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Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)
Multi-Scale Clustering for Gene Expression Profiling Data
Minneapolis, Minnesota
October 19-October 21
ISBN: 0-7695-2476-1
Shigeyuki Oba, Nara Institute of Science and Technology
Kikuya Kato, Osaka Medical Center for Cancer and Cardiovascular Diseases
Shin Ishii, Nara Institute of Science and Technology
In cluster analyses, setting the scale parameter which is implicitly related to the complexity of the data distribution is an important issue; different scale values lead to different results and hence cause different interpretation. In this study, we discuss a framework of multi-scale clustering, where clustering is done with multiple scale values and then the obtained results are compiled into a visually appropriate form to observe overall structures of the clusters. For such purpose, a brick view method is proposed in this study. The construction of a brick view diagram consists of a re-indexing procedure of clusters obtained with various scale values and a sorting procedure of samples so as to minimize the distortion defined based on the multiple clustering results. Although some popular clustering methods, such as K-means, spherical K-means, and hierarchical clustering, have been used within the multi-scale framework, we introduce mean-shift clustering based on the kernel density estimation for directional data. We evaluate our approach and existing hierarchical clustering by using an artificial data set and a real data set of gene expression profiles. The results show global structures of distributions can be observed well and in a stable manner, in the brick view diagram.
Citation:
Shigeyuki Oba, Kikuya Kato, Shin Ishii, "Multi-Scale Clustering for Gene Expression Profiling Data," bibe, pp.210-217, Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05), 2005
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