Pathfinder: Visual Analysis of Paths in Graphs

The analysis of paths in graphs is highly relevant in many domains. Typically, path‐related tasks are performed in node‐link layouts. Unfortunately, graph layouts often do not scale to the size of many real world networks. Also, many networks are multivariate, i.e., contain rich attribute sets associated with the nodes and edges. These attributes are often critical in judging paths, but directly visualizing attributes in a graph layout exacerbates the scalability problem. In this paper, we present visual analysis solutions dedicated to path‐related tasks in large and highly multivariate graphs. We show that by focusing on paths, we can address the scalability problem of multivariate graph visualization, equipping analysts with a powerful tool to explore large graphs. We introduce Pathfinder, a technique that provides visual methods to query paths, while considering various constraints. The resulting set of paths is visualized in both a ranked list and as a node‐link diagram. For the paths in the list, we display rich attribute data associated with nodes and edges, and the node‐link diagram provides topological context. The paths can be ranked based on topological properties, such as path length or average node degree, and scores derived from attribute data. Pathfinder is designed to scale to graphs with tens of thousands of nodes and edges by employing strategies such as incremental query results. We demonstrate Pathfinder's fitness for use in scenarios with data from a coauthor network and biological pathways.     

Smashing peacocks further: drawing quasi-trees from biconnected components

We extend the popular force-directed approach to network (or graph) layout to allow separation constraints, which enforce a minimum horizontal or vertical separation between selected pairs of nodes. This simple class of linear constraints is expressive enough to satisfy a wide variety of application-specific layout requirements, including: layout of directed graphs to better show flow; layout with non-overlapping node labels; and layout of graphs with grouped nodes (called clusters). In the stress majorization force-directed layout process, separation constraints can be treated as a quadratic programming problem. We give an incremental algorithm based on gradient projection for efficiently solving this problem. The algorithm is considerably faster than using generic constraint optimization techniques and is comparable in speed to unconstrained stress majorization. We demonstrate the utility of our technique with sample data from a number of practical applications including gene-activation networks, terrorist networks and visualization of high-dimensional data     

A stable graph layout algorithm for processes

Process mining enables organizations to analyze data about their (business) processes. Visualization is key to gaining insight into these processes and the associated data. Process visualization requires a high‐quality graph layout that intuitively represents the semantics of the process. Process analysis additionally requires interactive filtering to explore the process data and process graph. The ideal process visualization therefore provides a high‐quality, intuitive layout and preserves the mental map of the user during the visual exploration. The current industry standard used for process visualization does not satisfy either of these requirements. In this paper, we propose a novel layout algorithm for processes based on the Sugiyama framework. Our approach consists of novel ranking and order constraint algorithms and a novel crossing minimization algorithm. These algorithms make use of the process data to compute stable, high‐quality layouts. In addition, we use phased animation to further improve mental map preservation. Quantitative and qualitative evaluations show that our approach computes layouts of higher quality and preserves the mental map better than the industry standard. Additionally, our approach is substantially faster, especially for graphs with more than 250 edges.     

Inverse Markov Process Based Constrained Dynamic Graph Layout

In online dynamic graph drawing,constraints over nodes and node pairs help preserve a coherent mental map in a sequence of graphs.Defining the constraints is challenging due to the requirements of both preserving mental map and satisfying the visual aesthetics of a graph layout.Most existing algorithms basically depend on local changes but fail to do proper evaluations on the global propagation when setting constraints.To solve this problem,we introduce a heuristic model derived from PageRank which simulates the node movement as an inverse Markov process hence to give a global analysis of the layout's change,according to which different constraints can be set.These constraints,along with stress function,generate layouts maintaining spatial positions and shapes of relatively stable substructures between adjacent graphs.Experiments demonstrate that our method preserves both structure and position similarity to help users track graph changes visually.     

Customizing a Fisheye View Algorithm to Preserve the Mental Map

Frequently, large knowledge bases are represented by graphs. Many visualization tools allow users or other applications to interact with and adjust the layouts of these graphs. One layout adjustment problem is that of showing more detail without eliding parts of the graph. Approaches based on a fisheye lens paradigm seem well suited to this task. However, many of these techniques are non-trivial to implement and their distortion techniques often cannot be altered to suit different graph layouts. When distorting a graph layout, it is often desirable to preserve various properties of the original graph in an adjusted view. Pertinent properties may include straightness of lines, graph topology, orthogonalities and proximities. However, it is normally not possible to preserve all of the original properties of the graph layout. The type of layout and its application should be considered when deciding which properties to preserve or distort. This paper describes a fisheye view algorithm which can be customized to suit various different graph layouts. In contrast to other methods, the user can select which properties of the original graph layout to preserve in an adjusted view. The technique is demonstrated through its application to visualizing structures in large software systems.     

