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2020
The distance geometry problem consists in finding a realization of a weighed graph in a Euclidean space of given dimension, where the edges are realized as straight segments of length equal to the edge weight. We propose and test a new mathematical programming formulation based on the incidence between cycles and edges in the given graph.
ArXiv, 2020
The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension K, where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation...
Journal of Global Optimization
Distance Geometry (DG) is based on distances rather than points and angles. The fundamental problem of DG is the Distance Geometry Problem (DGP), which is an inverse problem to "given a set of points in R K , compute some of the pairwise distances". More precisely, given an integer K > 0 and a simple undirected graph G = (V , E) with a non-negative weight function d : E → R + defined on the edges, it asks whether there exists a realization x : V → R K such that ∀{i, j} ∈ E x i − x j = d i j. (1) DIMACS generously supported the Distance Geometry Theory and Applications workshop to which this special issue is dedicated. NSF support (through DIMACS) is also gratefully acknowledged.
ArXiv, 2021
The Distance Geometry Problem asks for a realization of a given weighted graph in R . Two variants of this problem, both originating from protein conformation, are based on a given vertex order (which abstracts the protein backbone). Both variants involve an element of discrete decision in the realization of the next vertex in the order using K preceding (already realized) vertices. The difference between these variants is that one requires the K preceding vertices to be contiguous. The presence of this constraint allows one to prove, via a combinatorial counting of the number of solutions, that the realization algorithm is fixed-parameter tractable. Its absence, on the other hand, makes it possible to efficiently construct the vertex order directly from the graph. Deriving a combinatorial counting method without using the contiguity requirement would therefore be desirable. In this paper we prove that, unfortunately, such a counting method cannot be devised in general.
2020
We propose a new algorithm for Discretizable Molecular Distance Geometry problems (DMDGPs), a class of Distance Geometry problems (DGPs) whose search space can be discretized and represented by a binary tree. By efficiently exploiting the many interesting symmetry properties of DMDGP instances, the new algorithm solves a sequence of nested and overlapped DMDGP subproblems rather than exploring the binary tree in a depth first manner as the classic Branch-and-Prune (BP) algorithm. Computational results on artificially generated instances show that the new algorithm outperforms the classic BP algorithm in sparse DMDGPs.
Optimization Letters, 2012
We introduce the Discretizable Distance Geometry Problem in R 3 (DDGP 3), which consists in a subclass of instances of the Distance Geometry Problem for which an embedding in R 3 can be found by means of a discrete search. We show that the DDGP 3 is a generalization of the Discretizable Molecular Distance Geometry Problem (DMDGP), and we discuss the main differences between the two problems. We prove that the DDGP 3 is NP-hard and we extend the Branch & Prune (BP) algorithm, previously used for the DMDGP, for solving instances of the DDGP 3. Protein graphs may or may not be in DMDGP and/or DDGP 3 depending on vertex orders and edge density. We show experimentally that as distance thresholds decrease, PDB protein graphs which fail to be in the DMDGP still belong to DDGP 3 , which means that they can still be solved using a discrete search.
In this paper we have made an effort to co-op up Graph Theory with Euclidian Geometry, we adopt the notion of diameter in Graph Theory (largest length of a path in graph) as length and height of a graph as breadth of graph. The breadth of the graph is defined to be the maximum of the heights taken over all the diametral paths and is denoted by . Therefore . A graph is said to be a square graph if . An algorithm is developed to find the breadth of graph.
2021
Abstract: Circular distance between vertices of a graph has a significant role, which is defined as summation of detour distance and geodesic distance. Attention is paid, this is metric on the set of all vertices of graph and it plays an important role in graph theory. Some bounds have been carried out for circular distance in terms of pendent vertices of graph . Some results and properties have been found for circular distance for some classes of graphs and applied this distance to Cartesian product of graphs〖 P〗_2×C_n. Including 〖 P〗_2×C_n, some graphs acted as a circular self-centered. Using this circular distance there exists some relations between various radii and diameters in path graphs. The possible applications were briefly discussed.
Discrete Applied Mathematics, 2015
When a weighted graph is an instance of the Distance Geometry Problem (DGP), certain types of vertex orders (called discretization orders) allow the use of a very efficient, precise and robust discrete search algorithm (called Branch-and-Prune). Accordingly, finding such orders is critically important in order to solve DGPs in practice. We discuss three types of discretization orders, the complexity of determining their existence in a given graph, and the inclusion relations between the three order existence problems. We also give three mathematical programming formulations of some of these ordering problems.
