Enhancing Cancer Classification through a Hybrid Bio-Inspired Evolutionary Algorithm for Biomarker Gene Selection

In this study,our aim is to address the problem of gene selection by proposing a hybrid bio-inspired evolutionary algorithm that combines Grey Wolf Optimization(GWO)with Harris Hawks Optimization(HHO)for feature selection.Themotivation for utilizingGWOandHHOstems fromtheir bio-inspired nature and their demonstrated success in optimization problems.We aimto leverage the strengths of these algorithms to enhance the effectiveness of feature selection in microarray-based cancer classification.We selected leave-one-out cross-validation(LOOCV)to evaluate the performance of both two widely used classifiers,k-nearest neighbors(KNN)and support vector machine(SVM),on high-dimensional cancer microarray data.The proposed method is extensively tested on six publicly available cancer microarray datasets,and a comprehensive comparison with recently published methods is conducted.Our hybrid algorithm demonstrates its effectiveness in improving classification performance,Surpassing alternative approaches in terms of precision.The outcomes confirm the capability of our method to substantially improve both the precision and efficiency of cancer classification,thereby advancing the development ofmore efficient treatment strategies.The proposed hybridmethod offers a promising solution to the gene selection problem in microarray-based cancer classification.It improves the accuracy and efficiency of cancer diagnosis and treatment,and its superior performance compared to other methods highlights its potential applicability in realworld cancer classification tasks.By harnessing the complementary search mechanisms of GWO and HHO,we leverage their bio-inspired behavior to identify informative genes relevant to cancer diagnosis and treatment.

A Survey on Acute Leukemia Expression Data Classification Using Ensembles

Acute leukemia is an aggressive disease that has high mortality rates worldwide.The error rate can be as high as 40%when classifying acute leukemia into its subtypes.So,there is an urgent need to support hematologists during the classification process.More than two decades ago,researchers used microarray gene expression data to classify cancer and adopted acute leukemia as a test case.The high classification accuracy they achieved confirmed that it is possible to classify cancer subtypes using microarray gene expression data.Ensemble machine learning is an effective method that combines individual classifiers to classify new samples.Ensemble classifiers are recognized as powerful algorithms with numerous advantages over traditional classifiers.Over the past few decades,researchers have focused a great deal of attention on ensemble classifiers in a wide variety of fields,including but not limited to disease diagnosis,finance,bioinformatics,healthcare,manufacturing,and geography.This paper reviews the recent ensemble classifier approaches utilized for acute leukemia gene expression data classification.Moreover,a framework for classifying acute leukemia gene expression data is proposed.The pairwise correlation gene selection method and the Rotation Forest of Bayesian Networks are both used in this framework.Experimental outcomes show that the classification accuracy achieved by the acute leukemia ensemble classifiers constructed according to the suggested framework is good compared to the classification accuracy achieved in other studies.

Deep Learning Enabled Microarray Gene Expression Classification for Data Science Applications

In bioinformatics applications,examination of microarray data has received significant interest to diagnose diseases.Microarray gene expression data can be defined by a massive searching space that poses a primary challenge in the appropriate selection of genes.Microarray data classification incorporates multiple disciplines such as bioinformatics,machine learning(ML),data science,and pattern classification.This paper designs an optimal deep neural network based microarray gene expression classification(ODNN-MGEC)model for bioinformatics applications.The proposed ODNN-MGEC technique performs data normalization process to normalize the data into a uniform scale.Besides,improved fruit fly optimization(IFFO)based feature selection technique is used to reduce the high dimensionality in the biomedical data.Moreover,deep neural network(DNN)model is applied for the classification of microarray gene expression data and the hyperparameter tuning of the DNN model is carried out using the Symbiotic Organisms Search(SOS)algorithm.The utilization of IFFO and SOS algorithms pave the way for accomplishing maximum gene expression classification outcomes.For examining the improved outcomes of the ODNN-MGEC technique,a wide ranging experimental analysis is made against benchmark datasets.The extensive comparison study with recent approaches demonstrates the enhanced outcomes of the ODNN-MGEC technique in terms of different measures.

