Abstract
Homology and persistent homology are fundamental tools for shape analysis and understanding that recently gathered a lot of interest, in particular for analyzing multidimensional data. In this context, discrete Morse theory, a combinatorial counterpart of smooth Morse theory, provides an excellent basis for reducing computational complexity in homology detection. A discrete Morse complex, computed over a given complex discretizing a shape, drastically reduces the number of cells of the latter while maintaining the same homology. Here, we consider the problem of shape analysis through discrete Morse theory, and we review and analyze algorithms for computing homology and persistent homology based on such theory.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Agoston, M.K.: Computer Graphics and Geometric Modeling: Mathematics. Springer, London (2005)
Alexandroff, P., Hopf, H.: Topologie i, vol. 1035. Springer, Berlin (1935)
Artin, M.: Algebra. Prentice Hall, Englewood Cliffs (1991)
Bendich, P., Edelsbrunner, H., Kerber, M.: Computing robustness and persistence for images. IEEE Trans. Vis. Comput. Graph. 16 (6), 1251–1260 (2010)
Benedetti, B., Lutz, F.H.: Random discrete Morse theory and a new library of triangulations. Exp. Math. 23 (1), 66–94 (2014)
Boissonnat, J.D., Dey, T.K., Maria, C.: The compressed annotation matrix: an efficient data structure for computing persistent cohomology. In: Algorithms–ESA 2013, Sophia Antipolis, pp. 695–706. Springer (2013)
Boltcheva, D., Canino, D., Merino Aceituno, S., Léon, J.C., De Floriani, L., Hétroy, F.: An iterative algorithm for homology computation on simplicial shapes. Comput. Aided Des. 43 (11), 1457–1467 (2011)
Bremer, P.T., Hamann, B., Edelsbrunner, H., Pascucci, V.: A topological hierarchy for functions on triangulated surfaces. IEEE Trans. Vis. Comput. Graph. 10 (4), 385–396 (2004)
Canino, D., De Floriani, L., Weiss, K.: IA*: an adjacency-based representation for non-manifold simplicial shapes in arbitrary dimensions. Comput. Graph. 35 (3), 747–753 (2011)
Carlsson, G., Ishkhanov, T., De Silva, V., Zomorodian, A.J.: On the local behavior of spaces of natural images. Int. J. Comput. Vis. 76 (1), 1–12 (2008)
Cazals, F., Chazal, F., Lewiner, T.: Molecular shape analysis based upon the Morse-Smale complex and the Connolly function. In: Proceedings of 9th Annual Symposium on Computational Geometry, pp. 351–360. ACM Press, New York (2003)
Cerri, A., Ferri, M., Giorgi, D.: Retrieval of trademark images by means of size functions. Graph. Models 68 (5), 451–471 (2006)
Chung, M.K., Bubenik, P., Kim, P.T.: Persistence diagrams of cortical surface data. In: Information Processing in Medical Imaging, pp. 386–397. Springer, Berlin/New York (2009)
Čomić, L., De Floriani, L., Iuricich, F.: Simplification operators on a dimension-independent graph-based representation of Morse complexes. In: Hendriks, C.L.L., Borgefors, G., Strand R. (eds.) ISMM. Lecture Notes in Computer Science, vol. 7883, pp. 13–24. Springer, Berlin/New York (2013)
Čomić, L., De Floriani, L., Iuricich, F., Fugacci, U.: Topological modifications and hierarchical representation of cell complexes in arbitrary dimensions. Comput. Vis. Image Underst. 121, 2–12 (2014)
Connolly, M.L.: Measurement of protein surface shape by solid angles. J. Mol. Graph. 4 (1), 3–6 (1986)
De Floriani, L., Hui, A.: Data structures for simplicial complexes: an analysis and a comparison. In: Desbrun, M., Pottmann, H. (eds.) Proceedings of 3rd Eurographics Symposium on Geometry Processing. ACM International Conference on Proceeding Series, vol. 255, pp. 119–128. Eurographics Association, Aire-la-Ville (2005)
Dequeant, M.L., Ahnert, S., Edelsbrunner, H., Fink, T.M., Glynn, E.F., Hattem, G., Kudlicki, A., Mileyko, Y., Morton, J., Mushegian, A.R., et al.: Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One 3 (8), e2856 (2008)