A regularized graph layout framework for dynamic network visualization

Many real-world networks, including social and information networks, are dynamic structures that evolve over time. Such dynamic networks are typically visualized using a sequence of static graph layouts. In addition to providing a visual representation of the network structure at each time step, the sequence should preserve the mental map between layouts of consecutive time steps to allow a human to interpret the temporal evolution of the network. In this paper, we propose a framework for dynamic network visualization in the on-line setting where only present and past graph snapshots are available to create the present layout. The proposed framework creates regularized graph layouts by augmenting the cost function of a static graph layout algorithm with a grouping penalty, which discourages nodes from deviating too far from other nodes belonging to the same group, and a temporal penalty, which discourages large node movements between consecutive time steps. The penalties increase the stability of the layout sequence, thus preserving the mental map. We introduce two dynamic layout algorithms within the proposed framework, namely dynamic multidimensional scaling and dynamic graph Laplacian layout. We apply these algorithms on several data sets to illustrate the importance of both grouping and temporal regularization for producing interpretable visualizations of dynamic networks.     

Semi‐Automatic Editing of Graphs with Customized Layouts

Usually visualization is applied to gain insight into data. Yet consuming the data in form of visual representation is not always enough. Instead, users need to edit the data, preferably through the same means used to visualize them. In this work, we present a semi‐automatic approach to visual editing of graphs. The key idea is to use an interactive EditLens that defines where an edit operation affects an already customized and established graph layout. Locally optimal node positions within the lens and edge routes to connected nodes are calculated according to different criteria. This spares the user much manual work, but still provides sufficient freedom to accommodate application‐dependent layout constraints. Our approach utilizes the advantages of multi‐touch gestures, and is also compatible with classic mouse and keyboard interaction. Preliminary user tests have been conducted with researchers from bio‐informatics who need to manually maintain a slowly, but constantly growing molecular network. As the user feedback indicates, our solution significantly improves the editing procedure applied so far.     

Scalable, Versatile and Simple Constrained Graph Layout

We describe a new technique for graph layout subject to constraints. Compared to previous techniques the proposed method is much faster and scalable to much larger graphs. For a graph with n nodes, m edges and c constraints it computes incremental layout in time O ( n log n + m + c ) per iteration. Also, it supports a much more powerful class of constraint: inequalities or equalities over the Euclidean distance between nodes. We demonstrate the power of this technique by application to a number of diagramming conventions which previous constrained graph layout methods could not support. Further, the constraint-satisfaction method—inspired by recent work in position-based dynamics—is far simpler to implement than previous methods.     

ImPrEd: An Improved Force‐Directed Algorithm that Prevents Nodes from Crossing Edges

PrEd [ [Ber00] ] is a force‐directed algorithm that improves the existing layout of a graph while preserving its edge crossing properties. The algorithm has a number of applications including: improving the layouts of planar graph drawing algorithms, interacting with a graph layout, and drawing Euler‐like diagrams. The algorithm ensures that nodes do not cross edges during its execution. However, PrEd can be computationally expensive and overly‐restrictive in terms of node movement. In this paper, we introduce ImPrEd: an improved version of PrEd that overcomes some of its limitations and widens its range of applicability. ImPrEd also adds features such as flexible or crossable edges, allowing for greater control over the output. Flexible edges, in particular, can improve the distribution of graph elements and the angular resolution of the input graph. They can also be used to generate Euler diagrams with smooth boundaries. As flexible edges increase data set size, we experience an execution/drawing quality trade off. However, when flexible edges are not used, ImPrEdproves to be consistently faster than PrEd.     

