Co-clustering numerical data under user-defined constraints

Statistical Analysis and Data Mining

Volumn 3, Issue 1, 2010, Pages 38-55

  Pensa, Ruggero G ^a,c   Boulicaut, Jean Francois ^b   Cordero, Francesca ^a   Atzori, Maurizio ^c  

^a UNIVERSITY OF TURIN   (Italy)

^b CNRS   (France)

^c ISTI CNR   (Italy)

Author keywords

Co clustering; Microarray analysis; Semi supervised clustering

Indexed keywords

CLUSTER ANALYSIS; DATA MINING; DOMAIN KNOWLEDGE; GENE EXPRESSION; ITERATIVE METHODS; NUMERICAL METHODS;

CANNOT LINKS; CO CLUSTERS; CO-CLUSTERING; MATRIX; MICROARRAY ANALYSIS; MUST LINKS; NUMERICAL DATA; OBJECT ATTRIBUTES; OBJECTIVE FUNCTIONS; SEMI-SUPERVISED CLUSTERING;

CLUSTERING ALGORITHMS;

EID: 77950210799     PISSN: 19321872     EISSN: 19321864     Source Type: Journal    
DOI: 10.1002/sam.10064     Document Type: Article

References (38)

1. M. N. Arbeitman, E. E. Furlong, F. Imam, E. Johnson, B. H. Null, B. S. Baker, M. A. Krasnow, M. P. Scott, R. W. Davis, and K. P. White, Gene expression during the life cycle of drosophila melanogaster, Science 297 (2002), 2270-2275.
2. C. Robardet and F. Feschet, Efficient local search in conceptual clustering, Proceedings DS 2001, Vol. 2226 of LNCS, Washington, DC, Springer, 2001, 323-335.
3. I. S. Dhillon, S. Mallela, and D. S. Modha, Information theoretic co-clustering, In Proceedings ACM SIGKDD 2003, Washington, DC, 2003, 89-98.
4. A. Banerjee, I. Dhillon, J. Ghosh, S. Merugu, and D. S. Modha, A generalized maximum entropy approach to bregman co-clustering and matrix approximation, J Mach Learn Res 8 (2007), 1919-1986.
5. Y. Cheng and G. M. Church, Biclustering of expression data, Proceedings ISMB 2000, San Diego, CA, AAAI Press, 2000, 93-103.
6. S. C. Madeira and A. L. Oliveira, Biclustering algorithms for biological data analysis: a survey, IEEE/ACM Trans Comput Biol Bioinform 1(1) (2004), 24-45.
7. K. Wagstaff, C. Cardie, S. Rogers, and S. Schrödl, Constrained k-means clustering with background knowledge, In Proceedings ICML 2001, Williamstown, MA, 2001, 577-584.
8. S. Basu, A. Banerjee, and R. J. Mooney, Semi-supervised clustering by seeding, In Proceedings ICML 2002, Sydney, 2002, 27-34.
9. D.Klein,S.D.Kamvar,andC.D.Manning, Frominstancelevel constraints to space-level constraints: Making the most of prior knowledge in data clustering, In Proceedings ICML 2002, Sydney, 2002, 307-314.
10. S. Basu, M. Bilenko, and R. J. Mooney, A probabilistic framework for semi-supervised clustering, In Proceedings ACM SIGKDD 2004, Seattle, WA, 2004, 59-68.
11. I. Davidson and S. S. Ravi, Clustering with constraints: feasibility issues and the k-means algorithm, In Proceedings SIAM SDM 2005, Newport Beach, CA, 2005.
12. I. Davidson and S. S. Ravi, Agglomerative hierarchical clustering with constraints: theoretical and empirical results, Proceedings PKDD 2005, Vol. 3721 of LNCS, Porto, Portugal, Springer, 2005, 59-70.
13. S. Basu, I. Davidson, and K. Wagstaff, eds, Constrained Clustering: Advances in Algorithms, Theory and Applications, Data Mining and Knowledge Discovery Series, Chapman & Hall/CRC Press, Boca Raton, FL, USA, 2008.
14. R. G. Pensa, C. Robardet, and J.-F. Boulicaut, Towards constrained co-clustering in ordered 0/1 data sets, Proceedings ISMIS 2006, Vol. 4203 of LNCS, Bari, Springer, 2006, 425-434.
15. R. G. Pensa, C. Robardet, and J.-F. Boulicaut, Constraintdriven co-clustering of 0/1 data, Constrained Clustering: Advances in Algorithms, Theory and Applications, Data Mining and Knowledge Discovery Series, Chapman & Hall/CRC Press, Boca Raton, FL, USA, 2008, 123-148.
