Abstract

Consider the set of solutions to a system of polynomial equations in many variables. An algebraic manifold is an open submanifold of such a set. We introduce a new method for computing integrals and sampling from distributions on algebraic manifolds. This method is based on intersecting with random linear spaces. It produces independent and identically distributed samples, works in the presence of multiple connected components, and is simple to implement. We present applications to computational statistical physics and topological data analysis.

Keywords

  1. sampling
  2. approximating integrals
  3. geometrical probability
  4. algebraic geometry
  5. statistical physics
  6. topological data analysis

MSC codes

  1. 60B05
  2. 62D05
  3. 51H30

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References

4.
D. Bates, J. Hauenstein, A. Sommese, and C. Wampler, Bertini: Software for Numerical Algebraic Geometry, https://doi.org/10.7274/R0H41PB5 (2013).
5.
U. Bauer, Ripser: A Lean C++ Code for Computation of Vietoris--Rips Persistence Barcodes, https://github.com/Ripser/ripser.
6.
G. Blekherman, P. Parrilo, and R. Thomas, Semidefinite Optimization and Convex Algebraic Geometry, MOS-SIAM Ser. Optim. 13, SIAM, Philadelphia, 2012.
7.
L. Blum, F. Cucker, M. Shub, and S. Smale, Complexity and Real Computation, Springer, New York, 1998, https://doi.org/10.1007/978-1-4612-0701-6.
8.
Y. Boykov and V. Kolmogorov, Computing geodesics and minimal surfaces via graph cuts, in Proceedings of the Ninth IEEE International Conference on Computer Vision, IEEE Computer Society, Los Alamitos, CA, 2003, pp. 23--33.
9.
C. Brammer and D. Nelson, Toward consistent terminology for cyclohexane conformers in introductory organic chemistry, J. Chem. Educ. 88 (2011), pp. 292--294.
10.
P. Breiding and S. Timme, HomotopyContinuation.jl - a package for solving systems of polynomial equations in Julia, Mathematical Software -- ICMS 2018, Lecture Notes in Computer Science 10931, Springer, Cham, Switzerland, 2018.
11.
W. H. Brown and L. S. Brown, Organic Chemistry, Enhanced Edition, Vol. 5, Brooks Cole, Pacific Grove, CA, 2010.
12.
M. Brubaker, M. Salzmann, and R. Urtasun, A family of MCMC methods on implicitly defined manifolds, Proc. Mach. Learn. Res. (PHLR), 22 (2012), pp. 161--172.
13.
P. Bürgisser and F. Cucker, Condition: The Geometry of Numerical Algorithms, Grundlehren Math. Wiss. 349, Springer, Heidelberg, 2013.
14.
S. Byrne and M. Girolami, Geodesic Monte Carlo on embedded manifolds, Scand. J. Stat., 41 (2013), pp. 825--845.
15.
B. Calderhead and M. Girolami, Riemann manifold Langevin and Hamiltonian Monte Carlo methods, J. Roy. Statist. Soc. Ser. B, 73 (2011), pp. 123--214.
16.
G. Casella and C. Robert, Monte Carlo Statistical Methods, Springer Texts Statist., Springer, New York, 2004.
17.
T. Chen, T. Lee, T. Li, and N. Ovenhouse, HOM4PS: A Software Package for Solving Polynomial Systems by the Polyhedral Homotopy Continuation Method.
18.
E. Dufresne, P. B. Edwards, H. A. Harrington, and J. D. Hauenstein, Sampling real algebraic varieties for topological data analysis, in International Conference on Machine Learning and Applications, IEEE, Piscataway, NJ, 2018, pp. 1531--1536.
19.
A. Edelman and O. Mangoubi, Integral Geometry for Markov Chain Monte Carlo: Overcoming the Curse of Search-Subspace Dimensionality, preprint, https://arxiv.org/abs/1503.03626, 2015.
20.
P. Edwards, private communication.
21.
M. Farber and F. Schütz, Homology of planar polygon spaces, Geom. Dedicata, 125 (2007), pp. 75--92.