Gene Expression Data Classification Using Consensus Independent Component Analysis

We propose a new method for tumor classification from gene expression data, which mainly contains three steps. Firstly, the original DNA microarray gene expression data are modeled by independent component analysis （ICA）. Secondly, the most discriminant eigenassays extracted by ICA are selected by the sequential floating forward selection technique. Finally, support vector machine is used to classify the modeling data. To show the validity of the proposed method, we applied it to classify three DNA microarray datasets involving various human normal and tumor tissue samples. The experimental results show that the method is efficient and feasible.

Cancer classification based on microarray gene expression data using a principal component accumulation method

The classification of cancer is a major research topic in bioinformatics. The nature of high dimensionality and small size associated with gene expression data,however,makes the classification quite challenging. Although principal component analysis (PCA) is of particular interest for the high-dimensional data,it may overemphasize some aspects and ignore some other important information contained in the richly complex data,because it displays only the difference in the first twoor three-dimensional PC subspaces. Based on PCA,a principal component accumulation (PCAcc) method was proposed. It employs the information contained in multiple PC subspaces and improves the class separability of cancers. The effectiveness of the present method was evaluated by four commonly used gene expression datasets,and the results show that the method performs well for cancer classification.

The expression and antigenicity identification of recombinant rat TGF-β1 in bacteria

In order to study structure-function details of TGF-beta1, the recombinant mature form of rat TGF-beta1 was expressed in bacteria. Synthesis of the 112 amino-acid carboxyl-terminal part of TGF-beta1 (amino acid 279-390) was controlled by an inducible gene expression system based on bacteriophage T7 RNA polymerase. This system allowed an active and selective synthesis of recombinant TGF-beta1. The molecular weight of expressed TGF-alpha1 monomer determined on SDS-polyacrylamide gel under reducing conditions was about 13 kD. Serial detergent washes combined with a single gel-filtration purification step were sufficient to purify the expression product to homogeneity. Amino-terminal sequencing revealed that the N-terminal of the recombinant protein was identical to the published data. In Western blot analysis the recombinant polypeptide showed excellent antigenicity against polyclonal TGF-beta1 antibody. The mature recombinant rat TGF-beta1 expressed in this study provides a useful tool for future detailed structural and functional studies.

Predictive Analysis of Microarray Data

Microarray gene expression data are analyzed by means of a Bayesian nonparametric model, with emphasis on prediction of future observables, yielding a method for selection of differentially expressed genes and the corresponding classifier.

基于混合进化算法的特征选择方法研究

特征选择(Feature Selection,FS)是一种有效的数据预处理方法,它可以通过选择高维数据中一组具有高相关性和低冗余性的特征,从而解决数据冗余引起的维数灾难.目前许多计算方法已经被应用于求解FS问题,其中基于教与学优化(Teaching and Learning-based Optimization Algorithm,TLBO)的特征选择模型由于其高效的全局搜索能力受到越来越多学者的关注.然而,随着数据规模的不断扩大,这些算法所具有的模型不稳定、模型精确度低和局部搜索能力差等局限性,使算法的研究逐步陷入困境.为解决上述问题,本文提出了融合教与学优化算法与局部搜索方法(Local Search,LS)的混合进化Wrapper算法模型(Teaching and Learning-based Optimization-Local Search Algorithm,TLBOLS).首先,由于传统的教与学优化算法不能直接用于求解特征选择问题,算法在初始化阶段将实数型编码转为二进制编码,然后为保证种群的多样性,在教阶段引入最差个体重启机制,并针对进化班级过程中学习者与教学者两种身份采用不同值的TF值,提出二进制的教与学特征选择算法(Binary Teaching and Learning-based Optimization-Local Search Algorithm,BTLBOLS).随后,提出结合多操作的局部搜索方法和变邻域搜索逐渐增强扰动力度,提高整个种群的个体质量.为优化特征选择结果,BTLBOLS利用综合评价指标作为目标函数指导整体进化过程.实验选取45个高维癌症基因表达数据集进行测试并与十种特征选择算法相比,实验结果表明,相比其他算法,BTLBOLS在分类准确率和特征个数上都具有一定优势,算法分类性能有效提高.