16. H. Cho, I. S. Dhillon, Y. Guan, and S. Sra, Minimum sum-squared residue co-clustering of gene expression data, In Proceedings SIAM SDM 2004, Lake Buena Vista, FL, 2004.
17. R. G. Pensa and J-F. Boulicaut, Constrained co-clustering of gene expression data, Proceedings SIAM SDM 2008, Atlanta, GA, 2008, 25-36.
18. E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman, Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nat Genet 34 (2003), 166-176.
19. E. E. Furlong, E. C. Andersen, B. Null, K. P. White, and M. P. Scott, Patterns of gene expression during drosophila mesoderm development, Science 293 (2001), 1629-1633.
20. Y. Kluger, R. Basri, J. T. Chang, and M. Gerstein, Spectral biclustering of microarray data: coclustering genes and conditions, Genome Res, 13 (2003), 703-716.
21. L. Lazzeroni and A. Owen, Plaid Models for Gene Expression Data, Stanford, CA, Technical Report Stanford University, 2000.
22. B. Hendrickson and T. G. Kolda, Partitioning rectangular and structurally unsymmetric sparse matrices for parallel processing, SIAM J Sci Comput 21 (1999), 2048-2072.
23. A. Anagnostopoulos, A. Dasgupta, and R. Kumar, Approximation algorithms for co-clustering, In Proceedings PODS 2008, Vancouver, BC, 2008, 201-210.
24. D. Ienco, R. G. Pensa, and R. Meo, Parameter-free hierarchical co-clustering by n-ary splits, Proceedings ECML PKDD 2009, Vol. 5781 of LNCS, Bled, Slovenia, Springer, 2009, 580-595.
25. M. Deodhar, G. Gupta, J. Ghosh, H. Cho, and I. S. Dhillon, A scalable framework for discovering coherent co-clusters in noisy data, In Proceedings ICML 2009, Montreal, Quebec, 2009, 241-248.
26. H. Shan and A. Banerjee, Bayesian co-clustering, Proceedings ICDM 2008, Pisa, IEEE Computer Society, 2008, 530-539.
27. J. Ihmels, G. Friedlander, S. Bergmann, O. Sarig, Y. Ziv, and N. Barkai, Revealing modular organization in the yeast transcriptional network, Nat Genet 31 (2002), 370-377.
28. M. Bilenko, S. Basu, and R. J. Mooney, Integrating constraints and metric learning in semi-supervised clustering, In Proceedings ICML 2004, Banff, 2004, 81-88.
29. A. Banerjee and J. Ghosh, On scaling up balanced clustering algorithms, In Proceedings SIAM SDM 2002, Arlington, VA, 2002.
30. A. Banerjee and J. Ghosh, Scalable clustering algorithms with balancing constraints, Data Min Knowl Discov 13(3) (2006), 365-395.
31. R. Ge, M. Ester, W. Jin, and I. Davidson, Constraint-driven clustering, In Proceedings of ACM SIGKDD 2007, San Jose, CA, 2007, 320-329.
32. J. A. Hartigan, Direct clustering of a data matrix, J Am Stat Assoc 67(337) (1972), 123-129.
33. L. Hubert and P. Arabie, Comparing partitions, J Classif 2(1) (1985), 193-218.
34. F. Cordero, A. Visconti, and M. Botta, A new protein motif extraction framework based on constrained coclustering, Proceedings SAC 2009, Honolulu, HI, ACM, 2009, 776-781.
35. A. Brazma, I. Jonassen, E. Ukkonen, and J. Vilo, Discovering patterns and subfamilies in biosequences, Proceedings ISMB, St. Louis, MO, AAAI Press, 1996, 34-43.
36. A. Bairoch, Prosite: a dictionary of sites and patterns in proteins, Nucleic Acids Res 19 (1991), 2241-2245.
37. G. E. Crooks, G. Hon, J.-M. Chandonia, and S. E. Brenner, Weblogo: a sequence logo generator, Genome Res 14 (2004), 1188-1190.
38. T. D. Schneider and R. M. Stephens, Sequence logos: a new way to display consensus sequences, Nucleic Acids Res 18 (1990), 6097-6100