Graph-based data mining in dynamic networks: Empirical comparison of compression-based and frequency-based subgraph mining

Proceedings - IEEE International Conference on Data Mining Workshops, ICDM Workshops 2008

Volumn , Issue , 2008, Pages 929-938

  You, Chang Hun ^a   Holder, Lawrence B ^a   Cook, Diane J ^a  

^a Washington State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; INFORMATION MANAGEMENT;

BIO-SYSTEMS; BIOLOGICAL NETWORKS; DYNAMIC GRAPHS; DYNAMIC NETWORKS; DYNAMIC PROPERTIES; EMPIRICAL COMPARISONS; EVALUATION METRICS; FREQUENT SUBGRAPH MININGS; GRAPH-BASED; GRAPH-REWRITING RULES; IN NETWORKS; STRUCTURAL CHANGES; STRUCTURAL TRANSFORMATIONS; SUBGRAPH MININGS; TEMPORAL PATTERNS;

TECHNICAL PRESENTATIONS;

EID: 62549141554     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICDMW.2008.68     Document Type: Conference Paper

References (30)

1. Biomodels database at European Bioinformatics Institute. http://www.ebi.ac.uk/biomodels.
2. Kegg. http://www.genome.jp.
3. H. Bunke, M. Kraetzl, P. Shoubridge, and W. Wallis. Detection of abnormal change in time series of graphs. Journal of Interconnection Networks, 3, Nos 1+2:85-101, 2002.
4. H. Bunke and K. Shearer. A graph distance metric based on the maximal common subgraph. Pattern Recogn. Lett., 19(3-4):255-259, 1998.
5. D. Cook and L. Holder. Substructure discovery using minimum description length and background knowledge. Journal of Artificial Intelligence Research, 1:231-255, 1994.
6. D. Cook and L. Holder. Graph-based data mining. IEEE Intelligent Systems, 15(2):32-41, 2000.
7. P. Dickinson, H. Bunke, A. Dadej, and M. Kraetzl. On graphs with unique node labels. In Proceedings of the IAPR Workshop on GBR, pages 13-23, 2003.
8. H. Dörr. Efficient Graph Rewriting and Its Implementation. Springer, 1995.
9. K. N. et. al. Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations. Biophysical Chemistry, 7:49-62, 1998.
10. M. Garey and D. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, 1979.
11. I. Jonyer, D. Cook, and L. Holder. Discovery and evaluation of graph-based hierarchical conceptual clusters. Journal of Machine Learning Research, 2:19-43, 2001.
12. I. Jonyer, L. Holder, and D. Cook. Mdl-based context-free graph grammar induction. In Proceedings of FLAIRS, 2003.
13. B. Kholodenko. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem, 267(6):1583-8, Mar 2000.
14. M. Koyuturk, A. Grama, and W. Szpankowski. An efficient algorithm for detecting frequent subgraphs in biological networks. Proceedings of the International Conference on Intelligent Systems for Molecular Biology, 20:200-207, 2004.
15. J. Kukluk, C. You, L. Holder, and D. Cook. Learning node replacement graph grammars in metabolic pathways. In Proceedings of BIOCOMP, 2007.
16. J. P. Kukluk, L. B. Holder, and D. J. Cook. Inference of node replacement recursive graph grammars. In Proceedings of the SIAM International Conference on Data Mining, 2006.
17. M. Kuramochi and G. Karypis. Frequent subgraph discovery. In Proceedings of the ICDM, pages 313-320, 2001.
18. M. Lahiri and T. Berger-Wolf. Structure prediction in temporal networks using frequent subgraphs. In Proceedings of CIDM, 2007.
19. M. Laub and W. Loomis. A molecular network that produces spontaneous oscillations in excitable cells of dictyostelium. Mol Biol Cell, 9(12):3521-32, Dec 1998.
20. J. Leloup and A. Goldbeter. A model for circadian rhythms in drosophila incorporating the formation of a complex between the per and tim proteins. J Biol Rhythms, 13(1):70-87, Feb 1998.
21. K. Nupponen. The design and implementation of a graph rewrite engine for model transformations. Master's thesis, Helsinki Univ. of Tech., Dept. of Comp. Sci. & Eng., 2005.
22. M. Obeyesekere, S. Zimmerman, E. Tecarro, and G. Auchmuty. A model of cell cycle behavior dominated by kinetics of a pathway stimulated by growth factors. Bull Math Bio, 61(5):917-34, Sep 1999.
23. J. F. Roddick and M. Spiliopoulou. A survey of temporal knowledge discovery paradigms and methods. IEEE TKDM, 14(4):750-767, 2002.
24. G. Rozenberg. Handbook of Graph Grammars and Computing by Graph Transformation. World Scientific, 1997.
25. S. B.-W. S, J. Wolf, H. Herzel, and A. Kramer. Modeling feedback loops of the mammalian circadian oscillator. Biophys J, 87(5):3023-34, Nov 2004.
26. J. Sun, C. Faloutsos, S. Papadimitriou, and P. S. Yu. Graphscope: parameter-free mining of large time-evolving graphs. In Proceedings of the ACM SIGKDD, pages 687-696, 2007.
27. J. Wolf, H. Sohn, R. Heinrich, and H. Kuriyama. Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of saccharomyces cerevisiae. FEBS Lett, 499(3):230-4, Jun 2001.
28. X. Yan and J. Han. gspan: Graph-based substructure pattern mining. In Proceedings of the ICDM, pages 721-724, 2002.
29. C. You, L. Holder, and D. Cook. Application of graph-based data mining to metabolic pathways. In Proceedings of IEEE ICDM Workshop on Data Mining in Bioinformatics, 2006.
30. Z. Q. Z, W. MacLellan, and J. Weiss. Dynamics of the cell cycle: checkpoints, sizers, and timers. Biophys J, 85(6):3600-11, Dec 2003.