22.
J. Goodman, M. Holme-Cerfon, and E. Zappa, Monte Carlo on manifolds: Sampling densities and integrating functions, Comm. Pure Appl. Math., 71 (2018), pp. 2609--2647.
23.
J. Harris, Algebraic Geometry, A First Course, Grad. Text in Math. 133, Springer, New York, 1992.
24.
R. Howard, The Kinematic Formula in Riemannian Homogeneous Spaces, Mem. Amer. Math. Soc. 106, 1993, https://doi.org/10.1090/memo/0509.
25.
J. D. Hunter, Matplotlib: A 2D graphics environment, Comput. Sci. Eng., 9 (2007), pp. 90--95, https://doi.org/10.1109/MCSE.2007.55.
26.
M. H. Kalos and P. A. Whitlock, Monte Carlo Methods, 2nd ed., Wiley-Blackwell, Weinheim, Germany, 2008, https://doi.org/10.1002/9783527626212.
27.
P. Lairez, Rigid continuation paths I. Quasilinear average complexity for solving polynomial systems, J. Amer, Math. Soc., 33 (2020), pp. 487--526.
28.
D. Legland, K. Kiêu, and M.-F. Devaux, Computation of Minkowski measures on 2D and 3D binary images, Image Anal. Stereol., 26 (2007), pp. 83--92.
29.
G. Lehmann and D. Legland, Efficient n-dimensional surface estimation using Crofton formula and run-length encoding, Insight J. (2012).
30.
K. Leichtweiss, Zur Riemannschen Geometrie in Grassmannschen Mannigfaltigkeiten, Math. Z., 76 (1961), pp. 334--366.
31.
T. Lelièvre, M. Rousset and G. Stoltz, Hybrid Monte Carlo methods for sampling probability measures on submanifolds, Numer. Math., 143 (2019), pp. 379--421.
32.
T. Lelièvre, M. Rousset, and G. Stoltz, Free Energy Computations: A Mathematical Perspective, Imperial College Press, London, 2010.
33.
T. Lelièvre, M. Rousset, and G. Stoltz, Langevin dynamics with constraints and computation of free energy differences, Math. Comp., 81 (2012), pp. 2071--2125, https://doi.org/10.1090/S0025-5718-2012-02594-4.
34.
A. Leykin, Homotopy continuation in macaulay2, Mathematical Software -- ICMS 2018. Lecture Notes in Comput. Sci. 10931, Springer, Cham, Switzerland, 2018, pp. 328--334.
35.
X. Li, W. Wang, R. R. Martin, and A. Bowyer, Using low-discrepancy sequences and the Crofton formula to compute surface areas of geometric models, Comput.-Aided Des., 35 (2003), pp. 771--782.
36.
O. Mangoubi, Integral Geometry, Hamiltonian Dynamics, and Markov Chain Monte Carlo, Ph.D Thesis, Massachusetts Institute of Technology, Cambridge, MA, 2016.
37.
R. Muirhead, Aspects of Multivariate Statistical Theory, Wiley, New York, 1982.
38.
L. Santaló, Integral Geometry and Geometric Probability, Encyclopedia Math. Appl., Addison-Wesley, Reading, PA, 1976.
39.
J. Skowron and A. Gould, General Complex Polynomial Root Solver and Its Further Optimization for Binary Microlenses, preprint, https://arxiv.org/abs/1203.1034, 2012.
40.
J. Verschelde, PHCpack: A General-Purpose Solver for Polynomial Systems by Homotopy Continuation.
41.
H. Whitney, Elementary structure of real algebraic varieties., Ann. of Math. (22), 66 (1957), pp. 545--556.

Information & Authors

Information

Published In

cover image SIAM Journal on Mathematics of Data Science
SIAM Journal on Mathematics of Data Science
Pages: 683 - 704
ISSN (online): 2577-0187

History

Submitted: 28 June 2019
Accepted: 29 May 2020
Published online: 24 August 2020

Keywords

  1. sampling
  2. approximating integrals
  3. geometrical probability
  4. algebraic geometry
  5. statistical physics
  6. topological data analysis

MSC codes

  1. 60B05
  2. 62D05
  3. 51H30

Authors

Affiliations

Funding Information

H2020 European Research Council https://doi.org/10.13039/100010663 : 787840

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