reduced datasets. The performance of the proposed method is estimated on 10 microarray datasets of numerous tumor. The comprehensive results and various comparisons disclose that EGS has a remarkable impact on the efficacy of the adaptive genetic algorithm with multipopulation strategy and enhance the capability of the proposed approach in terms of convergence rate and solution quality. The experiments results demonstrate the superiority of the proposed method when compared to other standard wrappers regarding classification accuracy and optimal number of genes.     

Gene selection using genetic algorithm and support vectors machines

In this paper, we present a gene selection method based on genetic algorithm (GA) and support vector machines (SVM) for cancer classification. First, the Wilcoxon rank sum test is used to filter noisy and redundant genes in high dimensional microarray data. Then, the different highly informative genes subsets are selected by GA/SVM using different training sets. The final subset, consisting of highly discriminating genes, is obtained by analyzing the frequency of appearance of each gene in the different gene subsets. The proposed method is tested on three open datasets: leukemia, breast cancer, and colon cancer data. The results show that the proposed method has excellent selection and classification performance, especially for breast cancer data, which can yield 100% classification accuracy using only four genes.     

采用S变换特征选择方法的心律失常分类

针对短时傅里叶变换与小波变换对心电图（Electrocardiogram,ECG）信号特征提取不足以及心律失常识别困难的问题,提出了一种基于S变换特征选择的心律失常分类算法。首先对ECG信号进行S变换,并从幅值和相位两个角度提取ECG信号的时频特征,与形态特征和RR间隔组成原始特征向量。然后将遗传算法与支持向量机（Support vector machine,SVM）结合组成Wrapper式特征选择方法,并在其中融入ReliefF算法,即采用ReliefF算法计算特征权重,并根据特征权重大小来指导遗传算法种群初始化,遗传算法以SVM的分类性能作为适应度函数来搜索特征子集。最后使用"一对多"（One against all,OAA）SVM对MIT-BIH心律失常数据库8种类型心拍进行分类。实验结果表明,该算法达到了较好的分类效果,灵敏度、特异性和准确率分别为96.14%,99.75%和99.81%。     

Analysis of high-dimensional genomic data employing a novel bio-inspired algorithm

Over the last decade, there has been a rapid growth in the generation and analysis of the genomics data. Though the existing data analysis methods are capable of handling a particular problem, they cannot guarantee to solve all problems with different nature. Therefore, there always lie a scope of a new algorithm to solve a problem which cannot be efficiently solved by the existing algorithms. In the present work, a novel hybrid approach is proposed based on the improved version of a recently developed bio-inspired optimization technique, namely, salp swarm algorithm (SSA) for microarray classification. Initially, the Fisher score filter is employed to pre-select a subset of relevant genes from the original high-dimensional microarray dataset. Later, a weighted-chaotic SSA (WCSSA) is proposed for the simultaneous optimal gene selection and parameter optimization of the kernel extreme learning machine (KELM) classifier. The proposed scheme is experimented on both binary-class and multi-class microarray datasets. An extensive comparison is performed against original SSA-KELM, particle swarm optimized-KELM (PSO-KELM), and genetic algorithm-KELM (GA-KELM). Lastly, the proposed method is also compared against the results of sixteen existing techniques to emphasize its capacity and competitiveness to successfully reduce the number of original genes by more than 98%. The experimental results show that the genes selected by the proposed method yield higher classification accuracy compared to the alternative techniques. The performance of the proposed scheme demonstrates its effectiveness in terms of number of selected genes (NSG), accuracy, sensitivity, specificity, Matthews correlation coefficient (MCC), and F-measure. The proposed WCSSA-KELM method is validated using a ten-fold cross-validation technique.     

Gene selection and sample classification on microarray data based on adaptive genetic algorithm/k-nearest neighbor method

Recently, microarray technology has widely used on the study of gene expression in cancer diagnosis. The main distinguishing feature of microarray technology is that can measure thousands of genes at the same time. In the past, researchers always used parametric statistical methods to find the significant genes. However, microarray data often cannot obey some of the assumptions of parametric statistical methods, or type I error may be over expanded. Therefore, our aim is to establish a gene selection method without assumption restriction to reduce the dimension of the data set. In our study, adaptive genetic algorithm/k-nearest neighbor (AGA/KNN) was used to evolve gene subsets. We find that AGA/KNN can reduce the dimension of the data set, and all test samples can be classified correctly. In addition, the accuracy of AGA/KNN is higher than that of GA/KNN, and it only takes half the CPU time of GA/KNN. After using the proposed method, biologists can identify the relevant genes efficiently from the sub-gene set and classify the test samples correctly.     