A new distributed feature selection technique for classifying gene expression data

Classification of gene expression data is a pivotal research area that plays a substantial role in diagnosis and prediction of diseases. Generally, feature selection is one of the extensively used techniques in data mining approaches, especially in classification. Gene expression data are usually composed of dozens of samples characterized by thousands of genes. This increases the dimensionality coupled with the existence of irrelevant and redundant features. Accordingly, the selection of informative genes (features) becomes difficult, which badly affects the gene classification accuracy. In this paper, we consider the feature selection for classifying gene expression microarray datasets. The goal is to detect the most possibly cancer-related genes in a distributed manner, which helps in effectively classifying the samples. Initially, the available huge amount of considered features are subdivided and distributed among several processors. Then, a new filter selection method based on a fuzzy inference system is applied to each subset of the dataset. Finally, all the resulted features are ranked, then a wrapper-based selection method is applied. Experimental results showed that our proposed feature selection technique performs better than other techniques since it produces lower time latency and improves classification performance.

基于输出不一致测度的极限学习机集成的基因表达数据分类

选择性集成学习已经成为分析基因表达数据、获取生物学信息的有力工具.为了更好地挖掘基因表达数据,利用极限学习机的集成,克服单个ELM用于数据分类时性能欠稳定的缺点,文中提出了一种基于输出不一致测度的ELM相异性集成算法(D-D-ELM).算法首先以输出不一致测度为标准对多个ELM模型进行相异性判断,其次根据ELM的平均分类精度剔除掉相应的模型,最后对筛选后的分类模型用多数投票法进行集成.算法被运用到Breast、Leukemia、Colon、Heart基因表达数据上,并通过理论和实验得到验证.实验结果的统计学分析表明D-D-ELM能够以更少的模型数量达到较稳定的分类精度.

肿瘤基因表达谱分类特征基因选取问题及分析方法研究

对肿瘤分类特征基因选取问题的研究是发现肿瘤特异表达基因、研究肿瘤基因表达模式的重要手段.文中基于多类别肿瘤基因表达谱数据集,从研究肿瘤与正常组织的分类入手,对肿瘤分类特征基因选取问题进行分析和研究.首先对基于Relief算法的特征选取策略加以改进生成候选特征集合;然后以支持向量机作为分类器对其分类性能进行检验以选取分类特征基因;最后结合分类模型,利用灵敏度分析方法进行特征基因的精确搜索以滤除冗余.基于该方法文中选出了52个具有良好分类性能的特征基因作为肿瘤的基因特征,并对其表达行为进行了简要分析.

基因表达谱聚类/分类技术研究及展望

随着人类及多种模式生物全基因组测序基本完成,人类基因组计划的研究进入后基因组时代.后基因组时代研究的焦点已经从测序转向功能研究。聚类/分类技术作为分析基因表达谱和识别基因功能的重要工具之一,近年来获得很大的发展。对目前基因表达谱聚类/分类技术及它们的发展,进行了综述性的研究,分析了它们的优缺点,结合我们的研究,提出了解决问题的思路和方法,为基因表达谱的进一步研究提供了新的途径。

嵌入代价敏感的极限学习机相异性集成的基因表达数据分类

极限学习机的相异性集成算法(Dissimilarity Based Ensemble of Extreme Learning Machine,D-ELM)在基因表达数据分类中能够得到较稳定的分类效果,然而这种分类算法是基于分类精度的,当所给样本的误分类代价不相等时,不能直接实现代价敏感分类过程中的最小平均误分类代价的要求。通过在分类过程中引入概率估计以及误分类代价和拒识代价重新构造分类结果,提出了基于相异性集成极限学习机的代价敏感算法(CS-D-ELM)。该算法被运用到基因表达数据集上,得到了较好的分类效果。

基于加权极限学习机的肿瘤基因表达谱数据分类

基因表达谱数据一般来源于临床试验,而在临床试验中,试验样本的类分布情况是不确定的,这就使得表达谱数据往往具有比较明显的不平衡性.采用加权极限学习机来对不平衡基因表达谱数据进行分类,为了减少因为不平衡数据引起的分类误差,一个临时的权重被分配给每一个样本以增强少样本类的影响,同时减少多样本类的影响,进而提高肿瘤分类的准确率.实验结果表明,所提方法能够提高少样本类的识别率,从而提高分类器的总体性能.

