An evolutionary clustering algorithm for gene expression microarray data analysis

Clustering is concerned with the discovery of interesting groupings of records in a database. Many algorithms have been developed to tackle clustering problems in a variety of application domains. In particular, some of them have been used in bioinformatics research to uncover inherent clusters in gene expression microarray data. In this paper, we show how some popular clustering algorithms have been used for this purpose. Based on experiments using simulated and real data, we also show that the performance of these algorithms can be further improved. For more effective clustering of gene expression microarray data, which is typically characterized by a lot of noise, we propose a novel evolutionary algorithm called evolutionary clustering (EvoCluster). EvoCluster encodes an entire cluster grouping in a chromosome so that each gene in the chromosome encodes one cluster. Based on such encoding scheme, it makes use of a set of reproduction operators to facilitate the exchange of grouping information between chromosomes. The fitness function that the EvoCluster adopts is able to differentiate between how relevant a feature value is in determining a particular cluster grouping. As such, instead of just local pairwise distances, it also takes into consideration how clusters are arranged globally. Unlike many popular clustering algorithms, EvoCluster does not require the number of clusters to be decided in advance. Also, patterns hidden in each cluster can be explicitly revealed and presented for easy interpretation even by casual users. For performance evaluation, we have tested EvoCluster using both simulated and real data. Experimental results show that it can be very effective and robust even in the presence of noise and missing values. Also, when correlating the gene expression microarray data with DNA sequences, we were able to uncover significant biological binding sites (both previously known and unknown) in each cluster discovered by EvoCluster.     

A simple method for screening variables before clustering microarray data

A simple and computationally fast procedure is proposed for screening a large number of variables prior to cluster analysis. Each variable is considered in turn, the sample is divided into the two groups that maximise the ratio of between-group to within-group sum of squares for that variable, and the achieved value of this ratio is tested to see if it is significantly greater than what would be expected when partitioning a sample from a single homogeneous population. Those variables that achieve significance are then used in the cluster analysis. It is suggested that significance levels be assessed using a Monte Carlo computational procedure; by assuming within-group normality an analytical approximation is derived, but caution in its use is advocated. Computational details are provided for both the partitioning and the testing. The procedure is applied to several microarray data sets, showing that it can often achieve good results both quickly and simply.     

利用连通分支对基因表示数据的聚类算法

在生命科学中,需要对物种及基因进行分类,以获得对种群固有结构的认识。利用数据聚类方法,有效地辨别／识别基因表示数据的模式,对它们进行分类。将特征相似性大的归为一类,特征相异性大的归为不同类。这对于研究基因的结构、功能、以及不同种类基因之间的关系都具有重要意义。利用图论的方法对分子生物学中基因表示数据进行初始聚类,然后再结合别的算法,如K－近邻自学习聚类算法或基于中心点的自学习聚类算法,对其进一步求精。对于某种聚类判别准则,能够产生全局最优簇。最后对算法进行了分析和讨论,并用模拟数据进行了实验验证。     

Assessing agreement of clustering methods with gene expression microarray data

In the rapidly evolving field of genomics, many clustering and classification methods have been developed and employed to explore patterns in gene expression data. Biologists face the choice of which clustering algorithm(s) to use and how to interpret different results from various clustering algorithms. No clear objective criteria have been developed to assess the agreement and compare the results from different clustering methods. We describe two generally applicable objective measures to quantify agreement between different clustering methods. These two measures are referred to as the local agreement measure, which is defined for each gene/subject, and the global agreement measure, which is defined for the whole gene expression experiment. The agreement measures are based on a probabilistic weighting scheme applied to the number of concordant and discordant pairs from two clustering methods. In the comparison and assessment process, newly-developed concepts are implemented under the framework of reliability of a cluster. The algorithms are illustrated by simulations and then applied to a yeast sporulation gene expression microarray data. Analysis of the sporulation data identified ∼5% (23 of 477) genes which were not consistently clustered using a neural net algorithm and K-means or pam. The two agreement measures provide objective criteria to conclude whether or not two clustering methods agree with each other. Using the local agreement measure, genes of unknown function which cluster consistently can more confidently be assigned functions based on co-regulation.     