基于聚类和微粒群优化的基因选择新方法

鉴于传统的基因选择方法会选出大量冗余基因从而导致较低的样本预测准确率,提出一种基于聚类和微粒群优化的基因选择算法。首先采用聚类算法将基因分成固定数目的簇;然后,采用极限学习机作为分类器进行簇中的特征基因分类性能评价,得到一个备选基因库;最后,采用基于微粒群优化和极限学习机的缠绕法从备选基因库中选择具有最大分类率、最小数目的基因子集。所选出的基因具有良好的分类性能。在两个公开的微阵列数据集上的实验结果表明,相对于一些经典的方法,新方法能够以较少的基因获得更高的分类性能。     

基于混合ABC和CRO的高维特征选择方法

高维数据集包含了成千上万可用于数据分析和预测的特征，然而这些数据集存在许多不相关或冗余特征，影响了数据分析和预测的准确性。现有分类技术难以准确地识别最佳特征子集。针对该问题，提出了一种基于wrapper模式的特征选择方法AB-CRO，该方法结合了人工蜂群算法（ABC）和改进的化学反应算法（CRO）的优点进行特征选择。针对迭代过程中较优的个体可能在化学反应过程中被消耗掉的现象，适当地加入精英策略来保持种群的优良性。实验结果表明，AB-CRO算法在最佳特征子集的识别和分类精度方面相对于基准算法ABC，CRO以及基于GA，PSO和混合蛙跳算法都所有改进。     

A random forest classifier for lymph diseases

Machine learning-based classification techniques provide support for the decision-making process in many areas of health care, including diagnosis, prognosis, screening, etc. Feature selection (FS) is expected to improve classification performance, particularly in situations characterized by the high data dimensionality problem caused by relatively few training examples compared to a large number of measured features. In this paper, a random forest classifier (RFC) approach is proposed to diagnose lymph diseases. Focusing on feature selection, the first stage of the proposed system aims at constructing diverse feature selection algorithms such as genetic algorithm (GA), Principal Component Analysis (PCA), Relief-F, Fisher, Sequential Forward Floating Search (SFFS) and the Sequential Backward Floating Search (SBFS) for reducing the dimension of lymph diseases dataset. Switching from feature selection to model construction, in the second stage, the obtained feature subsets are fed into the RFC for efficient classification. It was observed that GA-RFC achieved the highest classification accuracy of 92.2%. The dimension of input feature space is reduced from eighteen to six features by using GA.     

基于文化算法的表面肌电信号特征选择*

为了提高假肢控制系统肌电信号的分类准确率,提出一种新的基于文化算法的特征选择方法,通过该方法选择出最佳特征向量,然后用线性分类器检验其分类性能。利用表面差分电极从人体上肢四块肌肉采集四通道的肌电信号,对十个健康受试者进行八个动作的肌电信号模式分类实验,并同时用标准遗传算法来与文化算法作比较。实验结果表明,文化算法与遗传算法相比,特征维数更小,分类准确度更高。     

Self-adaptive Bat Algorithm With Genetic Operations

Swarm intelligence in a bat algorithm (BA) provides social learning. Genetic operations for reproducing individuals in a genetic algorithm (GA) offer global search ability in solving complex optimization problems. Their integration provides an opportunity for improved search performance. However, existing studies adopt only one genetic operation of GA, or design hybrid algorithms that divide the overall population into multiple subpopulations that evolve in parallel with limited interactions only. Differing from them, this work proposes an improved self-adaptive bat algorithm with genetic operations (SBAGO) where GA and BA are combined in a highly integrated way. Specifically, SBAGO performs their genetic operations of GA on previous search information of BA solutions to produce new exemplars that are of high-diversity and high-quality. Guided by these exemplars, SBAGO improves both BA’s efficiency and global search capability. We evaluate this approach by using 29 widely-adopted problems from four test suites. SBAGO is also evaluated by a real-life optimization problem in mobile edge computing systems. Experimental results show that SBAGO outperforms its widely-used and recently proposed peers in terms of effectiveness, search accuracy, local optima avoidance, and robustness.      

基于边缘分布模型的基因选择方法

一个微阵列数据集包含了成千上万的基因、相对少量的样本,而在这成千上万的基因中,只有一少部分基因对肿瘤分类是有贡献的,因此,对于肿瘤分类来说,最重要的一个问题就是识别选择出对肿瘤分类最有贡献的基因。为了能有效地进行微阵列基因选择,提出用一个边缘分布模型(marginal distribution model,MDM)来描述微阵列数据。该模型不仅能区分基因是否在两样本中差异表达,而且能区分出基因在哪一类样本中表达,从而选择出的基因更具有生物学意义。模拟数据及真实微阵列数据集上的实验结果表明,该方法能有效地进行微阵列基因选择。     

A genetic algorithm-based method for feature subset selection

As a commonly used technique in data preprocessing, feature selection selects a subset of informative attributes or variables to build models describing data. By removing redundant and irrelevant or noise features, feature selection can improve the predictive accuracy and the comprehensibility of the predictors or classifiers. Many feature selection algorithms with different selection criteria has been introduced by researchers. However, it is discovered that no single criterion is best for all applications. In this paper, we propose a framework based on a genetic algorithm (GA) for feature subset selection that combines various existing feature selection methods. The advantages of this approach include the ability to accommodate multiple feature selection criteria and find small subsets of features that perform well for a particular inductive learning algorithm of interest to build the classifier. We conducted experiments using three data sets and three existing feature selection methods. The experimental results demonstrate that our approach is a robust and effective approach to find subsets of features with higher classification accuracy and/or smaller size compared to each individual feature selection algorithm.     

