The Grasper-CL graph management system

Grasper-CL is a system for manipulating and displaying graphs, and for building graph-based user interfaces for application programs. It is implemented in COMMON LISP and CLIM, and has been proven by use in a number of applications. Grasper-CL includes several advances in graph drawing. It contains a graph abstract datatype plus a comprehensive and novel language of operations on that datatype. The appearance of Grasper-CL graphs can be tailored by a wide variety of shape parameters that allow the application to customize the display of nodes and edges for different domains. Default values for shape parameters can be established at several levels. Grasper-CL employs a toolbox approach to graph layout: the system contains a suite of graph layout algorithms that can be applied individually, or in combination to produce hierarchical graph layouts. The system also contains an interactive graph browser.     

Visual exploration of complex time-varying graphs

Quasi-trees, namely graphs with tree-like structure, appear in many application domains, including bioinformatics and computer networks. Our new SPF approach exploits the structure of these graphs with a two-level approach to drawing, where the graph is decomposed into a tree of biconnected components. The low-level biconnected components are drawn with a force-directed approach that uses a spanning tree skeleton as a starting point for the layout. The higher-level structure of the graph is a true tree with meta-nodes of variable size that contain each biconnected component. That tree is drawn with a new area-aware variant of a tree drawing algorithm that handles high-degree nodes gracefully, at the cost of allowing edge-node overlaps. SPF performs an order of magnitude faster than the best previous approaches, while producing drawings of commensurate or improved quality     

Exploring large graphs in 3D hyperbolic space

Drawing graphs as nodes connected by links is visually compelling but computationally difficult. Hyperbolic space and spanning trees can reduce visual clutter, speed up layout, and provide fluid interaction. This article briefly describes a software system that explicitly attempts to handle much larger graphs than previous systems and support dynamic exploration rather than final presentation. It then discusses the applicability of this system to goals beyond simple exploration. A software system that supports graph exploration should include both a layout and an interactive drawing component. I have developed new algorithms for both layout and drawing (H3 and H3Viewer). The H3Viewer drawing algorithm remains under development, so this article presents preliminary results. I have implemented a software library that uses these algorithms. It can handle graphs of more than 100,000 edges by using a spanning tree as the backbone for the layout and drawing algorithms     

Parametric graph drawing

A diagram is a drawing on the plane that represents a graph like structure, where nodes are represented by symbols and edges are represented by curves connecting pairs of symbols. An automatic layout facility is a tool that receives as input a graph like structure and is able to produce a diagram that nicely represents such a structure. Many systems use diagrams in the interaction with the users; thus, automatic layout facilities and algorithms for graphs layout have been extensively studied in the last years. We present a new approach in designing an automatic layout facility. Our approach is based on a modular management of a large collection of algorithms and on a strategy that, given the requirements of an application, selects a suitable algorithm for such requirements. The proposed approach has been used for designing the automatic layout facility of Diagram Server, a network server that offers to its clients several facilities for managing diagrams     

A browser for directed graphs

A general-purpose browser for directed graphs is described. The browser provides operations to examine and edit graphs and to generate a layout for a graph automatically that minimizes edge crossings. Two layout algorithms were implemented. A hierarchical graph layout algorithm was found to be best for directed graphs. The graph browser also has facilities that allow it to be integrated with other applications (e.g. a program browser). These facilities and our experiences building a program call-graph browser are described.     

Online dynamic graph drawing

This paper presents an algorithm for drawing a sequence of graphs online. The algorithm strives to maintain the global structure of the graph and thus the user's mental map, while allowing arbitrary modifications between consecutive layouts. The algorithm works online and uses various execution culling methods in order to reduce the layout time and handle large dynamic graphs. Techniques for representing graphs on the GPU allow a speedup by a factor of up to 17 compared to the CPU implementation. The scalability of the algorithm across GPU generations is demonstrated. Applications of the algorithm to the visualization of discussion threads in Internet sites and to the visualization of social networks are provided.     

Coherent time-varying graph drawing with multifocus+context interaction

We present a new approach for time-varying graph drawing that achieves both spatiotemporal coherence and multifocus+context visualization in a single framework. Our approach utilizes existing graph layout algorithms to produce the initial graph layout, and formulates the problem of generating coherent time-varying graph visualization with the focus+context capability as a specially tailored deformation optimization problem. We adopt the concept of the super graph to maintain spatiotemporal coherence and further balance the needs for aesthetic quality and dynamic stability when interacting with time-varying graphs through focus+context visualization. Our method is particularly useful for multifocus+context visualization of time-varying graphs where we can preserve the mental map by preventing nodes in the focus from undergoing abrupt changes in size and location in the time sequence. Experiments demonstrate that our method strikes a good balance between maintaining spatiotemporal coherence and accentuating visual foci, thus providing a more engaging viewing experience for the users.     