A novel clustering algorithm by clubbing GHFCM and GWO for microarray gene data

The Journal of Supercomputing - The advancement of data mining technology presents a way to examine and analyse the medical databases. Microarray data help in analysing the gene expressions, and...     

Simulated annealing based automatic fuzzy clustering combined with ANN classification for analyzing microarray data

Microarray technology has made it possible to monitor the expression levels of many genes simultaneously across a number of experimental conditions. Fuzzy clustering is an important tool for analyzing microarray gene expression data. In this article, a real-coded Simulated Annealing (VSA) based fuzzy clustering method with variable length configuration is developed and combined with popular Artificial Neural Network (ANN) based classifier. The idea is to refine the clustering produced by VSA using ANN classifier to obtain improved clustering performance. The proposed technique is used to cluster three publicly available real life microarray data sets. The superior performance of the proposed technique has been demonstrated by comparing with some widely used existing clustering algorithms. Also statistical significance test has been conducted to establish the statistical significance of the superior performance of the proposed clustering algorithm. Finally biological relevance of the clustering solutions are established.     

Mining microarray gene expression data with unsupervised possibilistic clustering and proximity graphs

Gene expression data generated by DNA microarray experiments provide a vast resource of medical diagnostic and disease understanding. Unfortunately, the large amount of data makes it hard, sometimes even impossible, to understand the correct behavior of genes. In this work, we develop a possibilistic approach for mining gene microarray data. Our model consists of two steps. In the first step, we use possibilistic clustering to partition the data into groups (or clusters). The optimal number of clusters is evaluated automatically from the data using the Information Entropy as a validity measure. In the second step, we select from each computed cluster the most representative genes and model them as a graph called a proximity graph. This set of graphs (or hyper-graph) will be used to predict the function of new and previously unknown genes. Experimental results using real-world data sets reveal a good performance and a high prediction accuracy of our model.     

A semi-supervised hierarchical approach: two-dimensional clustering of microarray gene expression data

Micro array technologies have become a widespread research technique for biomedical researchers to assess tens of thousands of gene expression values simultaneously in a single experiment. Micro array data analysis for biological discovery requires computational tools. In this research a novel two-dimensional hierarchical clustering is presented. From the review, it is evident that the previous research works have used clustering which have been applied in gene expression data to create only one cluster for a gene that leads to biological complexity. This is mainly because of the nature of proteins and their interactions. Since proteins normally interact with different groups of proteins in order to serve different biological roles, the genes that produce these proteins are therefore expected to co express with more than one group of genes. This constructs that in micro array gene expression data, a gene may makes its presence in more than one cluster. In this research, multi-level micro array clustering, performed in two dimensions by the proposed two-dimensional hierarchical clustering technique can be used to represent the existence of genes in one or more clusters consistent with the nature of the gene and its attributes and prevent biological complexities.     

Gene clustering for time-series microarray with production outputs

The identification of coexpressed genes from microarray data is a challenging problem in bioinformatics and computational biology. The objective of this study is to obtain knowledge about the most important genes and clusters related to production outputs of real-world time-series microarray data in the industrial microbiology area. Each sample in the microarray data experiment is complemented with the measurement of the corresponding production and growth values. A novel aspect of this research refers to considering the relation of coexpression patterns with the measured outputs to guide the biological interpretation of results. Shape-based clustering models are developed using the pattern of gene expression values over time and further incorporating knowledge about the correlation between the change in the gene expression level and the output value. Experiments are performed for time-series microarray of bacteria, and an analysis from a biological perspective is carried out. The obtained results confirm the existence of relationships between output variables and gene expressions. Moreover, the shape-based clustering methods show promising results, being able to guide metabolic engineering actions with the identification of potential targets.     