Dey, T.K., Fan, F., Wang, Y.: Computing topological persistence for simplicial maps. arXiv preprint arXiv:1208.5018 (2012)
Dey, T.K., Hirani, A.N., Krishnamoorthy, B., Smith, G.: Edge contractions and simplicial homology. arXiv preprint arXiv:1304.0664 (2013)
Dłotko, P., Kaczynski, T., Mrozek, M., Wanner, T.: Coreduction homology algorithm for regular cw-complexes. Discret. Comput. Geom. 46 (2), 361–388 (2011)
Dłotko, P., Wagner, H.: Simplification of complexes of persistent homology computations. Homol. Homotopy Appl. 16 (1), 49–63 (2014)
Edelsbrunner, H.: Algorithms in Combinatorial Geometry. Springer, Berlin (1987)
Edelsbrunner, H., Harer, J.: Persistent homology-a survey. Contemp. Math. 453, 257–282 (2008)
Edelsbrunner, H., Letscher, D., Zomorodian, A.J.: Topological persistence and simplification. Discret. Comput. Geom. 28 (4), 511–533 (2002)
Fellegara, R., Iuricich, F., De Floriani, L., Weiss, K.: Efficient computation and simplification of discrete Morse decompositions on triangulated terrains. In: 22th ACM SIGSPATIAL International Symposium on Advances in Geographic Information Systems, ACM-GIS 2014, Dallas, 4–7 Nov 2014 (2014)
Forman, R.: Combinatorial vector fields and dynamical systems. Mathematische Zeitschrift 228, 629–681 (1998)
Forman, R.: Morse theory for cell complexes. Adv. Math. 134, 90–145 (1998)
Fugacci, U., Iuricich, F., De Floriani, L.: Efficient computation of simplicial homology through acyclic matching. In: Proceedings of 5th International Workshop on Computational Topology in Image Context (CTIC 2014), Timisoara (2014)
Ghrist, R.: Barcodes: the persistent topology of data. Bull. Am. Math. Soc. 45 (1), 61–75 (2008)
Günther, D., Reininghaus, J., Wagner, H., Hotz, I.: Efficient computation of 3D Morse-Smale complexes and persistent homology using discrete Morse theory. Vis. Comput. 28 (10), 959–969 (2012)
Gyulassy, A., Bremer, P.T., Pascucci, V.: Computing Morse-Smale complexes with accurate geometry. IEEE Trans. Vis. Comput. Graph. 18 (12), 2014–2022 (2012). doi:10.1109/TVCG.2012.209
Gyulassy, A., Bremer, P.T., Hamann, B., Pascucci, V.: A practical approach to Morse-Smale complex computation: scalability and generality. IEEE Trans. Vis. Comput. Graph. 14 (6), 1619–1626 (2008)
Gyulassy, A., Bremer, P.T., Hamann, B., Pascucci, V.: Practical considerations in Morse-Smale complex computation. In: Pascucci, V., Tricoche, X., Hagen, H., Tierny, J. (eds.) Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, Mathematics and Visualization, pp. 67–78. Springer, Heidelberg (2011)
Gyulassy, A., Kotava, N., Kim, M., Hansen, C., Hagen, H., Pascucci, V.: Direct feature visualization using Morse-Smale complexes. IEEE Trans. Vis. Comput. Graph. 18 (9), 1549–1562 (2012)
Harker, S., Mischaikow, K., Mrozek, M., Nanda, V.: Discrete Morse theoretic algorithms for computing homology of complexes and maps. Found. Comput. Math. 14 (1), 151–184 (2014)
Harker, S., Mischaikow, K., Mrozek, M., Nanda, V., Wagner, H., Juda, M., Dłotko, P.: The efficiency of a homology algorithm based on discrete Morse theory and coreductions. In: Proceedings of 3rd International Workshop on Computational Topology in Image Context (CTIC 2010), Cádiz. Image A, vol. 1, pp. 41–47 (2010)
Hatcher, A.: Algebraic Topology. Cambridge University Press, Cambridge/New York (2002)
King, H., Knudson, K., Mramor, N.: Generating discrete Morse functions from point data. Exp. Math. 14 (4), 435–444 (2005)
Lewiner, T., Lopes, H., Tavares, G.: Optimal discrete Morse functions for 2-manifolds. Comput. Geom. 26 (3), 221–233 (2003)
Lewis, R.H., Zomorodian, A.J.: Multicore homology via Mayer Vietoris. arXiv preprint arXiv:1407.2275 (2014)
Lundell, A.T., Weingram, S.: The topology of CW complexes. Van Nostrand Reinhold Company, New York (1969)