GraphSET,a tool for simultaneous graph drawing

Problems in simultaneous graph drawing involve the layout of several graphs on a shared vertex set. This paper describes a Graph Simultaneous Embedding Tool, GraphSET, designed to allow the investigation of a wide range of graph embedding problems. GraphSET can be used in the study of several variants of simultaneous embedding including simultaneous geometric embedding, simultaneous embedding with fixed edges, and colored simultaneous embedding with the vertex set partitioned into color classes. The tool has three primary uses: (i) studying theoretical problems in simultaneous graph drawing through the production of examples and counterexamples, (ii) producing layouts of given classes of graphs using built‐in implementations of known algorithms, and (iii) providing a platform for development and implementation of new algorithms and data structures for all variants of simultaneous graph embedding. We also describe the design decisions involved in the construction of GraphSET in terms of the requirements dictated by its applications. GraphSET along with movies illustrating its utility are available at http://graphset.cs.arizona.edu . Copyright © 2010 John Wiley & Sons, Ltd.     

Cerebral: visualizing multiple experimental conditions on a graph with biological context

Systems biologists use interaction graphs to model the behavior of biological systems at the molecular level. In an iterative process, such biologists obser ve the reactions of living cells under various experimental conditions, view the results in the context of the interaction graph, and then propose changes to the graph model. These graphs ser ve as a form of dynamic knowledge representation of the biological system being studied and evolve as new insight is gained from the experimental data. While numerous graph layout and drawing packages are available, these tools did not fully meet the needs of our immunologist collaborators. In this paper, we describe the data information display needs of these immunologists and translate them into design decisions. These decisions led us to create Cerebral, a system that uses a biologically guided graph layout and incor porates experimental data directly into the graph display. Small multiple views of different experimental conditions and a data-driven parallel coordinates view enable correlations between experimental conditions to be analyzed at the same time that the data is viewed in the graph context. This combination of coordinated views allows the biologist to view the data from many different perspectives simultaneously. To illustrate the typical analysis tasks performed, we analyze two datasets using Cerebral. Based on feedback from our collaboratorsweconcludethat Cerebral is a valuable tool for analyzing experimental data in the context of an interaction graph model.      

A tabu search based approach for graph layout

This paper describes an automated tabu search based method for drawing general graph layouts with straight lines. To our knowledge, this is the first time tabu methods have been applied to graph drawing. We formulated the task as a multi-criteria optimization problem with a number of metrics which are used in a weighted fitness function to measure the aesthetic quality of the graph layout. The main goal of this work is to speed up the graph layout process without sacrificing layout quality. To achieve this, we use a tabu search based method that goes through a predefined number of iterations to minimize the value of the fitness function. Tabu search always chooses the best solution in the neighbourhood. This may lead to cycling, so a tabu list is used to store moves that are not permitted, meaning that the algorithm does not choose previous solutions for a set period of time. We evaluate the method according to the time spent to draw a graph and the quality of the drawn graphs. We give experimental results applied on random graphs and we provide statistical evidence that our method outperforms a fast search-based drawing method (hill climbing) in execution time while it produces comparably good graph layouts. We also demonstrate the method on real world graph datasets to show that we can reproduce similar results in a real world setting.     

EvoGeneSys,a new evolutionary approach to graph generation

Graphs are widely used to represent complex and structured information of interest in various fields of science and engineering. When using graph representations, problems of special interest often imply searching. For example, searching for the prototypes representing a dataset of graphs or for the graph that optimizes a set of parameters. In any case, it is necessary that the problem solution be expressed in terms of graphs. Therefore, defining effective methods for automatically generating single graphs, or sets of graphs, representing problem solutions, is a key issue. A new evolutionary computation-based approach specifically devised for generating graphs is presented. The method is based on a special data structure, called multilist, which allows the encoding of any type of graph, directed or undirected, with or without attributes. Graph encoding by multilists makes it possible to define effective crossover and mutation operators, overcoming the problems normally encountered when implementing genetic operators on graphs. Further advantages of the proposed approach are that it does not require any problem specific knowledge and it is able to search for graphs whose number of nodes is not known a priori. Three sets of experiments were performed to test the proposed approach and the solutions found were compared with those obtained by other approaches proposed in the literature.     

Visualization of graph products

Graphs are a versatile structure and abstraction for binary relationships between objects. To gain insight into such relationships, their corresponding graph can be visualized. In the past, many classes of graphs have been defined, e.g. trees, planar graphs, directed acyclic graphs, and visualization algorithms were proposed for these classes. Although many graphs may only be classified as "general" graphs, they can contain substructures that belong to a certain class. Archambault proposed the TopoLayout framework: rather than draw any arbitrary graph using one method, split the graph into components that are homogeneous with respect to one graph class and then draw each component with an algorithm best suited for this class. Graph products constitute a class that arises frequently in graph theory, but for which no visualization algorithm has been proposed until now. In this paper, we present an algorithm for drawing graph products and the aesthetic criterion graph product's drawings are subject to. We show that the popular High-Dimensional Embedder approach applied to cartesian products already respects this aestetic criterion, but has disadvantages. We also present how our method is integrated as a new component into the TopoLayout framework. Our implementation is used for further research of graph products in a biological context.     

