Machine Learning
COOLCAT: an entropy-based algorithm for categorical clustering
Proceedings of the eleventh international conference on Information and knowledge management
Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Values
Data Mining and Knowledge Discovery
Discretization: An Enabling Technique
Data Mining and Knowledge Discovery
Biclustering of Expression Data
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Clustering Categorical Data: An Approach Based on Dynamical Systems
VLDB '98 Proceedings of the 24rd International Conference on Very Large Data Bases
ROCK: A Robust Clustering Algorithm for Categorical Attributes
ICDE '99 Proceedings of the 15th International Conference on Data Engineering
HARP: A Practical Projected Clustering Algorithm
IEEE Transactions on Knowledge and Data Engineering
A bi-clustering framework for categorical data
PKDD'05 Proceedings of the 9th European conference on Principles and Practice of Knowledge Discovery in Databases
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We propose and study the notion of dense regions for the analysis of categorized gene expression data and present some searching algorithms for discovering them. The algorithms can be applied to any categorical data matrices derived from gene expression level matrices. We demonstrate that dense regions are simple but useful and statistically significant patterns that can be used to 1) identify genes and/or samples of interest and 2) eliminate genes and/or samples corresponding to outliers, noise, or abnormalities. Some theoretical studies on the properties of the dense regions are presented which allow us to characterize dense regions into several classes and to derive tailor-made algorithms for different classes of regions. Moreover, an empirical simulation study on the distribution of the size of dense regions is carried out which is then used to assess the significance of dense regions and to derive effective pruning methods to speed up the searching algorithms. Real microarray data sets are employed to test our methods. Comparisons with six other well-known clustering algorithms using synthetic and real data are also conducted which confirm the superiority of our methods in discovering dense regions. The DRIFT code and a tutorial are available as supplemental material, which can be found on the Computer Society Digital Library at http://computer.org/tcbb/archives.htm.