A layout algorithm for undirected compound graphs

We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other possible application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions.     

Visual comparison of metabolic pathways

Biological databases contain a large amount of data about metabolic pathways, in particular about similar pathways in different species. Biologists are familiar with visual representations of metabolic pathways. Pathway diagrams help them to understand the complex relationships between the components of the pathways, to extract information from the data, and to compare pathways between different species. However, visual interfaces to metabolic pathway databases cannot cope well with the visual comparison of similar pathways in different species.This paper presents a new approach for the visual comparison of metabolic pathways which uses a graph drawing algorithm. Using layout constraints, identical parts of similar pathways in different species are placed side by side, thereby highlighting similarities and differences between these pathways. This visualization method can be used as a visual interface to databases. It supports different layout styles and has been tested with data obtained from the BioPath system and the KEGG database.     

Techniques for Edge Stratification of Complex Graph Drawings

We propose an approach that allows a user (e.g., an analyst) to explore a layout produced by any graph drawing algorithm, in order to reduce the visual complexity and clarify its presentation. Our approach is based on stratifying the drawing into layers with desired properties; to this aim, heuristics are presented. The produced layers can be explored and combined by the user to gradually acquire details. We present a user study to test the effectiveness of our approach. Furthermore, we performed an experimental analysis on popular force-directed graph drawing algorithms, in order to evaluate what is the algorithm that produces the smallest number of layers and if there is any correlation between the number of crossings and the number of layers of a graph layout. The proposed approach is useful to explore graph layouts, as confirmed by the presented user study. Furthermore, interesting considerations arise from the experimental evaluation, in particular, our results suggest that the number of layers of a graph layout may represent a reliable measure of its visual complexity. The algorithms presented in this paper can be effectively applied to graph layouts with a few hundreds of edges and vertices. For larger drawings that contain lots of crossings, the time complexity of our algorithms grows quadratically in the number of edges and more efficient techniques need to be devised. The proposed approach takes as input a layout produced by any graph drawing algorithm, therefore it can be applied in a variety of application domains. Several research directions can be explored to extend our framework and to devise new visualization paradigms to effectively present stratified drawings.     

BioPW+:基于Linked Data的生物途径数据可视化系统

自Linked Data项目被提出以来,大量的开放关联数据被发布到语义Web上,这其中就包含了许多的生物途径数据集。为了使生物学家能够有效地利用这些开放的数据集,对基于Linked Data的生物途径数据可视化系统进行研究,提出了生物途径可视化模型和展示布局方案,并且采用标识符动态映射实现了多源生物途径数据的浏览,最终开发了基于Linked Data的生物途径数据查询可视化系统——BioPW+。该系统应用语义Web技术,依靠SPARQL查询来定位生物途径的基本信息,然后基于Open PHACTS平台获取生物途径元素的详细信息,最终Web界面采用力导向图布局、Sankey图布局对生物途径数据进行展示并提供多种交互操作。与已有的仅仅基于某一特定数据库的生物途径工具相比,BioPW+系统基于Linked Data,可以同时一次性展示多个数据集中的生物途径数据及与其相关的其他生物化学数据,极大节省了时间并增强了数据的完整性。     

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.     

Constrained Graph Layout

Most current graph layout technology does not lend itself to interactive applications such as animation or advanced user interfaces. We introduce the constrained graph layout model which is better suited for interactive applications. In this model, input to the layout module includes suggested positions for nodes and constraints over the node positions in the graph to be laid out. We describe four implementations of layout modules which are based on the constrained graph layout model. The first three implementations are for undirected graph layout while the fourth is for tree layout. The implementations use active set techniques to solve the layout. Our empirical evaluation shows that they are quite fast and give reasonable layout.     

一种基于遗传算法的优化排料方法

采用遗传算法和排料约束条件相结合的方式来解决优化排料问题.详细介绍待排零件最优位置的计算方法,并对优化排料问题中的快速靠紧问题提出了一种有效的解决方案.实验结果表明提出的方法是有效的.     