FMR:基于FR的快速多层次算法

图可视化技术是可视化研究的重要内容,近年来大图的绘制问题一直是图可视化 技术的焦点。为此,提出了一种快速多层次算法用于解决大图绘制问题。采用多层次方法作为 算法的框架,以 FR 力导向算法的变体结合质心算法以及四叉树空间分解等方法对单层布局进 行优化。另外,还使用了约束规范化和能量模型 2 种加速方法。实验表明,该算法具有高效的 性能和良好的布局效果。其效率非常高,在单核 CPU 下,可以在大约 5 s 内很好地绘制出 10 000 个顶点的图。并与几种经典的算法进行了比较,也证明了该算法的有效性和实用性。此外,该 算法易于实现,可被轻易推广到其他布局算法上,以加速其运算。     

Aesthetics-based Graph Layout for Human Consumption

Automatic graph layout is an important and long-studied problem. The basic straight-edge graph layout problem is to find spatial positions for the nodes of an input graph that maximize some measure of desirability. When graph layout is intended for human consumption, we call this measure of desirability an aesthetic. We seek an algorithm that produces graph layouts of high aesthetic quality not only for general graphs, but also for specific classes of graphs, such as trees and directed acyclic graphs. The Aesthetic Graph Layout (AGLO) approach described in this paper models graph layout as a multiobjective optimization problem, where the value of a layout is determined by multiple user-controlled layout aesthetics. The current AGLO algorithm combines the power and flexibility of the simulated annealing approach of Davidson and Harel (1989) with the relative speed of the method of Fruchterman and Reingold (1991). In addition, it is more general, and incorporates several new layout aesthetics to support new layout styles. Using these aesthetics, we are able to produce pleasing displays for graphs on which these other methods flounder.     

Mental map preserving graph drawing using simulated annealing

Visualizing graphs has been studied extensively in the community of graph drawing and information visualization over the years. In some applications, the user is required to interact with a graph by making slight changes to the underlying graph structure. To visualize graphs in such an interactive environment, it is desirable that the differences between the displays of the original and the modified graphs be kept minimal, allowing the user to comprehend the changes in the graph structure faster. As the mental map concept refers to the presentation of a person’s mind while exploring visual information, the better the mental map is preserved, the easier the structure change of a graph is understood. It is somewhat surprising that preserving the user’s mental map has largely been ignored in the graph drawing community in the past. We propose an effective mental-map-preserving graph drawing algorithm for straight-line drawings of general undirected graphs based on the simulated-annealing technique. Our experimental results and questionnaire analysis suggest this new approach to be promising.     

Cut-tree construction for facility layout

The Gomory-Hu cut tree corresponding to a material flow graph provides important structural relationships to layout designers. The cut tree generation is not trivial to the programmer. In this paper, we present a simple technique which generates and constructs a cut tree of a given flow graph. The method differs from previous cut tree generation methods in the sense that its output also facilitates computer construction of the graph of the cut tree with only a few lines of additional coding, which makes its implementation attractive for computerized graph theoretic layout design approaches. The algorithm actually draws the cut tree automatically. Example graphs and the corresponding computer generated cut trees are illustrated. Also, an example is given where the cut tree information provides the optimal layout configuration.     

A graph grammar‐based approach for graph layout

As a two‐dimensional formal tool, graph grammars are capable of handling the layout problems of visual programming languages. Based on an edge‐based graph grammar (EGG), this paper proposes a novel layout approach that uses the unique features of EGG and overcomes the weakness of existing layout approaches. In order to make the approach rigorous yet concise, the graph grammar mechanisms with layout constraints and quantitative analysis techniques are combined together as an integrity. First, the basic notions of EGG are briefly introduced; second, the layout approach is presented that consists of two phases, ie, bottom‐up parsing and top‐down derivation. Finally, a case study is given by taking the standard flowchart as an example to demonstrate the working process of the proposed approach.     

Convergent drawing for mutually connected directed graphs

Directed graphs are used to represent a variety of datasets, including friendship on social networking services (SNS), pathways of genes, and citations of research papers. Graph drawing is useful in representing such datasets. At the international conference on Information Visualization (IV), we have presented a convergent edge drawing and a node layout technique for tightly and mutually connected directed graphs. The edge drawing technique in the IV paper includes three features: ordinary bundling of edges connecting pairs of node clusters, convergence of multiple bundles that connect to the same node cluster, and shape adjustment of two bundles connecting the same pair of node clusters. In this paper, we present improved node layout and edge drawing techniques, which make our edge bundling more effective. This paper also introduces a case study with a directed paper citation graph dataset.vvvvv     

A technique for compiling execution graph expressions for restricted and-parallelism in logic programs

The restricted and-parallelism (RAP) execution model of logic programs is described. This model uses a compile-time data-dependence analysis to generate execution graph expressions for the clauses in a Prolog program. These expressions use simple run-time tests to determine the possibilities of parallelism and produce multiple parallel execution graphs from a single execution graph expression. A simple algorithm is then presented which automatically produces these execution graphs for Prolog clauses. Several ways in which the algorithm can be significantly improved by using the results of program-level data-dependence analysis are discussed.