Abstract
The Distance Geometry Problem (DGP) is the problem of determining whether a realization for a simple weighted undirected graph \(G=(V,E,d)\) in a given Euclidean space exists so that the distances between pairs of realized vertices u, \(v \in V\) correspond to the weights \(d_{uv}\), for each \(\{u,v\} \in E\). We focus on a special class of DGP instances, referred to as the Discretizable DGP (DDGP), and we introduce the K-discretization and the K-incident graphs for the DDGP class. The K-discretization graph is independent on the vertex order that can be assigned to V, and can be useful for discovering whether one of such orders actually exists so that the DDGP assumptions are satisfied. The use of a given vertex order allows the definition of another important graph, the K-incident graph, which is potentially useful for performing pre-processing analysis on the solution set of DDGP instances.
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References
Alves, R., Lavor, C.: Geometric algebra to model uncertainties in the discretizable molecular distance geometry problem. Adv. Appl. Clifford Algebras 27, 439–452 (2017)
Gonçalves, D., Mucherino, A.: Optimal partial discretization orders for discretizable distance geometry. Int. Trans. Oper. Res. 23, 947–967 (2016)
Gonçalves, D., Mucherino, A., Lavor, C., Liberti, L.: Recent advances on the interval distance geometry problem. J. Global Optim. 69, 525–545 (2017)
Lavor, C., Lee, J., Lee-St.John, A., Liberti, L., Mucherino, A., Sviridenko, M.: Discretization orders for distance geometry problems. Optim. Lett. 6, 783–796 (2012)
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. Global Optim. 56, 855–871 (2013)
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, 3–69 (2014)
Liberti, L., Lavor, C., Mucherino, A., Maculan, N.: Molecular distance geometry methods: from continuous to discrete. Int. Trans. Oper. Res. 18, 33–51 (2011)
Liberti, L., Masson, B., Lee, J., Lavor, C., Mucherino, A.: On the number of realizations of certain Henneberg graphs arising in protein conformation. Discrete Appl. Math. 165, 213–232 (2014)
Mucherino, A., Lavor, C., Liberti, L.: The discretizable distance geometry problem. Optim. Lett. 6, 1671–1686 (2012)
Mucherino, A., Lavor, C., Liberti, L.: Exploiting symmetry properties of the discretizable molecular distance geometry problem. J. Bioinform. Comput. Biol. 10(3), 1242009(1–15) (2012)
Saxe J (1979) Embeddability of weighted graphs in \(k\)-space is strongly NP-hard. In: Proceedings of 17th Allerton conference in communications, control and computing, pp 480–489
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We wish to thank the anonymous referees for the very fruitful comments. We are also grateful to the Brazilian research agencies FAPESP and CNPq for financial support.
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Abud, G., Alencar, J., Lavor, C. et al. The K-discretization and K-incident graphs for discretizable Distance Geometry. Optim Lett 14, 469–482 (2020). https://doi.org/10.1007/s11590-018-1294-2
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DOI: https://doi.org/10.1007/s11590-018-1294-2