Projected Clustering for Biological Data Analysis

Projected Clustering for Biological Data Analysis

Ping Deng (University of Illinois at Springfield, USA), Qingkai Ma (Utica College, USA) and Weili Wu (The University of Texas at Dallas, USA)
Copyright: © 2009 |Pages: 6
DOI: 10.4018/978-1-60566-010-3.ch247
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Abstract

Clustering can be considered as the most important unsupervised learning problem. It has been discussed thoroughly by both statistics and database communities due to its numerous applications in problems such as classification, machine learning, and data mining. A summary of clustering techniques can be found in (Berkhin, 2002). Most known clustering algorithms such as DBSCAN (Easter, Kriegel, Sander, & Xu, 1996) and CURE (Guha, Rastogi, & Shim, 1998) cluster data points based on full dimensions. When the dimensional space grows higher, the above algorithms lose their efficiency and accuracy because of the so-called “curse of dimensionality”. It is shown in (Beyer, Goldstein, Ramakrishnan, & Shaft, 1999) that computing the distance based on full dimensions is not meaningful in high dimensional space since the distance of a point to its nearest neighbor approaches the distance to its farthest neighbor as dimensionality increases. Actually, natural clusters might exist in subspaces. Data points in different clusters may be correlated with respect to different subsets of dimensions. In order to solve this problem, feature selection (Kohavi & Sommerfield, 1995) and dimension reduction (Raymer, Punch, Goodman, Kuhn, & Jain, 2000) have been proposed to find the closely correlated dimensions for all the data and the clusters in such dimensions. Although both methods reduce the dimensionality of the space before clustering, the case where clusters may exist in different subspaces of full dimensions is not handled well. Projected clustering has been proposed recently to effectively deal with high dimensionalities. Finding clusters and their relevant dimensions are the objectives of projected clustering algorithms. Instead of projecting the entire dataset on the same subspace, projected clustering focuses on finding specific projection for each cluster such that the similarity is reserved as much as possible.
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Background

Projected clustering algorithms generally fall into two categories: density-based algorithms (Agrawal, Gehrke, Gunopulos, & Raghavan, 1998; Procopiuc, Jones, Agarwal, & Murali, 2002; Liu & Mamoulis, 2005; Ng, Fu, & Wong, 2005; Moise, Sander, & Ester, 2006) and distance-based algorithms (Aggarwal, Procopiuc, Wolf, Yu, & Park, 1999; Aggarwal & Yu, 2000; Deng, Wu, Huang, & Zhang, 2006; Yip, Cheung, & Ng, 2003; Tang, Xiong, Zhong, & Wu, 2007). Density-based algorithms define a cluster as a region that has a higher density of data points than its surrounding regions. Dense regions only in their corresponding subspaces need to be considered in terms of projected clustering. Distance-based algorithms define a cluster as a partition such that the distance between objects within the same cluster is minimized and the distance between objects from different clusters is maximized. A distance measure is defined between data points. Compared to density-based methods in which each data point is assigned to all clusters with a different probability, distance-based methods assign data to a cluster with probability 0 or 1. Three criteria (Yip, Cheung, & Ng, 2003) have been proposed to evaluate clusters: the number of data points in a cluster, the number of selected dimensions in a cluster, and the distance between points at selected dimensions.

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