Permu-pattern: Discovery of mutable permutation patterns with proximity constraint

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

Volumn , Issue , 2008, Pages 318-326

  Hu, Meng ^a   Yang, Jiong ^a   Su, Wei ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

Permutation pattern; Proximity pattern; Sequential pattern

Indexed keywords

A-PRIORI; COMPUTATIONAL BIOLOGIES; DATA SETS; GENE CLUSTERS; PATTERN DISCOVERIES; PERMUTATION PATTERN; PROXIMITY PATTERN; REACHABILITY; SEQUENCE DATABASE; SEQUENCE DATUM; SEQUENTIAL PATTERN; SYNTHETIC DATUM; TEXT MININGS;

BIOINFORMATICS; INFORMATION MANAGEMENT; MINING;

DATA MINING;

EID: 65449136773     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1401890.1401932     Document Type: Conference Paper

References (27)

1. A. Bergeron, J. Stoye. On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. COCOON 2003.
2. R. Eres, G.M. Landau, L. Parida. Permutation Pattern Discovery in Biosequences. Journal of Computational Biology, 2004, 11(6): 1050-1060. doi: 10.1089/cmb.2004.11.1050.
3. R. Agrawal, R. Srikant. Mining Sequential. Patterns. ICDE, 1995.
4. BLAST, available at http://ncbi.nih.gov/BLAST/.
5. S. Cong, J. Han, D.A. Padua. Parallel Mining of Closed Sequential Patterns. KDD, 2005.
6. G. Deckers-Hebestreit, K. Altendorf. THE FOFl-TYPE ATP SYNTHASES OF BACTERIA: Structure and Function of the F0 Complex. Annual Review of Microbiology, Vol. 50: 791 -824.
7. R. Durbin, S. Eddy, A. Krogh, G. Mitchison. Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.
8. C. Fellbaum. WordNet: An Electronic Lexical Database. The MIT Press, 1998.
9. M.N. Garofelakis, R. Rastogi, K. Shim. SPIRIT: Sequential Pattern Mining with Regular Expression Constraints. VLDB, 1999.
10. D.Graur, W.H. Li. Fundamentals of Molecular Evolution. Ed. Sinauer Associates, Inc., 1991.
11. J. Han, J. Pei. Mining Frequent Patterns by Pattern-growth: Methodology and Implications. KDD, 2000.
12. S. Heber, J. Stoye. Finding AU Common Intervals of k Permutations. CPM, 2001.
13. M. Hu, J. Yang, and W. Su. Permu-pattern: Discovery of Mutable Permutation Patterns with Proximity Constraint. CWRU EECS Dept. Tech. Report, 2007.
14. M. Joshi, G. Karypis, V. Kumar. A Universal Formulation of Sequential Patterns. KDD workshop on Temporal Data Mining, 2001.
15. G.M. Landau, L. Parida, O. Weimann. Gene Proximity Analysis Across Whole Genomes via PQ Trees. Journal of Computational Biology, 12(10), pp 1289-1306, 2005.
16. R. Overbeek, M. Fonstein, M. D'Souza, G. D. Pusch, N. Maltsev. The Use of Gene Clusters to Infer Functional Coupling. Proc. Natl. Acad. Sci. U.S.A., 96(6):28961́C2901, 1999.
17. J. Pei, J. Han, B. Mortazavi-Asl, H. Pinto, Q. Chen, U. Dayal and M-C. Hsu. PrefixSpan: Mining Sequential Patterns Efficiently by PrefixProjected Pattern Growth. ICDE, 2001.
18. J. Pei, J. Han, W. Wang. Mining Sequential. Patterns with Constraints in Large Databases. CIKM, 2002.
19. J. Pei, J. Liu, H. Wang, K. Wang, P.S. Yu, J. Wang. Efficiently Mining Frequent Closed Partial Orders. ICDM, 2005.
20. R. Rymon. Search Through Systematic Set Enumeration. In Int'l. Conf. on Principles of Knowledge Representation and Reasoning, 1992.
21. R. Srikant, R. Agrawal. Mining Sequential. Patterns: Generalization and Performance Improvements. EDBT, 1996.
22. T. Schmidt, J. Stoye. Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. CPM, 2004.
23. Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale. The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 2003, 4:41.
24. K. Wang, Y. Xu, J. Xu Yu. Scalable Sequential Pattern Mining for Biological Sequences. CIKM, 2004.
25. W. Wang and J. Yang. Mining Sequential Patterns from Large Data Sets. Kluwer Publisher, 2005.
26. J. Yang, W. Wang, P. Yu, J. Han. Mining Long Sequential Patterns in a Noisy Environment. SIGMOD, 2002.
27. M.J. Zaki, 2001. SPADE: An efficient algorithm for mining frequent sequences. Machine Learning 42, 1/2, 31(60).