Discrete & Computational Geometry, 1994
Given an undirected edge-weighted graph G = (V, E), a subgraph G' = (IT, E') is a t-spanner of G if, for every u, v ~ V, the weighted distance between u and v in G' is at most t times the weighted distance between u and v in G. We consider the problem of approximating the distances among points of a Euclidean metric space: given a finite set V of points in ~a, we want to construct a sparse t-spanner of the complete weighted graph induced by V. The weight of an edge in these graphs is the Euclidean distance between the endpoints of the edge. We show by a simple greedy argument that, for any t > 1 and any V c R a, a t-spanner G of V exists such that G has degree bounded by a function of d and r The analysis of our bounded degree spanners improves over previously known upper bounds on the minimum number of edges of Euclidean t-spanners, even compared with spanners of bounded average degree. Our results answer two open problems, one proposed by Vaidya and the other by Keil and Gutwin. The main result of the paper concerns the case of dimension d = 2. It is fairly easy to see that, for some t (t > 7.6), t-spanners of maximum degree 6 exist for any set of points in the Euclidean plane, but it was not known that degree 5 would suffice. We prove that for some (fixed) t, t-spanners of degree 5 exist for any set of points in the plane. We do not know if 5 is the best possible upper bound on the degree. * This research was supported by Conselho Nacional de Desenvolvimento Cientifico e Tecnol6gico, Proc 203039/87.4 (Brazil). 214 J. Soares shortest path between x and y. We say that a subgraph G' = (V, E') (with the same weights on E') is a t-spanner of G if, for every x, y 6 V, dG,(x, y) < t" da(x, y). The number t is a measure of how well G' approximates G with respect to the distances. The construction of t-spanners has received recent attention in several works: [2], [3], [5], [8], [9], [11], and [18], among others. Given a set V ~ •a the complete Euclidean graph on V is the complete graph on V where each edge weight is the Euclidean distance I[x-Y]I. In this paper we consider the problem of constructing bounded degree spanners of complete Euclidean graphs. For brevity we write t-spanner of V instead of t-spanner of the complete Euclidean graph on V. Let A(G) denote the maximum degree of a graph G. Dobkin et al. [5] mention that Feder and others had shown that, for some fixed t and for any set V of points in the Euclidean plane, a t-spanner G of V exists such that A(G) < 7. Then they ask what would be the minimum A for which such a result is possible? This paper has a partial answer to this question. Our main result (Section 4) is that, for some fixed t, t-spanners with A < 5 exist. Nisan [10] has proved the same for A < 6. Section 2 contains the basic algorithm used to construct bounded degree t-spanners. Although the algorithm has been used before by Althrfer et al. [1] and Soares [16] to construct t-spanners for arbitrary graphs, it was not known that the algorithm also constructs bounded degree spanners for complete Euclidean graphs. Section 3 contains a brief analysis of the problem when V is in d-dimensional Euclidean space. We show that, for any t > 1 and any V c ~d, a t-spanner G of V exists where A(G) is bounded by a function that depends only on d and t. This answers a question proposed by Keil and Gutwin in [8]. This bound on the maximum degree implies an improvement on the previously known upper bounds on the number of edges sufficient to build Euclidean spanners. Then we show that, for each dimension d, the least A(G) for which our algorithm constructs Od(1)spanners coincides with the kissing number in dimension d. (Od(1) denotes some function of d, i.e., a constant for each d.) Section 4 contains our main result, the construction of O(1)-spanners of degree 5 for any set of points in the Euclidean plane.
Journal of Computational Geometry, 2012
A ball graph is an intersection graph of a set of balls with arbitrary radii. Given a real number t > 1, we say that a subgraph G ′ of a graph G is a t-spanner of G, if for every pair of vertices u, v in G, there exists a path in G ′ of length at most t times the distance between u and v in G. In this paper, we consider the problem of efficiently constructing sparse spanners of ball graphs which supports fast shortest path distance queries. We present the first algorithm for constructing spanners of ball graphs. For a disk graph in R 2 , we construct a (1 + ǫ)-spanner for any ǫ > 0 with O(nǫ −2) edges in O(n 4/3+δ ǫ −4/3 log 2/3 S) time, using an efficient partitioning of the plane into squares and solving intersection problems. Here δ is any positive constant, and S is the ratio between the largest and smallest radius. For the special case when the disks all have unit size, we show that the complexity of constructing a (1+ ǫ)-spanner is almost equal to the complexity of constructing a Euclidean minimum spanning tree. The algorithm extends naturally to other "disk-like" objects, also in higher dimensions. The algorithm uses an efficient subdivision of space to construct a sparse graph having many of the same distance properties as the input ball graph. Additionally, the constructed spanners have a small vertex separator decomposition (hereditary). In dimension 2, the disk graph spanner has an O(√ nǫ −3/2 + ǫ −3 log S) separator. The presence of a small separator is then exploited to obtain very efficient data structures for approximate distance queries. The results on geometric graph separators might be of independent interest. For example, since complete Euclidean graphs are just a special case of (unit) ball graphs, our results also provide a new approach for constructing spanners with small separators in these graphs.
