5,616 research outputs found
Techniques for clustering gene expression data
Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered
On-line evolving fuzzy clustering
In this paper, a novel on-line evolving fuzzy clustering method that extends the evolving clustering method (ECM) of Kasabov and Song (2002) is presented, called EFCM. Since it is an on-line algorithm, the fuzzy membership matrix of the data is updated whenever the existing cluster expands, or a new cluster is formed. EFCM does not need the numbers of the clusters to be pre-defined. The algorithm is tested on several benchmark data sets, such as Iris, Wine, Glass, E-Coli, Yeast and Italian Olive oils. EFCM results in the least objective function value compared to the ECM and Fuzzy C-Means. It is significantly faster (by several orders of magnitude) than any of the off-line batch-mode clustering algorithms. A methodology is also proposed for using theXie-Beni cluster validity measure to optimize the number of clusters. © 2007 IEEE
Overlapping modularity at the critical point of k-clique percolation
One of the most remarkable social phenomena is the formation of communities
in social networks corresponding to families, friendship circles, work teams,
etc. Since people usually belong to several different communities at the same
time, the induced overlaps result in an extremely complicated web of the
communities themselves. Thus, uncovering the intricate community structure of
social networks is a non-trivial task with great potential for practical
applications, gaining a notable interest in the recent years. The Clique
Percolation Method (CPM) is one of the earliest overlapping community finding
methods, which was already used in the analysis of several different social
networks. In this approach the communities correspond to k-clique percolation
clusters, and the general heuristic for setting the parameters of the method is
to tune the system just below the critical point of k-clique percolation.
However, this rule is based on simple physical principles and its validity was
never subject to quantitative analysis. Here we examine the quality of the
partitioning in the vicinity of the critical point using recently introduced
overlapping modularity measures. According to our results on real social- and
other networks, the overlapping modularities show a maximum close to the
critical point, justifying the original criteria for the optimal parameter
settings.Comment: 20 pages, 6 figure
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Local search: A guide for the information retrieval practitioner
There are a number of combinatorial optimisation problems in information retrieval in which the use of local search methods are worthwhile. The purpose of this paper is to show how local search can be used to solve some well known tasks in information retrieval (IR), how previous research in the field is piecemeal, bereft of a structure and methodologically flawed, and to suggest more rigorous ways of applying local search methods to solve IR problems. We provide a query based taxonomy for analysing the use of local search in IR tasks and an overview of issues such as fitness functions, statistical significance and test collections when conducting experiments on combinatorial optimisation problems. The paper gives a guide on the pitfalls and problems for IR practitioners who wish to use local search to solve their research issues, and gives practical advice on the use of such methods. The query based taxonomy is a novel structure which can be used by the IR practitioner in order to examine the use of local search in IR
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