Nonmetric Multidimensional Scaling As a Data-Mining Tool: New Algorithm and New Targets

Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems

Volumn 130, Issue , 2005, Pages 315-351

  Taguchi, Y H ^a   Oono, Yoshitsugu ^b  

^a CHUO UNIVERSITY   (Japan)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

Data mining; Large samples; Multi variate analysis; Nonmetric multidimensional scaling

Indexed keywords

CHAOS THEORY; COMPUTER SCIENCE;

DATA SET; DATA-MINING TOOLS; ECOLOGICAL DATA; MULTI VARIATE ANALYSIS; NON-METRIC MULTIDIMENSIONAL SCALING; QUALITATIVE FEATURES; VERY LARGE DATUM;

DATA MINING;

EID: 84907229922     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471712531.ch18     Document Type: Chapter

References (23)

1. A. C. Rencher, Methods of Multivariate Analysis, 2nd ed, John Wiley & Sons, New York.
2. D. L. Donoho, M. Vetterli, R. A. DeVore, and I. Daubechies, IEEE Trans. Inf. Theory 44, 2435 (1998).
3. J. B. Kruskal and R. N. Shepard, Am. Psychol. 19, 557 (1964).
4. Y-h. Taguchi, Y. Oono, and K. Yokoyama, Proc. Inst. Stat. Math. 49(1), 133 (2001) (in Japanese).
5. I. Borg and P. Groenen, Modern Multidimensional Scaling, Springer, New York, 1997.
6. It should be noted that there is a different stress-free proposal: M.W. Trosset, J. Classif. 15, 15 (1998).
7. S. Rajaram, unpublished (2004).
8. E. L. Lehman, Nonparametrics, Holden-Day, San Francisco, 1975.
9. T. D. Kocher, J. A. Conroy, K. R. McKaye, J. R. Stauffer, and S. F. Lockwood, Mol. Phyl. Evol. 4, 420 (1995).
10. M. Hasegawa and H. Kishino Molecular Phylogenetics, Iwanami, Tokyo 1996 (in Japanese).
11. K. Hayasaka, T. Gojobori, and S. Horai, Mol. Biol. Evol. 5, 626 (1988).
12. M. Barbieri, The Organic Codes-An Introduction to Semantic Biology, Cambridge University Press, New York, 2002.
13. Both DNA sequence and phenotypes tables are taken from http://ucjeps.berkeley.edu/ bryolab/ GPphylo/ferndata/. DNA sequence: P95rbcl.nex, phenotypes: P95morph.nex.
14. K. M. Pryer, A. R. Smith, and J. E. Skog. Am. Fern J. 85(4), 205 (1995).
15. Both DNA sequence and phenotypes tables are taken from morph: http://ucjeps.berkeley. edu/ bryolab/GPphylo/Nexus/GPMorph.txt.
16. DNA sequence: http://ucjeps.berkeley. edu/bryolab/ GPphylo/Nexus/GPMolecular.txt.
17. B. D. Mishler, L. A. Lewis, M. A. Buchheim, K. S. Renzaglia, D. J. Garbary, C. F. Delwiche, F. W. Zechman,T. S. Kantz, and R. L. Chapman. Ann. Missouri Botanical Garden 81, 451 (1994).
18. http://www.science.siu.edu/landplants/Alignments/Alignments.html.
19. K. Yokoyama, Soil Microorganisms 47, 1 (1996) (in Japanese).
20. X. L. Zhang, H. Begleiter, B. Porjesz,W. Wang, and A. Litke, Brain Res. Bull. 38, 531 (1995).
21. S. K. Kim, J. Lund, M. Kiraly, K. Duke, M. Jiang, J. M. Stuart, A. Eizinger, B. N.Wylie, and G. S. Davidson, Science 293 2087 (2001).
22. V. R. Iyer,M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, J. C. F. Lee, J. M.Trent, L. M. Staudt, J. S. Hudson Jr., M. S. Boguski, D. Lashkari, D. Shalon, D. Botstein, and P. O. Brown, Science 283, 83 (1999).
23. Y-h. Taguchi and Y. Oono, Bioinformatics, in press.