UML类图层次化自动布图算法

UML类图能够有效地帮助软件工程师理解大规模的软件系统,而优化图元的空间布局可以增强类图的可读性和可理解性.由于类图中继承关系具有明显的层次特性,因此类图自动布局大多采用层次化的布图算法.此外,类图布局需要考虑相关的领域知识以及绘制准则,因而通用嵌套有向图层次化布局算法不能直接用于类图的绘制,它们必须加以扩展.但是,已有的类图层次化方法并没有考虑类图中图元的嵌套关系,这将导致自动布局方法不能处理类图中包与类、接口之间的包含关系.在考虑图绘制美学、UML类图绘制以及软件可视化等相关知识的基础上,选取了一组布     

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 linear time layout algorithm for business process models

The layout of a business process model influences how easily it can be understood. Existing layout features in process modeling tools often rely on graph representations, but do not take the specific properties of business process models into account. In this paper, we propose an algorithm that is based on a set of constraints which are specifically identified toward establishing a readable layout of a process model. Our algorithm exploits the structure of the process model and allows the computation of the final layout in linear time. We explain the algorithm, show its detailed run-time complexity, compare it to existing algorithms, and demonstrate in an empirical evaluation the acceptance of the layout generated by the algorithm. The data suggests that the proposed algorithm is well perceived by moderately experienced process modelers, both in terms of its usefulness as well as its ease of use.     

基于社区探测的层次自适应并行布局算法

针对大规模网络高效布局和递进式结构分析的需求,提出基于社区发现的多层级力导向布局算法.首先,该算法采用Louvain算法对网络进行多层级社团结构划分,根据划分结果压缩网络并进行骨架布局,确定网络整体架构;然后,采用自适应的力导向变体算法对各个社团内部的原始节点并行布局,细化社区内部网络结构,并引入补偿力减少社区划分带来的网络结构信息缺失;最后,设计了初始布局算法、改良了振颤模型来减少布局所需的迭代次数.实验结果表明,与现有网络布局算法相比,该算法能够更清晰、高效地展示大规模社交网络数据,满足大规模复杂网络可视化的需要.     

Interactive visual analysis of time-series microarray data

Estimating dynamic regulatory pathways using DNA microarray time-series can provide invaluable information about the dynamic interactions among genes and result in new methods of rational drug design. Even though several purely computational methods have been introduced for DNA pathway analysis, most of these techniques do not provide a fully interactive method to explore and analyze these dynamic interactions in detail, which is necessary to obtain a full understanding. In this paper, we present a unified modeling and visual approach focusing on visual analysis of gene regulatory pathways over time. As a preliminary step in analyzing the gene interactions, the method applies two different techniques, a clustering algorithm and an auto regressive (AR) model. This approach provides a successful prediction of the dynamic pathways involved in the biological process under study. At this level, these pure computational techniques lack the transparency required for analysis and understanding of the gene interactions. To overcome the limitations, we have designed a visual analysis method that applies several visualization techniques, including pixel-based gene representation, animation, and multi-dimensional scaling (MDS), in a new way. This visual analysis framework allows the user to quickly and thoroughly search for and find the dynamic interactions among genes, highlight interesting gene information, show the detailed annotations of the selected genes, compare regulatory behaviors for different genes, and support gene sequence analysis for the interesting genes. In order to enhance these analysis capabilities, several methods are enabled, providing a simple graph display, a pixel-based gene visualization technique, and a relation-displaying technique among gene expressions and gene regulatory pathways.     

Pathway Preserving Representation of Metabolic Networks

Improvements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while respecting biological drawing conventions. These constraints complicate the automatic generation of such visualization as it raises graph drawing issues. In this paper we propose a method to lay out the entire metabolic network while preserving the pathway information as much as possible. That method is flexible as it enables the user to define whether or not node duplication should be performed, to preserve or not the network topology. Our technique combines partitioning, node placement and edge bundling to provide a pseudo‐orthogonal visualization of the metabolic network. To ease pathway information retrieval, we also provide complementary interaction tools that emphasize relevant pathways in the entire metabolic context.     

