Multidimensional data distributions can have complex topologies and variable local dimensions. To approximate complex data, we propose a new type of low-dimensional “principal object”: a principal cubic complex. This complex is a generalization of linear and non-linear principal manifolds and includes them as a particular case. To construct such an object, we combine a method of topological grammars with the minimization of an elastic energy defined for its embedment into multidimensional data space. The whole complex is presented as a system of nodes and springs and as a product of one-dimensional continua (represented by graphs), and the grammars describe how these continua transform during the process of optimal complex construction
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Bishop, C. M., Svensén, M., and Williams, C. K. I.: GTM: The generative topo-graphic mapping. Neural Computation 10 (1), 215-234 (1998)
Crick, F. H. C., Barnett, L., Brenner, S., and Watts-Tobin, R. J.: General nature of the genetic code for proteins. Nature, 192, 1227-1232 (1961)
Dergachev, V. A., Gorban, A. N., Rossiev, A. A., Karimova, L. M., Kuandykov, E. B., Makarenko, N. G., and Steier, P.: The filling of gaps in geophysical time series by artificial neural networks Radiocarbon 43, 2A, 365-371 (2001)
Einbeck, J., Tutz, G., and Evers, L.: Local principal curves. Statistics and Computing, 15, 301-313 (2005)
Erwin, E., Obermayer, K., and Schulten, K.: Self-organizing maps: ordering, convergence properties and energy functions. Biological Cybernetics 67, 47-55 (1992)
Gorban, A. N., Popova, T. G., and Zinovyev, A. Yu.: Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences. Physica A: Statistical and Theoretical Physics, 353, 365-387 (2005)
Gorban, A. N., Zinovyev, A. Yu., and Popova, T. G.: Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences. In Silico Biology 5, 0025 (2005)
Gorban, A. N. and Rossiev, A. A.: Neural network iterative method of principal curves for data with gaps. Journal of Computer and System Sciences Interna-tional 38 (5), 825-831 (1999)
Gorban, A. N, Sumner, N. R. and Zinovyev, A. Y.: Topological grammars for data approximation, Applied Mathematics Letters 20 (4), 382-386 (2005)
Gorban, A. N. and Zinovyev, A. Y.: Visualization of data by method of elastic maps and its applications in genomics, economics and sociology Preprint of Institut des Hautes Etudes Scientiques, M/01/36 (2001) http://www.ihes. fr/PREPRINTS/M01/Resu/resu-M01-36. html
Gorban, A. N. and Zinovyev, A. Y.: Method of elastic maps and its applications in data visualization and data modeling. International Journal of Computing Anticipatory Systems, CHAOS, 12, 353-369 (2001)
Gorban, A. N., Zinovyev, A. Yu. and Wunsch, D. C.: Application of the method of elastic maps in analysis of genetic texts. In: Proceedings of International Joint Conference on Neural Networks (IJCNN). Portland, Oregon (2003).
Gorban, A. N., Zinovyev, A. Yu. and Pitenko, A. A.: Visualization of data using method of elastic maps (in Russian). Informatsionnie technologii 6, 26-35 (2000)
Gorban, A. and Zinovyev, A.: Elastic Principal Graphs and Manifolds and their Practical Applications. Computing 75, 359-379 (2005)
Gorban, A. N. and Zinovyev, A. Y.: Elastic maps and nets for approximating principal manifolds and their application to microarray data visualization. In this book.
Gusev, A.: Finite element mapping for spring network representations of the mechanics of solids. Phys. Rev. Lett. 93 (2), 034302 (2004)
Hastie, T. and Stuetzle, W.: Principal curves. Journal of the American Statistical Association 84 (406) (1989), 502-516 (1989)
Kégl, B. and Krzyzak, A.: Piecewise linear skeletonization using principal curves. IEEE Transactions on Pattern Analysis and Machine Intelligence 24 (1), 59-74 (2002)
Kohonen, T.: Self-organized formation of topologically correct feature maps. Biological Cybernetics 43, 59-69 (1982)
Leung, Y. F. and Cavalieri, D.: Fundamentals of cDNA microarray data analysis. Trends Genet. 19 (11), 649-659 (2003)
Löwe, M.: Algebraic approach to single-pushout graph transformation. Theor. Comp. Sci. 109, 181-224 (1993)
Martinetz, T. M., Berkovich, S. G., and Schulten K. J.: Neural-gas network for vector quantization and its application to time-series prediction. IEEE Trans-actions on Neural Networks, 4 4, 558-569 (1993)
Matveev, S. and Polyak, M.: Cubic complexes and finite type invariants. In: Geometry & Topology Monographs, Vol. 4: Invariants of knots and 3-manifolds. Kyoto, 215-233 (2001)
Mulier, F. and Cherkassky, V.: Self-organization as an iterative kernel smoothing process. Neural Computation 7, 1165-1177 (1995)
“Principal manifolds for data cartography and dimension reduction”, Leices-ter, UK, August 2006. A web-page with test microarrays datasets provided for participants of the workshop: http://www. ihes. fr/∼zinovyev/princmanif2006
Pearson, K.: On lines and planes of closest fit to systems of points in space. Philosophical Magazine, series 6 (2), 559-572 (1901)
Shyamsundar, R., Kim, Y. H., Higgins, J. P. et al.: A DNA microarray survey of gene expression in normal human tissues. Genome Biology, 6, R22 (2005)
Nagl, M.: Formal languages of labelled graphs: Computing, 16, 113-137 (1976)
Ritter, H., Martinetz, T. and Schulten, K.: Neural Computation and Self-Organizing Maps: An Introduction. Addison-Wesley Reading, Massachusetts (1992)
Zinovyev, A.: Visualization of Multidimensional Data. Krasnoyarsk State University Press Publ. (2000)
Zinovyev, A. Yu., Gorban, A. N. and Popova, T. G.: Self-organizing approach for automated gene identification. Open Systems and Information Dynamics 10 (4), 321-333 (2003)
Cluster structures in genomic word frequency distributions. Web-site with sup-plementary materials. http://www.ihes. fr/~zinovyev/7clusters/index.htm
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Gorban, A.N., Sumner, N.R., Zinovyev, A.Y. (2008). Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes. In: Gorban, A.N., Kégl, B., Wunsch, D.C., Zinovyev, A.Y. (eds) Principal Manifolds for Data Visualization and Dimension Reduction. Lecture Notes in Computational Science and Enginee, vol 58. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73750-6_9
Download citation
DOI: https://doi.org/10.1007/978-3-540-73750-6_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73749-0
Online ISBN: 978-3-540-73750-6
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)