非负矩阵分解在微阵列数据分类和聚类发现中的应用

基因芯片是微阵列技术的典型代表,它具有高通量的特性和同时检测全部基因组基因表达水平的能力。应用微阵列芯片的一个主要目的是基因表达模式的发现,即在基因组水平发现功能相似,生物学过程相关的基因簇;或者将样本分类,发现样本的各种亚型。例如根据基因表达水平对癌症样本进行分类,发现疾病的分子亚型。非负矩阵分解NMF方法是一种非监督的、非正交的、基于局部表示的矩阵分解方法。近年来这种方法被越来越多地应用在微阵列数据的分类分析和聚类发现中。系统地介绍了非负矩阵分解的原理、算法和应用,分解结果的生物学解释,分类结果的质量评估和基于NMF算法的分类软件。总结并评估了NMF方法在微阵列数据分类和聚类发现应用中的表现。     

Reusable components for partitioning clustering algorithms

Clustering algorithms are well-established and widely used for solving data-mining tasks. Every clustering algorithm is composed of several solutions for specific sub-problems in the clustering process. These solutions are linked together in a clustering algorithm, and they define the process and the structure of the algorithm. Frequently, many of these solutions occur in more than one clustering algorithm. Mostly, new clustering algorithms include frequently occurring solutions to typical sub-problems from clustering, as well as from other machine-learning algorithms. The problem is that these solutions are usually integrated in their algorithms, and that original algorithms are not designed to share solutions to sub-problems outside the original algorithm easily. We propose a way of designing cluster algorithms and to improve existing ones, based on reusable components. Reusable components are well-documented, frequently occurring solutions to specific sub-problems in a specific area. Thus we identify reusable components, first, as solutions to characteristic sub-problems in partitioning cluster algorithms, and, further, identify a generic structure for the design of partitioning cluster algorithms. We analyze some partitioning algorithms (K-means, X-means, MPCK-means, and Kohonen SOM), and identify reusable components in them. We give examples of how new cluster algorithms can be designed based on them.     

基于张量分析的链接聚类算法的研究*

针对复杂信息网络中多链接高维数据聚类难以处理且效率较低问题,提出了一种新颖的基于高阶张量分析方法和模块化网络分析方法相结合的链接聚类算法。利用模块化方法分析网络,利用张量的形式表示多维的复杂的多链接数据,利用Tucker张量分解的方法对数据降维处理,降低了算法的时间和空间复杂度。并在复杂网络环境下,通过实验验证了算法的有效性和健壮性。     

Robust data envelopment analysis approaches for evaluating algorithmic performance

Recent advances in state-of-the-art meta-heuristics feature the incorporation of probabilistic operators aiming to diversify search directions or to escape from being trapped in local optima. This feature would result in non-deterministic output in solutions that vary from one run to another of a meta-heuristic. Consequently, both the average and variation of outputs over multiple runs have to be considered in evaluating performances of different configurations of a meta-heuristic or distinct meta-heuristics. To this end, this work considers each algorithm as a decision-making unit (DMU) and develops robust data envelopment analysis (DEA) models taking into account not only average but also standard deviation of an algorithm’s output for evaluating relative efficiencies of a set of algorithms. The robust DEA models describe uncertain output using an uncertainty set, and aim to maximize a DMU’s worst-case relative efficiency with respect to that uncertainty set. The proposed models are employed to evaluate a set of distinct configurations of a genetic algorithm and a set of parameter settings of a simulated annealing heuristic. Evaluation results demonstrate that the robust DEA models are able to identify efficient algorithmic configurations. The proposed models contribute not only to the evaluation of meta-heuristics but also to the DEA methodology.     

Self-tuning clustering for high-dimensional data

Spectral clustering is an important component of clustering method, via tightly relying on the affinity matrix. However, conventional spectral clustering methods 1). equally treat each data point, so that easily affected by the outliers; 2). are sensitive to the initialization; 3). need to specify the number of cluster. To conquer these problems, we have proposed a novel spectral clustering algorithm, via employing an affinity matrix learning to learn an intrinsic affinity matrix, using the local PCA to resolve the intersections; and further taking advantage of a robust clustering that is insensitive to initialization to automatically generate clusters without an input of number of cluster. Experimental results on both artificial and real high-dimensional datasets have exhibited our proposed method outperforms the clustering methods under comparison in term of four clustering metrics.     

