An association analysis approach to biclustering

Gaurav Pandey, Gowtham Atluri, Michael Steinbach, Chad L. Myers, Vipin Kumar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

41 Scopus citations

Abstract

The discovery of biclusters, which denote groups of items that show coherent values across a subset of all the transactions in a data set, is an important type of analysis performed on real-valued data sets in various domains, such as biology. Several algorithms have been proposed to find different types of biclusters in such data sets. However, these algorithms are unable to search the space of all possible biclusters exhaustively. Pattern mining algorithms in association analysis also essentially produce biclusters as their result, since the patterns consist of items that are supported by a subset of all the transactions. However, a major limitation of the numerous techniques developed in association analysis is that they are only able to analyze data sets with binary and/or categorical variables, and their application to real-valued data sets often involves some lossy transformation such as discretization or binarization of the attributes. In this paper, we propose a novel association analysis framework for exhaustively and efficiently mining "range support" patterns from such a data set. On one hand, this framework reduces the loss of information incurred by the binarization- and discretization-based approaches, and on the other, it enables the exhaustive discovery of coherent biclusters. We compared the performance of our framework with two standard biclustering algorithms through the evaluation of the similarity of the cellular functions of the genes constituting the patterns/biclusters derived by these algorithms from microarray data. These experiments show that the real-valued patterns discovered by our framework are better enriched by small biologically interesting functional classes. Also, through specific examples, we demonstrate the ability of the RAP framework to discover functionally enriched patterns that are not found by the commonly used biclustering algorithm ISA. The source code and data sets used in this paper, as well as the supplementary material, are available at http://www.cs.umn.edu/vk/ gaurav/rap.

Original languageEnglish (US)
Title of host publicationKDD '09
Subtitle of host publicationProceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Pages677-685
Number of pages9
DOIs
StatePublished - Nov 16 2009
Event15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD '09 - Paris, France
Duration: Jun 28 2009Jul 1 2009

Publication series

NameProceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Other

Other15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD '09
CountryFrance
CityParis
Period6/28/097/1/09

Keywords

  • Association analysis
  • Biclustering
  • Functional modules
  • Microarray data
  • Range support
  • Real-valued data

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