Node Overlap Removal by Growing a Tree

Node overlap removal is a necessary step in many scenarios including laying out a graph, or visualizing a tag cloud. Our contribution is a new overlap removal algorithm that iteratively builds a Minimum Spanning Tree on a Delaunay triangulation of the node centers and removes the node overlaps by “growing” the tree. The algorithm is simple to implement yet produces high quality layouts. According to our experiments it runs several times faster than the current state-of-the-art methods.

In the context of graph layout, many algorithms have been designed to remove node overlapping, and many quality criteria and associated metrics have been proposed to evaluate those algorithms. Unfortunately, a complete comparison of the algorithms based on some metrics that evaluate their quality has never been provided and it is thus difficult for a visualisation designer to select the algorithm that best suits their needs. In this paper, we review 22 metrics available in the literature, classify them according to the quality criteria they try to capture, and select a representative one for each class. Based on the selected metrics,we compare 9 node overlap removal algorithms. Our experiment involves 854 synthetic and real-world graphs. Finally, we propose a JavaScript library containing both the algorithms and the criteria, and we provide a Web platform, AGORA, in which one can upload graphs, apply the algorithms and compare/download the results.

The problem of node overlap removal is to adjust the layout generated by typical graph drawing methods so that nodes of non-zero width and height do not overlap, yet are as close as possible to their original positions. We give an O(n log n) algorithm for achieving this assuming that the number of nodes overlapping any single node is bounded by some constant. This method has two parts, a constraint generation algorithm which generates a linear number of “separation” constraints and an algorithm for finding a solution to these constraints “close” to the original node placement values. We also extend our constraint solving algorithm to give an active set based algorithm which is guaranteed to find the optimal solution but which has considerably worse theoretical complexity. We compare our method with convex quadratic optimization and force scan approaches and find that it is faster than either, gives results of better quality than force scan methods and similar quality to the quadratic optimisation approach.Keywordsgraph layoutconstrained optimizationseparation constraints

N points are given in the Euclidean plane, and the minimum spanning tree problem seeks for a minimum spanning tree interconnecting the n points so that there is only one path between any two points. One of the classic and frequently-used algorithms for minimum spanning tree problem is Prim's algorithm, but it consumes large time and space complexity for the plane minimum spanning tree problem is of O(n2) numbers of edges. Luckily, it was proved that the plane minimum spanning tree is a sub-graph of Delaunay triangulation for the given points in the plane, and the number of edges in the triangulation is O(n). This motivates us to efficiently compute the Delaunay triangulation of the given points and then find the minimum spanning tree in the triangulation. This paper presents an algorithm based on the divide and conquer for Delaunay triangulation together with the Prim's algorithm to produce an O(nlogn) algorithm for minimum spanning tree problem in the plane, implements the visual graphic interface with various selected algorithms for plane minimum spanning tree and compares their running time.

In a previous article, using underlying graph theoretical properties, Gouveia and Magnanti (2003) described several network flow‐based formulations for diameter‐constrained tree problems. Their computational results showed that, even with several enhancements, models for situations when the tree diameter D is odd proved to be more difficult to solve than those when D is even. In this article we provide an alternative modeling approach for the situation when D is odd. The approach views the diameter‐constrained minimum spanning tree as being composed of a variant of a directed spanning tree (from an artificial root node) together with two constrained paths, a shortest and a longest path, from the root node to any node in the tree. We also show how to view the feasible set of the linear programming relaxation of the new formulation as the intersection of two integer polyhedra, a so‐called triangle‐tree polyhedron and a constrained path polyhedron. This characterization improves upon a model of Gouveia and Magnanti (2003) whose linear programming relaxation feasible set is the intersection of three rather than two integer polyhedra. The linear programming gaps for the tightened model are very small, typically less than 0.5%, and are usually one third to one tenth of the gaps of the best previous model described in Gouveia and Magnanti (2003). Moreover, using the new model, we have been able to solve large Euclidean problem instances that are not solvable by the previous approaches. © 2004 Wiley Periodicals, Inc.