Genetic algorithm for text clustering based on latent semantic indexing

In this paper, we develop a genetic algorithm method based on a latent semantic model (GAL) for text clustering. The main difficulty in the application of genetic algorithms (GAs) for document clustering is thousands or even tens of thousands of dimensions in feature space which is typical for textual data. Because the most straightforward and popular approach represents texts with the vector space model (VSM), that is, each unique term in the vocabulary represents one dimension. Latent semantic indexing (LSI) is a successful technology in information retrieval which attempts to explore the latent semantics implied by a query or a document through representing them in a dimension-reduced space. Meanwhile, LSI takes into account the effects of synonymy and polysemy, which constructs a semantic structure in textual data. GA belongs to search techniques that can efficiently evolve the optimal solution in the reduced space. We propose a variable string length genetic algorithm which has been exploited for automatically evolving the proper number of clusters as well as providing near optimal data set clustering. GA can be used in conjunction with the reduced latent semantic structure and improve clustering efficiency and accuracy. The superiority of GAL approach over conventional GA applied in VSM model is demonstrated by providing good Reuter document clustering results.     

The improvement of breast cancer prognosis accuracy from integrated gene expression and clinical data

Predicting the accurate prognosis of breast cancer from high throughput microarray data is often a challenging task. Although many statistical methods and machine learning techniques were applied to diagnose the prognosis outcome of breast cancer, they are suffered from the low prediction accuracy (usually lower than 70%). In this paper, we propose a better method (genetic algorithm-support vector machine, we called GASVM) to significant improve the prediction accuracy of breast cancer from gene expression profiles. To further improve the classification performance, we also apply GASVM model using combined clinical and microarray data. In this paper, we evaluate the performance of the GASVM model based on data provided by 97 breast cancer patients. Four kinds of gene selection methods are used: all genes (All), 70 correlation-selected genes (C70), 15 medical literature-selected genes (R15), and 50 T-test-selected genes (T50). With optimized parameter values identified from GASVM model, the average predictive accuracy of our model approaches 95% for T50 and 90% for C70 or R15 in all four kernel functions using integrated clinical and microarray data. Our model produces results more accurately than the average 70% predictive accuracy of other machine learning methods. The results indicate that the GASVM model has the potential to better assist physicians in the prognosis of breast cancer through the use of both clinical and microarray data.     

改进的基于粒子群优化的支持向量机特征选择和参数联合优化算法

针对支持向量机(SVM)中特征选择和参数优化对分类精度有较大影响,提出了一种改进的基于粒子群优化(PSO)的SVM特征选择和参数联合优化算法(GPSO-SVM),使算法在提高分类精度的同时选取尽可能少的特征数目。为了解决传统粒子群算法在进行优化时易出现陷入局部最优和早熟的问题,该算法在PSO中引入遗传算法(GA)中的交叉变异算子,使粒子在每次迭代更新后进行交叉变异操作来避免这一问题。该算法通过粒子之间的不相关性指数来决定粒子之间的交叉配对,由粒子适应度值的大小决定其变异概率的大小,由此产生新的粒子进入到群体中。这样使得粒子跳出当前搜索到的局部最优位置,提高了群体的多样性,在全局范围内寻找更优值。在不同数据集上进行实验,与基于PSO和GA的特征选择和SVM参数联合优化算法相比,GPSO-SVM的分类精度平均提高了2%~3%,选择的特征数目减少了3%~15%。实验结果表明,所提算法的特征选择和参数优化效果更好。     

Diversification for better classification trees

Classification trees are widely used in the data mining community. Typically, trees are constructed to try and maximize their mean classification accuracy. In this paper, we propose an alternative to using the mean accuracy as the performance measure of a tree. We investigate the use of various percentiles (representing the risk aversion of a decision maker) of the distribution of classification accuracy in place of the mean. We develop a genetic algorithm (GA) to build decision trees based on this new criterion. We develop this GA further by explicitly creating diversity in the population by simultaneously considering two fitness criteria within the GA. We show that our bicriterion GA performs quite well, scales up to handle large data sets, and requires a small sample of the original data to build a good decision tree.