2017
The fundamental problem of distance geometry consists in finding a realization of a given weighted graph in a Euclidean space of given dimension, in such a way that vertices are realized as points and edges as straight segments having the same lengths as their given weights. This problem arises in structural proteomics, wireless sensor networks, and clock synchronization protocols to name a few applications. The well-known Isomap method is a dimensionality reduction heuristic which projects finite but high dimensional metric spaces into the "most significant" lower dimensional ones, where significance is measured by the magnitude of the corresponding eigenvalues. We start from a simple observation, namely that Isomap can also be used to provide approximate realizations of weighted graphs very eciently, and then derive and benchmark six new heuristics.
2014
We propose a set of formulations and reformulations of the Distance Geometry Problem, which we evaluate with both local and global off-the-shelf solvers. The local solvers are cast in a global optimization metaheuristic (Variable Neighbourhood Search) since the problem is nonconvex and non-global optima are usually of limited practical interest.
2020
With the most recent releases of MD-JEEP, new relevant features have been included to our software tool. MD-JEEP solves instances of the class of Discretizable Distance Geometry Problems (DDGPs), which ask to find possible realizations, in a Euclidean space, of a simple weighted undirected graph for which distance constraints between vertices are given, and for which a discretization of the search space can be supplied. Since its version 0.3.0, MD-JEEP is able to deal with instances containing interval data. We focus in this short paper on the most recent release MD-JEEP 0.3.2: among the new implemented features, we will focus our attention on three features: (i) an improved procedure for the generation and update of the boxes used in the coarse-grained representation (necessary to deal with instances containing interval data); (ii) a new procedure for the selection of the so-called discretization vertices (necessary to perform the discretization of the search space); (iii) the impl...
Optimization Letters
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 ∈ V correspond to the weights d uv , for each {u, v} ∈ 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.
TOP
Data are often represented as graphs. Many common tasks in data science are based on distances between entities. While some data science methodologies natively take graphs as their input, there are many more that take their input in vectorial form. In this survey, we discuss the fundamental problem of mapping graphs to vectors, and its relation with mathematical programming. We discuss applications, solution methods, dimensional reduction techniques, and some of their limits. We then present an application of some of these ideas to neural networks, showing that distance geometry techniques can give competitive performance with respect to more traditional graph-to-vector mappings.
Optimization Letters, 2017
Discretizable distance geometry problems (DDGPs) constitute a class of graph realization problems where the vertices can be ordered in such a way that the search space of possible positions becomes discrete, usually represented by a binary tree. Finding such vertex order is an essential step to identify and solve DDGPs. Here we look for discretization orders that minimize an indicator of the size of the search tree. This paper sets the ground for exact solution of the discretization order problem by proposing two integer programming formulations and a constraint generation procedure for an extended formulation. We discuss some theoretical aspects of the problem and numerical experiments on protein-like instances of DDGP are also reported.
Lecture Notes in Computer Science, 2017
We introduce the dynamical distance geometry problem (dynDGP), where vertices of a given simple weighted undirected graph are to be embedded at different times t. Solutions to the dynDGP can be seen as motions of a given set of objects. In this work, we focus our attention on a class of instances where motion inter-frame distances are not available, and reduce the problem of embedding every motion frame as a static distance geometry problem. Some preliminary computational experiments are presented.
Pattern Recognition Letters, 1994
We present a novel graph-theoretic approach to the Distance Transformation (DT) problem. The binary digital image is considered as a graph and the DT problem reduces to a shortest path forest problem. An algorithm is presented which solves the chamfer DT, and the Euclidian DT for a given bound.
RAIRO - Operations Research, 2015
In this paper, we study the efficiency (both theoretically and computationally) of a class of valid inequalities for the minimum weighted elementary directed cycle problem (MWEDCP) in planar digraphs with negative weight elementary directed cycles. These valid inequalities are called cycle valid inequalities and are parametrized by an integer called inequality's order. From a theoretical point of view, we prove that separating cycle valid inequalities of order 1 in planar digraph can be done in polynomial time. From a computational point of view, we present a cutting plane algorithm featuring the efficiency of a lifted form of the cycle valid inequalities of order 1. In addition to these lifted valid inequalities, our algorithm is also based on a mixed integer linear formulation of the MWEDCP. The computational results are carried out on randomly generated planar digraph instances of the MWEDCP. For all 29 instances considered, we obtain in average 26.47% gap improvement. Moreover, for some of our instances the strengthening process directly displays the optimal integer elementary directed cycle.
Distance Geometry, 2012
Given a weighted undirected graph G = (V, E, d) with d : E → Q + and a positive integer K, the Distance Geometry Problem (DGP) asks to find an embedding x : V → R K of G such that for each edge {i, j} we have x i − x j = d i j. Saxe proved in 1979 that the DGP is NP-complete with K = 1 and doubted the applicability of the Turing machine model to the case with K > 1, because the certificates for YES instances might involve real numbers. This chapter is an account of an unfortunately failed attempt to prove that the DGP is in NP for K = 2. We hope that our failure will motivate further work on the question.
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