Boolean property encoding for local set pattern discovery: An application to gene expression data analysis

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3539 LNAI, Issue , 2005, Pages 115-134

  Pensa, Ruggero G ^a   Boulicaut, Jean François ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOTECHNOLOGY; BOOLEAN FUNCTIONS; DATA MINING; DATA REDUCTION; HEURISTIC METHODS;

BIOINFORMATICS; ENCODING TECHNIQUE; GENE EXPRESSION;

PATTERN RECOGNITION;

EID: 26944451261     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11504245_8     Document Type: Conference Paper

References (26)

1. DeRisi, J., Iyer, V., Brown, P.: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 (1997) 680-686
2. Velculescu, V., Zhang, L., Vogelstein, B., Kinzler, K.: Serial analysis of gene expression. Science 270 (1995) 484-487
3. Piatetsky-Shapiro, G., Tamayo, P., eds.: Special issue on microrray data mining. SIGKDD Explorations, Volume 5, Issue 2 (2003)
4. Eisen, M., Spellman, P., Brown, P., Botstein, D.: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 05 (1998) 14863-14868
5. Niehrs, C., Pollet, N.: Synexpression groups in eukaryotes. Nature 402 (1999) 483-487
6. Boulicaut, J.F., Bykowski, A.: Frequent closures as a concise representation for binary data mining. In: Proceedings PAKDD'00. Volume 1805 of LNAI., Kyoto, JP, Springer-Verlag (2000) 62-73
7. Pei, J., Han, J., Mao, R.: CLOSET an efficient algorithm for mining frequent closed itemsets. In: Proceedings ACM SIGMOD Workshop DMKD'00, Dallas, USA (2000) 21-30
8. Zaki, M.J., Hsiao, C.J.: CHARM: An efficient algorithm for closed itemset mining. In: Proccedings SIAM DM'02, Arlington, USA (2002)
9. Becquet, C., Blachon, S., Jeudy, B., Boulicaut, J.F., Gandrillon, O.: Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human sage data. Genome Biology 12 (2002)
10. Creighton, C., Hanash, S.: Mining gene expression databases for association rules. Bioinformatics 10 (2003) 79 - 86
11. Wille, R.: Restructuring lattice theory: an approach based on hierarchies of concepts. In Rival, I., ed.: Ordered sets. Reidel (1982) 445-470
12. Rioult, F., Boulicaut, J.F., Crémilleux, B., Besson, J.: Using transposition for pattern discovery from microarray data. In: Proceedings ACM SIGMOD Workshop DMKD'03, San Diego (USA) (2003) 73-79
13. Rioult, F., Robardet, C., Blachon, S., Crémilleux, B., Gandrillon, O., Boulicaut, J.F.: Mining concepts from large sage gene expression matrices. In: Proceedings KDID'03 co-located with ECML-PKDD 2003, Catvat-Dubrovnik (Croatia) (2003) 107-118
14. Besson, J., Robardet, C., Boulicaut, J.F.: Constraint-based mining of formal concepts in transactional data. In: Proceedings PAKDD'04. Volume 3056 of LNAI., Sydney (Australia), Springer-Verlag (2004) 615-624
15. Besson, J., Robardet, C., Boulicaut, J.F., Rome, S.: Constraint-based concept mining and its application to microarray data analysis. Intelligent Data Analysis journal 9 (2004) To appear.
16. Pensa, R.G., Leschi, C., Besson, J., Boulicaut, J.F.: Assessment of discretization techniques for relevant pattern discovery from gene expression data. In: Proceedings ACM BIOKDD'04 co-located with SIGKDD'04, Seattle, USA (2004) 24-30
17. Parthasarathy, S.: Efficient progressive sampling for association rules. In: Proceedings IEEE ICDM'02, Maebashi City, Japan (2002) 354-361
18. Moore, G.W., Goodman, M., Barnabas, J.: An iterative approach from the standpoint of the additive hypothesis to the dendrogram problem posed by molecular data sets. Journal of Theoretical Biology 38 (1973) 423-457
19. Robinsons, D.F.: Comparison of labeled trees with valency three. Journal of Combinatorial Theory, Series B 11 (1971) 105-119
20. DasGupta, B., He, X., Jiang, T., Li, M., Tromp, J., Zhang, L.: On distances between phylogenetic trees. In: Proceedings ACM-SIAM SODA'97. Volume 55. (1997) 427-436
21. DasGupta, B., He, X., Jiang, T., Li, M., Tromp, J., Zhang, L.: On computing the nearest neighbor interchange distance. In: Discrete mathematical problems with medical applications (New Brunswick, NJ, 1999), Providence, RI, Amer. Math. Soc. (2000) 125-143
22. Finden, C., Gordon, A.: Obtaining common pruned trees. Journal of Classification 2 (1985) 255-276
23. Cole, R., Hariharan, R.: An o(n log n) algorithm for the maximum agreement subtree problem for binary trees. In: Proceedings of the 7th annual ACM-SIAM symposium on Discrete algorithms, Atlanta, Georgia, United States (1996) 323-332
24. Bozdech, Z., Llinás, M., Pulliam, B.L., Wong, E., Zhu, J., DeRisi, J.: The transcriptome of the intraerythrocytic developmental cycle of plasmodium falciparum. PLoS Biology 1 (2003) 1-16
25. Arbeitman, M., Furlong, E., Imam, F., Johnson, E., Null, B., Baker, B., Krasnow, M., Scott, M., Davis, R., White, K.: Gene expression during the life cycle of drosophila melanogaster. Science 207 (2002) 2270-2275
26. Lash, A., Tolstoshev, C., Wagner, L., Schuler, G., Strausberg, R., Riggins, G., Altschul, S.: SAGEmap: A public gene expression resource. Genome Research 10 (2000) 1051-1060