Genetic algorithm for the personnel assignment problem with multiple objectives

The assignment problem is a well-known graph optimization problem defined on weighted-bipartite graphs. The objective of the standard assignment problem is to maximize the summation of the weights of the matched edges of the bipartite graph. In the standard assignment problem, any node in one partition can be matched with any node in the other partition without any restriction. In this paper, variations of the standard assignment problem are defined with matching constraints by introducing structures in the partitions of the bipartite graph, and by defining constraints on these structures. According to the first constraint, the matching between the two partitions should respect the hierarchical-ordering constraints defined by forest and level graph structures produced by using the nodes of the two partitions respectively. In order to define the second constraint, the nodes of the partitions of the bipartite graph are distributed into mutually exclusive sets. The set-restriction constraint enforces the rule that in one of the partitions all the elements of each set should be matched with the elements of a set in the other partition. Even with one of these constraints the assignment problem becomes an NP-hard problem. Therefore, the extended assignment problem with both the hierarchical-ordering and set-restriction constraints becomes an NP-hard multi-objective optimization problem with three conflicting objectives; namely, minimizing the numbers of hierarchical-ordering and set-restriction violations, and maximizing the summation of the weights of the edges of the matching. Genetic algorithms are proven to be very successful for NP-hard multi-objective optimization problems. In this paper, we also propose genetic algorithm solutions for different versions of the assignment problem with multiple objectives based on hierarchical and set constraints, and we empirically show the performance of these solutions.     

The State of the Art in Multilayer Network Visualization

Modelling relationship between entities in real‐world systems with a simple graph is a standard approach. However, reality is better embraced as several interdependent subsystems (or layers). Recently, the concept of a multilayer network model has emerged from the field of complex systems. This model can be applied to a wide range of real‐world data sets. Examples of multilayer networks can be found in the domains of life sciences, sociology, digital humanities and more. Within the domain of graph visualization, there are many systems which visualize data sets having many characteristics of multilayer graphs. This report provides a state of the art and a structured analysis of contemporary multilayer network visualization, not only for researchers in visualization, but also for those who aim to visualize multilayer networks in the domain of complex systems, as well as those developing systems across application domains. We have explored the visualization literature to survey visualization techniques suitable for multilayer graph visualization, as well as tools, tasks and analytic techniques from within application domains. This report also identifies the outstanding challenges for multilayer graph visualization and suggests future research directions for addressing them.     

TreeMatrix: A Hybrid Visualization of Compound Graphs

We present a hybrid visualization technique for compound graphs (i.e. networks with a hierarchical clustering defined on the nodes) that combines the use of adjacency matrices, node‐link and arc diagrams to show the graph, and also combines the use of nested inclusion and icicle diagrams to show the hierarchical clustering. The graph visualized with our technique may have edges that are weighted and/or directed. We first explore the design space of visualizations of compound graphs and present a taxonomy of hybrid visualization techniques. We then present our prototype, which allows clusters (i.e. subtrees) of nodes to be grouped into matrices or split apart using a radial menu. We also demonstrate how our prototype can be used in the software engineering domain, and compare it to the commercial matrix‐based visualization tool Lattix using a qualitative user study.     

Using adjacency matrices to lay out larger small-world networks

Many networks exhibit small-world properties. The structure of a small-world network is characterized by short average path lengths and high clustering coefficients. Few graph layout methods capture this structure well which limits their effectiveness and the utility of the visualization itself. Here we present an extension to our novel graphTPP layout method for laying out small-world networks using only their topological properties rather than their node attributes. The Watts–Strogatz model is used to generate a variety of graphs with a small-world network structure. Community detection algorithms are used to generate six different clusterings of the data. These clusterings, the adjacency matrix and edgelist are loaded into graphTPP and, through user interaction combined with linear projections of the adjacency matrix, graphTPP is able to produce a layout which visually separates these clusters. These layouts are compared to the layouts of two force-based techniques. graphTPP is able to clearly separate each of the communities into a spatially distinct area and the edge relationships between the clusters show the strength of their relationship. As a secondary contribution, an edge-grouping algorithm for graphTPP is demonstrated as a means to reduce visual clutter in the layout and reinforce the display of the strength of the relationship between two communities.     

The Perception of Graph Properties in Graph Layouts

When looking at drawings of graphs, questions about graph density, community structures, local clustering and other graph properties may be of critical importance for analysis. While graph layout algorithms have focused on minimizing edge crossing, symmetry, and other such layout properties, there is not much known about how these algorithms relate to a user's ability to perceive graph properties for a given graph layout. In this study, we apply previously established methodologies for perceptual analysis to identify which graph drawing layout will help the user best perceive a particular graph property. We conduct a large scale (n = 588) crowdsourced experiment to investigate whether the perception of two graph properties (graph density and average local clustering coefficient) can be modeled using Weber's law. We study three graph layout algorithms from three representative classes (Force Directed ‐ FD, Circular, and Multi‐Dimensional Scaling ‐ MDS), and the results of this experiment establish the precision of judgment for these graph layouts and properties. Our findings demonstrate that the perception of graph density can be modeled with Weber's law. Furthermore, the perception of the average clustering coefficient can be modeled as an inverse of Weber's law, and the MDS layout showed a significantly different precision of judgment than the FD layout.     