Fuzzy clustering for symbolic data

Most of the techniques used in the literature in clustering symbolic data are based on the hierarchical methodology, which utilizes the concept of agglomerative or divisive methods as the core of the algorithm. The main contribution of this paper is to show how to apply the concept of fuzziness on a data set of symbolic objects and how to use this concept in formulating the clustering problem of symbolic objects as a partitioning problem. Finally, a fuzzy symbolic c-means algorithm is introduced as an application of applying and testing the proposed algorithm on real and synthetic data sets. The results of the application of the new algorithm show that the new technique is quite efficient and, in many respects, superior to traditional methods of hierarchical nature     

结构复杂数据的半监督聚类

基于成对限制,提出一种半监督聚类算法（ＳＣＣＤ）,它能够处理存在多种密度结构复杂的数据且识别任意形状的簇．利用成对限制反映的多密度分布信息计算基于密度的聚类算法（ＤＢＳＣＡＮ）的邻域半径参数Ｅｐｓ,并利用不同参数的ＤＢＳＣＡＮ 算法处理复杂形状且密度变化的数据集．实验结果表明,ＳＣＣＤ 算法能在噪声环境下发现任意形状且多密度的簇,性能优于已有同类算法．     

Random walk biclustering for microarray data

A biclustering algorithm, based on a greedy technique and enriched with a local search strategy to escape poor local minima, is proposed. The algorithm starts with an initial random solution and searches for a locally optimal solution by successive transformations that improve a gain function. The gain function combines the mean squared residue, the row variance, and the size of the bicluster. Different strategies to escape local minima are introduced and compared. Experimental results on several microarray data sets show that the method is able to find significant biclusters, also from a biological point of view.     

Model-based clustering for longitudinal data

A model-based clustering method is proposed for clustering individuals on the basis of measurements taken over time. Data variability is taken into account through non-linear hierarchical models leading to a mixture of hierarchical models. We study both frequentist and Bayesian estimation procedures. From a classical viewpoint, we discuss maximum likelihood estimation of this family of models through the EM algorithm. From a Bayesian standpoint, we develop appropriate Markov chain Monte Carlo (MCMC) sampling schemes for the exploration of target posterior distribution of parameters. The methods are illustrated with the identification of hormone trajectories that are likely to lead to adverse pregnancy outcomes in a group of pregnant women.     

Algorithms for clustering clickstream data

Clustering is a classic problem in the machine learning and pattern recognition area, however a few complications arise when we try to transfer proposed solutions in the data stream model. Recently there have been proposed new algorithms for the basic clustering problem for massive data sets that produce an approximate solution using efficiently the memory, which is the most critical resource for streaming computation. In this paper, based on these solutions, we present a new model for clustering clickstream data which applies three different phases in the data processing, and is validated through a set of experiments.     

Effective fuzzy c-means clustering algorithms for data clustering problems

Clustering is a well known technique in identifying intrinsic structures and find out useful information from large amount of data. One of the most extensively used clustering techniques is the fuzzy c-means algorithm. However, computational task becomes a problem in standard objective function of fuzzy c-means due to large amount of data, measurement uncertainty in data objects. Further, the fuzzy c-means suffer to set the optimal parameters for the clustering method. Hence the goal of this paper is to produce an alternative generalization of FCM clustering techniques in order to deal with the more complicated data; called quadratic entropy based fuzzy c-means. This paper is dealing with the effective quadratic entropy fuzzy c-means using the combination of regularization function, quadratic terms, mean distance functions, and kernel distance functions. It gives a complete framework of quadratic entropy approaching for constructing effective quadratic entropy based fuzzy clustering algorithms. This paper establishes an effective way of estimating memberships and updating centers by minimizing the proposed objective functions. In order to reduce the number iterations of proposed techniques this article proposes a new algorithm to initialize the cluster centers.In order to obtain the cluster validity and choosing the number of clusters in using proposed techniques, we use silhouette method. First time, this paper segments the synthetic control chart time series directly using our proposed methods for examining the performance of methods and it shows that the proposed clustering techniques have advantages over the existing standard FCM and very recent ClusterM-k-NN in segmenting synthetic control chart time series.