This paper studies the minimum spanning tree problem on a graph with uncertain edge weights, which are formulated as uncertain variables. The concept of ideal uncertain minimum spanning tree (ideal UMST) is initiated by extending the definition of the uncertain [Formula: see text]-minimum spanning tree to reect the overall properties of the α-minimum spanning tree weights at any confidence level [Formula: see text]. On the basis of this new concept, the definition of uncertain distribution-minimum spanning tree is proposed in three ways. Particularly, by considering the tail value at risk from the perspective of risk management, the notion of uncertain [Formula: see text]-distribution-minimum spanning tree ([Formula: see text]-distribution-UMST) is suggested. It is shown that the [Formula: see text]-distribution-UMST is just the uncertain expected minimum spanning tree when [Formula: see text] = 0. For any [Formula: see text], this problem can be effectively solved via the proposed deterministic graph transformation-based approach with the aid of the [Formula: see text]-distribution-path optimality condition. Furthermore, the proposed definitions and solutions are illustrated by some numerical examples.

BackgroundDrug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to identify protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. Few studies, however, have assessed the evolution of resistance from genotype–phenotype data.ResultsThe machine learning produced highly accurate and robust classification of resistance to HIV protease inhibitors. Genotype data were mapped to the enzyme structure and encoded using Delaunay triangulation. Estimates of evolutionary relationships, based on this encoding, and using Minimum Spanning Trees, showed clusters of mutations that closely resemble the wild type. These clusters appear to evolve uniquely to more resistant phenotypes.ConclusionsUsing the triangulation metric and spanning trees results in paths that are consistent with evolutionary theory. The majority of the paths show bifurcation, namely they switch once from non-resistant to resistant or from resistant to non-resistant. Paths that lose resistance almost uniformly have far lower levels of resistance than those which either gain resistance or are stable. This strongly suggests that selection for stability in the face of a rapid rate of mutation is as important as selection for resistance in retroviral systems.

This paper introduces a polygon-based method for removing overlaps of printed circuit board (PCB) pattern with circular-arc. The algorithm takes a sequence of object contours in Gerber files which consist of circular-arc polygons (i.e., polygons that have straight or circular boundary edges) in a plane as input, and outputs high quality and non-overlapping layouts. Instead of combining circular-arc polygons together, we adopt a new clipping strategy so that the bounding boxes of circular-arc polygons should remain as small as possible. The clipping algorithm is simple, robust and efficient yet it produce high quality layouts. It employs bounding boxes and spatial binning to avoid the quadratic complexity of exact intersection tests. A comparison with a brute force overlap tester are given. A number of PCB pattern experiments suggests it benefits the real-time rasterizer in decreasing running time.

Degree-bounded minimum spanning trees

Motivated by the increasing need for fast distributed processing of large-scale graphs such as the Web graph and various social networks, we study a number of fundamental graph problems in the message-passing model, where we have k machines that jointly perform computation on an arbitrary n-node (typically, n > k) input graph. The graph is assumed to be randomly partitioned among the k ≥ 2 machines (a common implementation in many real world systems). The communication is point-to-point, and the goal is to minimize the time complexity i.e., the number of communication rounds, of solving various fundamental graph problems.We present lower bounds that quantify the fundamental time limitations of distributively solving graph problems. We first show a lower bound of Ω(n/k) rounds for computing a spanning tree (ST) of the input graph. This result also implies the same bound for other fundamental problems such as computing a minimum spanning tree (MST), breadth-first tree (BFS), and shortest paths tree (SPT). We also show an Ω(n/k2) lower bound for connectivity ST verification and other related problems. Our lower bounds develop and use new bounds in random-partition communication complexity.To complement our lower bounds, we also give algorithms for various fundamental graph problems, e.g., PageRank, MST, connectivity, ST verification, shortest paths, cuts, spanners, covering problems, densest subgraph, subgraph isomorphism, finding triangles, etc. We show that problems such as PageRank, MST, connectivity, and graph covering can be solved in O(n/k) time (the notation O hides polylog(n) factors and an additive polylog(n) term); this shows that one can achieve almost linear (in k) speedup, whereas for shortest paths, we present algorithms that run in O(n/Ok) time (for (1 + e)-factor approximation) and in O(n/k) time (for O(log n)-factor approximation) respectively.Our results are a step towards understanding the complexity of distributively solving large-scale graph problems.