Game level layout from design specification

The design of video game environments, or levels, aims to control gameplay by steering the player through a sequence of designer‐controlled steps, while simultaneously providing a visually engaging experience. Traditionally these levels are painstakingly designed by hand, often from pre‐existing building blocks, or space templates. In this paper, we propose an algorithmic approach for automatically laying out game levels from user‐specified blocks. Our method allows designers to retain control of the gameplay flow via user‐specified level connectivity graphs, while relieving them from the tedious task of manually assembling the building blocks into a valid, plausible layout. Our method produces sequences of diverse layouts for the same input connectivity, allowing for repeated replay of a given level within a visually different, new environment. We support complex graph connectivities and various building block shapes, and are able to compute complex layouts in seconds. The two key components of our algorithm are the use of configuration spaces defining feasible relative positions of building blocks within a layout and a graph‐decomposition based layout strategy that leverages graph connectivity to speed up convergence and avoid local minima. Together these two tools quickly steer the solution toward feasible layouts. We demonstrate our method on a variety of real‐life inputs, and generate appealing layouts conforming to user specifications.     

Perceptual organization in user-generated graph layouts

Many graph layout algorithms optimize visual characteristics to achieve useful representations. Implicitly, their goal is to create visual representations that are more intuitive to human observers. In this paper, we asked users to explicitly manipulate nodes in a network diagram to create layouts that they felt best captured the relationships in the data. This allowed us to measure organizational behavior directly, allowing us to evaluate the perceptual importance of particular visual features, such as edge crossings and edge-lengths uniformity. We also manipulated the interior structure of the node relationships by designing data sets that contained clusters, that is, sets of nodes that are strongly interconnected. By varying the degree to which these clusters were "masked" by extraneous edges we were able to measure observers' sensitivity to the existence of clusters and how they revealed them in the network diagram. Based on these measurements we found that observers are able to recover cluster structure, that the distance between clusters is inversely related to the strength of the clustering, and that users exhibit the tendency to use edges to visually delineate perceptual groups. These results demonstrate the role of perceptual organization in representing graph data and provide concrete recommendations for graph layout algorithms.     

空间布局的约束图方法

空间布局的自动化是智能CAD领域的研究方向之一,旨在为设计师提供智能辅助工具，用于求解在建筑、厂房设备、大规模集成电路以及产品包装等等若干领域出现的布局问题.图论方法是空间布局研究的主要途径之一.以往的布局模型由于难以充分表达知识与约束,使得设计过程与结果难以控制.本文提出一种可应用于2D及3D布局的规范约束图及层次约束图模型,给出了约束图解的存在条件.该模型可以表示精细的布局知识与约束,在一定程度上克服了以往图模型不能充分表达布局知识与约束的不足.本文还给出了基于约束图的布局生成算法.     

Multidimensional Projections for Visual Analysis of Social Networks

Visual analysis of social networks is usually based on graph drawing algorithms and tools.However,social networks are a special kind of graph in the sense that interpretation of displayed relationships is heavily dependent on context.Context,in its turn,is given by attributes associated with graph elements,such as individual nodes,edges,and groups of edges,as well as by the nature of the connections between individuals.In most systems,attributes of individuals and communities are not taken into consideration during graph layout,except to derive weights for force-based placement strategies.This paper proposes a set of novel tools for displaying and exploring social networks based on attribute and connectivity mappings.These properties are employed to layout nodes on the plane via multidimensional projection techniques.For the attribute mapping,we show that node proximity in the layout corresponds to similarity in attribute,leading to easiness in locating similar groups of nodes.The projection based on connectivity yields an initial placement that forgoes force-based or graph analysis algorithm,reaching a meaningful layout in one pass.When a force algorithm is then applied to this initial mapping,the final layout presents better properties than conventional force-based approaches.Numerical evaluations show a number of advantages of pre-mapping points via projections.User evaluation demonstrates that these tools promote ease of manipulation as well as fast identification of concepts and associations which cannot be easily expressed by conventional graph visualization alone.In order to allow better space usage for complex networks,a graph mapping on the surface of a sphere is also implemented.