Identification of functional modules in a PPI network by clique percolation clustering

Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein–protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein–protein interaction data for any species and even other biological networks.     

基于对象多属性差异的灰色发展聚类方法及应用

在现实决策问题中,决策对象在不同时期行为状态和所属类型往往呈现一定的发展规律,而现有聚类方法难以充分挖掘聚类对象的发展信息、对象间的关系信息和发展属性的差异信息。为有效处理此类问题,考虑到研究对象的发展趋势、发展行为和发展绝对量与增长量的属性差异,采用GM(1,1)和灰色定权聚类方法,构建了基于对象多属性差异的灰色发展聚类方法,并以我国区域高新技术产业化聚类评估问题为例验证了模型的有效性与合理性。结果表明,所构建模型能够有效描述研究对象呈现发展趋势或未来行为,并实现对研究对象的有效聚类。     

Sparse Convex Clustering

Convex clustering, a convex relaxation of k-means clustering and hierarchical clustering, has drawn recent attentions since it nicely addresses the instability issue of traditional nonconvex clustering methods. Although its computational and statistical properties have been recently studied, the performance of convex clustering has not yet been investigated in the high-dimensional clustering scenario, where the data contains a large number of features and many of them carry no information about the clustering structure. In this article, we demonstrate that the performance of convex clustering could be distorted when the uninformative features are included in the clustering. To overcome it, we introduce a new clustering method, referred to as Sparse Convex Clustering, to simultaneously cluster observations and conduct feature selection. The key idea is to formulate convex clustering in a form of regularization, with an adaptive group-lasso penalty term on cluster centers. To optimally balance the trade-off between the cluster fitting and sparsity, a tuning criterion based on clustering stability is developed. Theoretically, we obtain a finite sample error bound for our estimator and further establish its variable selection consistency. The effectiveness of the proposed method is examined through a variety of numerical experiments and a real data application. Supplementary material for this article is available online.     

Clustering Categorical Data via Ensembling Dissimilarity Matrices

We present a technique for clustering categorical data by generating many dissimilarity matrices and combining them. We begin by demonstrating our technique on low-dimensional categorical data and comparing it to several other techniques that have been proposed. We show through simulations and examples that our method is both more accurate and more stable. Then we give conditions under which our method should yield good results in general. Our method extends to high-dimensional categorical data of equal lengths by ensembling over many choices of explanatory variables. In this context, we compare our method with two other methods. Finally, we extend our method to high-dimensional categorical data vectors of unequal length by using alignment techniques to equalize the lengths. We give an example to show that our method continues to provide useful results, in particular, providing a comparison with phylogenetic trees. Supplementary material for this article is available online.     

基于FCM算法的小脑基因模糊聚类分析

探讨基因表达数据的聚类分析方法,结合一种聚类结果的评判准则,应用于胎儿小脑基因表达数据,得到了最优的聚类结果,并做出了生物学解释.利用Matlab软件进行了仿真,利用模糊聚类Xie-Beni指数得到了最优聚类数,并把每一类对应的基因标号输出到txt文件,最后进行生物学解释.得到的小脑基因最优聚类数为3类,与生物学意义比较吻合,各类中的基因功能接近.基于FCM算法的基因模糊聚类是有效的,结果具有一定生物学意义,能对生物学基因聚类有一定指导作用.     

Edge-Weighted Centroidal Voronoi Tessellations

<正>Most existing applications of centroidal Voronoi tessellations(CVTs) lack consideration of the length of the cluster boundaries.In this paper we propose a new model and algorithms to produce segmentations which would minimize the total energy—a sum of the classic CVT energy and the weighted length of cluster boundaries.To distinguish it with the classic CVTs,we call it an Edge-Weighted CVT(EWCVT).The concept of EWCVT is expected to build a mathematical base for all CVT related data classifications with requirement of smoothness of the cluster boundaries.The EWCVT method is easy in implementation,fast in computation,and natural for any number of clusters.     

Community detection in complex networks by density-based clustering

We proposed a method to find the community structure in a complex network by density-based clustering. Physical topological distance is introduced in density-based clustering for determining a distance function of specific influence functions. According to the distribution of the data, the community structures are uncovered. The method keeps a better connection mode of the community structure than the existing algorithms in terms of modularity, which can be viewed as a basic characteristic of community detection in the future. Moreover, experimental results indicate that the proposed method is efficient and effective to be used for community detection of medium and large networks.     

多指标面板数据融合聚类分析

针对多指标面板数据的样品分类和历史时期划分问题,从多元统计分析理论角度提出一个多指标面板数据的融合聚类分析方法。该方法改进了多指标面板数据的因子分析和系统聚类方法,依据Fisher有序聚类理论,构造了Frobenius范数形式的离差平方和函数,提出了多指标面板数据的有序聚类方法。实证结果表明,该方法能够满足系统分析的统一性要求,保证指标之间的不相关;能够克服时间维度上均值处理造成的偏误,信息损失较少;能够解决面板数据有序聚类的问题;弥补了单一分析的片面性和局限性。     

Ant colony clustering with fitness perception and pheromone diffusion for community detection in complex networks

Community structure detection in complex networks has been intensively investigated in recent years. In this paper, we propose an adaptive approach based on ant colony clustering to discover communities in a complex network. The focus of the method is the clustering process of an ant colony in a virtual grid, where each ant represents a node in the complex network. During the ant colony search, the method uses a new fitness function to percept local environment and employs a pheromone diffusion model as a global information feedback mechanism to realize information exchange among ants. A significant advantage of our method is that the locations in the grid environment and the connections of the complex network structure are simultaneously taken into account in ants moving. Experimental results on computer-generated and real-world networks show the capability of our method to successfully detect community structures.