Wavelet transformation and cluster ensemble for gene expression analysis

This paper introduces a wavelet transformation and a cluster ensemble framework using graph theory for clustering gene expression data sets. The experiment results indicate that wavelet transformation and cluster ensemble approaches together yield better clustering results than the single best clustering algorithm on both synthetic and yeast gene expression data sets.

[1]  L. Hubert,et al.  Quadratic assignment as a general data analysis strategy. , 1976 .

[2]  George Karypis,et al.  Multilevel k-way Partitioning Scheme for Irregular Graphs , 1998, J. Parallel Distributed Comput..

[3]  Richard M. Karp,et al.  CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts , 2001, ISMB.

[4]  L. A. Goodman,et al.  Measures of Association for Cross Classifications, IV: Simplification of Asymptotic Variances , 1972 .

[5]  Anil K. Jain,et al.  Data clustering: a review , 1999, CSUR.

[6]  James C. Bezdek,et al.  Pattern Recognition with Fuzzy Objective Function Algorithms , 1981, Advanced Applications in Pattern Recognition.

[7]  Stéphane Mallat,et al.  A Theory for Multiresolution Signal Decomposition: The Wavelet Representation , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[8]  Joydeep Ghosh,et al.  Cluster Ensembles --- A Knowledge Reuse Framework for Combining Multiple Partitions , 2002, J. Mach. Learn. Res..

[9]  Robert R. Klevecz,et al.  Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data , 2000, Functional & Integrative Genomics.

[10]  F. Azuaje In silico approaches to microarray-based disease classification and gene function discovery , 2002, Annals of medicine.

[11]  Teuvo Kohonen,et al.  Self-Organizing Maps , 2010 .

[12]  Thomas G. Dietterich Multiple Classifier Systems , 2000, Lecture Notes in Computer Science.

[13]  Vipin Kumar,et al.  A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs , 1998, SIAM J. Sci. Comput..

[14]  I. Guyon,et al.  Detecting stable clusters using principal component analysis. , 2003, Methods in molecular biology.

[15]  Werner Dubitzky,et al.  A Practical Approach to Microarray Data Analysis , 2003, Springer US.

[16]  Richard Lippmann,et al.  Neural Network Classifiers Estimate Bayesian a posteriori Probabilities , 1991, Neural Computation.

[17]  Jiawei Han,et al.  Data Mining: Concepts and Techniques , 2000 .

[18]  John A. Hartigan,et al.  Clustering Algorithms , 1975 .

[19]  J. Dunn Well-Separated Clusters and Optimal Fuzzy Partitions , 1974 .

[20]  Francisco Azuaje,et al.  Clustering Genomic Expression Data: Design and Evaluation Principles , 2003 .

[21]  George Karypis,et al.  Clustering in life sciences. , 2003, Methods in molecular biology.

[22]  Sankar K. Pal,et al.  Fuzzy models for pattern recognition , 1992 .

[23]  John Reinitz,et al.  Registration of the expression patterns of Drosophila segmentation genes by two independent methods , 2001, Bioinform..

[24]  Donald W. Bouldin,et al.  A Cluster Separation Measure , 1979, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[25]  Guang R. Gao,et al.  An adaptive meta-clustering approach: combining the information from different clustering results , 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

[26]  Zohar Yakhini,et al.  Clustering gene expression patterns , 1999, J. Comput. Biol..

[27]  Abdelghani Bellaachia,et al.  E-CAST: A Data Mining Algorithm for Gene Expression Data , 2002, BIOKDD.

[28]  Vipin Kumar,et al.  Partitioning-based clustering for Web document categorization , 1999, Decis. Support Syst..

[29]  Xiaohua Hu,et al.  Using rough sets theory and database operations to construct a good ensemble of classifiers for data mining applications , 2001, Proceedings 2001 IEEE International Conference on Data Mining.