In this paper, we aim at improving the vector lifting scheme dedicated to lossless coding of hyperspectral images by an optimal components ordering. For this purpose, we propose a three-stage algorithm. The first one consists in classifying the spectral components into separate clusters sharing similar characteristics. Then, within each cluster, the problem of ordering the components for inter-component coding is addressed. It is formulated as the design of a minimum spanning tree whose vertices are the spectral components. Finally, at the last stage, the spatial and spectral redundancies are simultaneously exploited by a vector lifting scheme. Experiments carried out on AVIRIS images indicate the outperformance of the proposed method w.r.t. the state-of-art coders.

Given an undirected, connected graph, the aim of the minimum branch-node spanning tree problem is to find a spanning tree with the minimum number of nodes of degree larger than 2. The problem is motivated by network design problems where junctions are significantly more expensive than simple end- or through-nodes, and are thus to be avoided. Unfortunately, it is NP-hard to recognize instances that admit an objective value of zero, rendering the search for guaranteed approximation ratios futile. We suggest to investigate a complementary formulation, called maximum path-node spanning tree, where the goal is to find a spanning tree that maximizes the number of nodes with degree at most two. While the optimal solutions (and the practical applications) of both formulations coincide, our formulation proves more suitable for approximation. In fact, it admits a trivial 1/2-approximation algorithm. Our main contribution is a local search algorithm that guarantees a ratio of 6/11, as well as showing that the problem is APX-hard, i.e., it does not allow a PTAS.

In a complete graphwith independent uniform(or exponential) edge weights, letbe the minimum‐weight spanning tree (MST), andthe MST after deleting the edges of all previous trees. We show that each tree's weightconverges in probability to a constant, with, and we conjecture that. The problem is distinct from Frieze and Johansson's minimum combined weightofkedge‐disjoint spanning trees; indeed,. With an edge of weightw“arriving” at time, Kruskal's algorithm defines forests, initially empty and eventually equal to, each edge added to the first possible. Using tools of inhomogeneous random graphs we obtain structural results including that the fraction of vertices in the largest component ofconverges to some. We conjecture that the functionstend to time translations of a single function.

Minimum Spanning Trees (MSTs) are ubiquitous in optimization problems in networks. Even though fast algorithms exist to solve the MST problem, real world applications are usually subject to constraints that do not let us apply such methods directly. In these cases we confront a version of the MST called the “Weighted Spanning Tree” (WST) in which we look for a spanning tree in a graph that satisfies other side constraints and is of minimum cost. In this paper we implement this constraint using a lower bound and learning to accelerate the search and thus reduce the solving time. We show that having this propagator is tremendously beneficial for solvers and we show the benefits of learning.

The concept of the minimum spanning tree (MST) plays an important role in topological network design, because it models a cheapest connected network. In a tree, however, the failure of a vertex can disconnect the network. In order to tolerate such a failure, we generalize the MST to the concept of a cheapest biconnected network. For a set of points in the Euclidean plane, we show that it is NP-hard to find a cheapest biconnected spanning graph, where edge costs are the Euclidean distances of the respective points. We propose a different type of subgraph, based on forbidding (due to failure) the use of a vertex. A minimum spanning multi-tree is a spanning graph that contains for each possible forbidden vertex a spanning tree that is minimum among the spanning trees that do not use the forbidden vertex. We propose a worst-case time optimal algorithm for computing a minimum spanning multi-tree for a planar Euclidean point set. A minimum spanning multi-tree is cheap, even though it embeds a linear number of MSTs: Its cost is more than the MST cost only by a constant factor. Furthermore, we propose a linear time algorithm for computing a cheap vertex failure tolerant graph, given the Delaunay triangulation. This graph bounds the cost of the minimum spanning multi-tree from above.