Abstract
Distance Geometry consists in embedding a simple weighted undirected graph in a given space so that the distances between embedded vertices correspond to the edge weights. Weights can be either exact real values, or real-valued intervals. In this work, the focus is on problems where the embedding space is the Euclidean 1-dimensional space, and the general situation where distances can be represented by intervals is taken into consideration. A previously proposed branch-and-prune algorithm is adapted to the 1-dimensional case, and the proposed variant turns out to be deterministic even in presence of interval distances. Backtracking pruning is introduced in the algorithm for guaranteeing that all vertex positions in a given solution are actually feasible. The proposed algorithm is tested on a set of artificially generated instances in dimension 1.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alipanahi, B., Krislock, N., Ghodsi, A., Wolkowicz, H., Donaldson, L., Li, M.: Determining protein structures from NOESY distance constraints by semidefinite programming. J. Comput. Biol. 20(4), 296–310 (2013)
Alves, R., Cassioli, A., Mucherino, A., Lavor, C., Liberti, L.: The integration of clifford algebra in the \(i\) BP algorithm for the DMDGP. In: Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO13), pp. 745–746. Granada, Spain (2013)
Alves, R., Cassioli, A., Mucherino, A., Lavor, C., Liberti, L.: Adaptive branching in iBP with clifford algebra. In: Proceedings of Distance Geometry and Applications (DGA13), pp. 65-69. Manaus, Amazonas, Brazil (2013)
Billinge, S.J.L., Duxbury, Ph.M., Gonçalves, D.S., Lavor, C., Mucherino, A.: Assigned and unassigned distance geometry: applications to biological molecules and nanostructures. Q. J. Oper. Res. 14(4), 337–376 (2016)
Biswas, P., Lian, T., Wang, T., Ye, Y.: Semidefinite programming based algorithms for sensor network localization. ACM Trans. Sens. Netw. 2, 188–220 (2006)
Crippen, G.M., Havel, T.F.: Distance Geometry and Molecular Conformation. Wiley, New York (1988)
Ding, Y., Krislock, N., Qian, J., Wolkowicz, H.: Sensor network localization, Euclidean distance matrix completions, and graph realization. Optim. Eng. 11(1), 45–66 (2010)
Freris, N.M., Graham, S.R., Kumar, P.R.: Fundamental limits on synchronizing clocks over networks. IEEE Trans. Autom. Control 56(6), 1352–1364 (2010)
Gonçalves, D.S., Mucherino, A., Lavor, C.: An adaptive branching scheme for the branch & prune algorithm applied to distance geometry. In: IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS14), Workshop on Computational Optimization (WCO14), pp. 463–469. Warsaw, Poland (2014)
Gonçalves, D.S., Mucherino, A., Lavor, C., Liberti, L.: Recent advances on the interval distance geometry problem. J. Glob. Optim. (2017). To appear
Lavor, C., Liberti, L., Maculan, N., Mucherino, A.: The discretizable molecular distance geometry problem. Comput. Optim. Appl. 52, 115–146 (2012)
Lavor, C., Liberti, L., Mucherino, A.: The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances. J. Glob. Optim. 56(3), 855–871 (2013)
Lavor, C., Alves, R., Figueiredo, W., Petraglia, A., Maculan, N.: Clifford algebra and the discretizable molecular distance geometry problem. Adv. Appl. Clifford Algebr. 25(4), 925–942 (2015)
Liberti, L., Lavor, C., Maculan, N.: A branch-and-prune algorithm for the molecular distance geometry problem. Int. Trans. Oper. Res. 15, 1–17 (2008)
Liberti, L., Lavor, C., Maculan, N., Mucherino, A.: Euclidean distance geometry and applications. SIAM Rev. 56(1), 3–69 (2014)
Mucherino, A., Lavor, C.: The branch and prune algorithm for the molecular distance geometry problem with inexact distances. In: Proceedings of World Academy of Science, Engineering and Technology 58, International Conference on Bioinformatics and Biomedicine (ICBB09), pp. 349–353. Venice, Italy (2009)
Mucherino, A., Lavor, C., Liberti, L.: The discretizable distance geometry problem. Optim. Lett. 6(8), 1671–1686 (2012)
Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.): Distance Geometry: Theory, Methods and Applications, 410 pp. Springer, New York (2013)
Mucherino, A., de Freitas, R., Lavor, C.: Distance geometry and applications. Discret. Appl. Math. 197, 1–144 (2015). Special issue
Petitjean, M.: Spheres unions and intersections and some of their applications in molecular modeling. In: [19], pp. 61–83 (2013)
Saxe, J.: Embeddability of weighted graphs in \(k\)-space is strongly NP-hard. In: Proceedings of \(17^{th}\) Allerton Conference in Communications, Control and Computing, pp. 480–489 (1979)
Wang, Z., Zheng, S., Ye, Y., Boyd, S.: Further relaxations of the semidefinite programming approach to sensor network localization. SIAM J. Optim. 19(2), 655–673 (2008)
Wu, Y.-C., Chaudhari, Q., Serpedin, E.: Clock synchronization of wireless sensor networks. IEEE Signal Process. Mag. 28(1), 124–138 (2011)
Acknowledgements
The author is thankful to the anonymous referees.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG
About this chapter
Cite this chapter
Mucherino, A. (2018). On the Exact Solution of the Distance Geometry with Interval Distances in Dimension 1. In: Fidanova, S. (eds) Recent Advances in Computational Optimization. Studies in Computational Intelligence, vol 717. Springer, Cham. https://doi.org/10.1007/978-3-319-59861-1_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-59861-1_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-59860-4
Online ISBN: 978-3-319-59861-1
eBook Packages: EngineeringEngineering (R0)