一种改进的基因表达数据分类方法

从分类算法和特征基因选择两个方面研究基因表达数据的分类,将传统的Support Vector Machines(SVM)算法和K-nearest neighbor(KNN)算法两者结合成为一种应用于基因表达数据分类的算法,并针对基因表达数据分类数据集“样本少,维数高”的特点,提出了一种改进的基于相关性的递归特征消除算法(简称为C-RFE),消除了数据冗余．实验结果表明,新方法可有效提高分类准确率和特征选取的效率．

支持向量机在基因表达数据分类中的应用研究

目的探讨支持向量机在基因表达数据分类研究中的应用条件和效果。方法使用支持向量机软件包,通过实际基因表达数据考核其应用效果,并通过模拟试验进一步验证和研究在含有大量无差异表达基因情况下对分类产生的影响。结果对四种疾病的真实基因表达数据的分类取得了良好的效果,模拟试验则显示了支持向量机对分类具有较高的准确性,但随无差异基因数量的增加其分类效果呈明显下降的趋势;在类间分离一定的情况下,差异表达基因数目较多、基因之间具有较高的相关性时,更容易获得好的分类效果。结论支持向量机在解决小样本、非线性及高维问题中表现出许多潜在的优势,可以有效地用于分析基因表达数据的分类问题。

癌症基因分类的Laplace谱方法

本文尝试着将图的Laplace谱理论应用于癌症基因表达谱数据的分类上.计算出训练集中每个类的均值作为类中心,选出与类中心欧式距离最小的若干样本用laplace矩阵构造完全图,记为代表该类的标准图.用待测样本依次替换标准图中所有的点,将生成的新图与标准图进行特征点匹配,并计算匹配点数总和.将待测样本划分为总匹配点数最多的那个类.通过对白血病两个亚型(ALL与AML)与结肠癌数据进行留一法实验,验证了本文方法的有效性.

两种基于偏最小二乘法的分类模型对肿瘤基因表达数据行多分类的比较研究

目的比较两种基于偏最小二乘法的分类模型对肿瘤基因表达数据行多分类分析的效果,比较不同差异基因选取方法对分类结果的影响。方法利用NCI60等4个肿瘤基因表达数据库,通过4种不同方法选取差异表达基因,在此基础上,用两种基于偏最小二乘的方法行多分类分析。一是偏最小二乘线性判别,首先运用偏最小二乘法行降维,再利用降维得到的成分作为输入变量作线性判别分析;二是偏最小二乘判别分析,利用偏最小二乘回归直接进行分类。分类效果采用留一法和10倍交叉验证法进行评价。结果偏最小二乘判别分析的分类效果略优于偏最小二乘降维后的线性判别。以变量重要性指标选取差异表达基因时分类效果较好,其次是SAM法。结论在对肿瘤基因表达数据行多分类分析时,偏最小二乘法既是一种高效的降维方法,也是一种实用的分类方法。

基因表达数据在邻域关系中的特征选择

基因特征选择是基因表达数据分析中的一种重要方法。粗糙集是一种处理不确定性、不一致性、不精确性数据的有效分类工具,其特点是保持基因表达数据集的分类能力不变,进行基因特征选择。为了避免传统粗糙集特征选择方法所必需的离散化过程带来的信息损失,将邻域粗糙集特征选择方法应用于基因的特征选取,提出了基于邻域粗糙集的基因选择方法。该方法从所有特征出发,根据特征重要度逐步删除冗余的特征,最后得到关键特征组进行分类研究。在2个标准的基因表达数据集上进行特征选取,并进行了分类实验,实验结果表明该方法是有效可行的。

基于层级规则树的跨平台基因表达数据分类

基因检测技术运用至今已积累大量来自不同平台的数据,针对传统数据分类模式难以在不同平台间进行有效迁移的问题,提出一种基于层级规则树的基因表达数据分类算法k-HRT。设计数据转换与规则预筛选策略,实现算法的快速挖掘,以解决由跨平台特性所带来的大规模数据问题。在真实基因表达数据集上的实验结果表明,相对k-TSP算法、SVM-RFE算法,k-HRT算法能够有效提高分类精度。