Martin, S., Thompson, A., Coutsias, E.A., Watson, J.P.: Topology of cyclo-octane energy landscape. J. Chem. Phys. 132 (23), 234115 (2010). doi:10.1063/1.3445267
Milnor, J.: Morse Theory. Princeton University Press, Princeton (1963)
Mischaikow, K., Nanda, V.: Morse theory for filtrations and efficient computation of persistent homology. Discret. Comput. Geom. 50 (2), 330–353 (2013)
Mrozek, M., Batko, B.: Coreduction homology algorithm. Discret. Comput. Geom. 41 (1), 96–118 (2009)
Mrozek, M., Wanner, T.: Coreduction homology algorithm for inclusions and persistent homology. Comput. Math. Appl. 60 (10), 2812–2833 (2010)
Munkres, J.: Elements of Algebraic Topology. Advanced Book Classics. Perseus Books, New York (1984)
Nanda, V.: The Perseus software project for rapid computation of persistent homology. http://www.math.rutgers.edu/~vidit/perseus/index.html
Rieck, B., Leitte, H.: Structural analysis of multivariate point clouds using simplicial chains. Comput. Graph. Forum 33 (8), 28–37 (2014). doi:10.1111/cgf.12398
Rieck, B., Mara, H., Leitte, H.: Multivariate data analysis using persistence-based filtering and topological signatures. IEEE Trans. Vis. Comput. Graph. 18 (12), 2382–2391 (2012). doi:10.1109/TVCG.2012.248
Robins, V., Wood, P.J., Sheppard, A.P.: Theory and algorithms for constructing discrete Morse complexes from grayscale digital images. IEEE Trans. Pattern Anal. Mach. Intell. 33 (8), 1646–1658 (2011)
Rosenfeld, A., Kak, A.C.: Digital Picture Processing. Academic Press, London (1982)
Shivashankar, N., Maadasamy, S., Natarajan, V.: Parallel computation of 2D Morse-Smale complexes. IEEE Trans. Vis. Comput. Graph. 18 (10), 1757–1770 (2012)
Shivashankar, N., Natarajan, V.: Parallel computation of 3D Morse-Smale complexes. Comput. Graph. Forum 31 (3), 965–974 (2012)
de Silva, V., Ghrist, R.: Coverage in sensor networks via persistent homology. Algebr. Geom. Topol. 7, 339–358 (2007). doi:10.2140/agt.2007.7.339
Wang, Y., Agarwal, P.K., Brown, P.H.E., Rudolph, J.: Coarse and reliable geometric alignment for protein docking. In: Proceedings of Pacific Symposium on Biocomputing, Hawaii, vol. 10, pp. 65–75 (2005)
Weiss, K., De Floriani, L., Fellegara, R., Velloso, M.: The PR-star octree: a spatio-topological data structure for tetrahedral meshes. In: GIS, Chicago, pp. 92–101 (2011)
Weiss, K., Iuricich, F., Fellegara, R., De Floriani, L.: A primal/dual representation for discrete Morse complexes on tetrahedral meshes. Comput. Graph. Forum 32 (3), 361–370 (2013)
Van de Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B.J., Pranav, P., Park, C., Hellwing, W.A., Eldering, B., Kruithof, N., Bos, E., et al.: Alpha, Betti and the megaparsec universe: on the topology of the cosmic web. In: Transactions on Computational Science XIV, pp. 60–101. Springer, Berlin/New York (2011). http://arxiv.org/abs/1306.3640
Zomorodian, A.J.: Topology for Computing, vol. 16. Cambridge University Press, Cambridge/New York (2005)
Acknowledgements
This work has been partially supported by the US National Science Foundation under grant number IIS-1116747 and by the University of Genova through PRA 2013. The authors wish to thank Davide Bolognini, Emanuela De Negri and Maria Evelina Rossi for their helpful comments and suggestions.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this paper
Cite this paper
De Floriani, L., Fugacci, U., Iuricich, F. (2016). Homological Shape Analysis Through Discrete Morse Theory. In: Breuß, M., Bruckstein, A., Maragos, P., Wuhrer, S. (eds) Perspectives in Shape Analysis. Mathematics and Visualization. Springer, Cham. https://doi.org/10.1007/978-3-319-24726-7_9
Download citation
DOI: https://doi.org/10.1007/978-3-319-24726-7_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-24724-3
Online ISBN: 978-3-319-24726-7
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)