Constraint-based document layout for the Web

Constraints can be used to specify declaratively the desired layout of a Web document. We present a system architecture in which both the author and the viewer can impose page layout constraints, some required and some preferential. The final appearance of the Web page is thus the result of negotiation between author and viewer, where this negotiation is carried out by solving the set of required and preferential constraints imposed by both parties. We identify two plausible system architectures, based on different ways of dividing the work of constraint solving between Web server and Web client. We describe a prototype constraint-based Web authoring system and viewing tool that provides linear arithmetic constraints for specifying the layout of the document as well as finite-domain constraints for specifying font size relationships. Finally, we provide an empirical evaluation of the prototype.     

结合因子图的多目的地地图布局优化

目的提出一种结合因子图的多目的地地图生成方法。方法首先,由用户选择多个感兴趣的目的地,系统根据相应规则自动地选择与目的地最相关的路线。然后,通过定义一组衡量布局质量的约束规则,采用因子图方法将定义的每条规则编码成因子,并采用Metropolis Hastings算法对由因子图构建得到的目标分布函数进行采样得到符合约束规则的多目的地地图。结果实验结果表明,使用这种方法得到的多目的地地图,可以在同一显示空间中显示多个目的地之间的道路信息,同时又保留了各目的地区域之间的拓扑和空间关系。结论提出的多目的地地图能有效地为用户提供导航,解决了当前在线地图无法在同一视野中为用户提供空间距离较远的区域道路信息的问题。     

带静不平衡约束的正交矩形布局问题的启发式模拟退火算法*

以卫星舱布局为背景,研究一类带静不平衡约束的正交矩形布局问题.借鉴拟物策略,定义矩形与矩形、矩形与圆形容器之间的嵌入度计算公式,将该问题转变为无约束的优化问题.通过将启发式格局更新策略、基于梯度法的局部搜索机制与具有全局优化功能的模拟退火算法相结合,提出一种求解带静不平衡约束的正交矩形布局问题的启发式模拟退火算法.算法中的启发式格局更新策略产生新格局和跳坑,梯度法搜索新格局附近能量更低的格局.另外,在布局优化过程中,通过在挤压弹性势能的基础上增加静不平衡量惩罚项,并采用质心平移的方法,使布局系统的静不平衡量达到约束要求.实验表明,文中算法是一种解决带静不平衡约束的正交矩形布局问题的有效算法.     

基于相似性推导的代谢数据集成

为了解决生物学代谢数据库数据集成的难题,通过结合生物数据库中代谢通路数据特点和自动模式匹配的集成方法,根据同种分子和酶在反应中有相同表现的特点,提出一种基于相似性推导的代谢通路数据集成方法。该方法通过在公共代谢数据库LIGAND、 EcoCyc和MetaCyc上的实验,验证了其有效性。最后,为了方便使用,采用动态布局的可视化用户界面,设计实现了一个代谢通路可视化集成工具。     

基于认知规律的用户界面信息布局设计方法

为进一步提高工作效率,提出一种基于人的认知因素和几何位置匹配因素的界面信息布局设计方法。建立任务模型,获取合理的待布局任务信息元素;从人的认知规律中提取3个布局原则,分别将其以定量化的形式构建数学模型,以目标函数变量的形式作用于界面布局过程中;引入带有惯性权重的粒子群算法求解目标函数,对界面中所有待布局元素的几何位置寻求最优布局方案。以隧道应急救援培训系统的决策界面布局为例,提出解决方案并验证该方法的可行性。实验结果表明,该方法具有一定的实用性。     

Drawing layered graphs with port constraints

Complex software systems are often modeled using data flow diagrams, in which nodes are connected to each other through dedicated connection points called ports. The influence a layout algorithm has on the placement of ports is determined by port constraints defined on the corresponding node.In this paper we present approaches for integrating port constraints into the layer-based approach to graph drawing pioneered by Sugiyama et al. We show how our layout algorithm, called KLay Layered, progresses from relaxed to more restricted port constraint levels as it executes, and how established algorithms for crossing minimization and edge routing can be extended to support port constraints. Compared to the previous layout algorithms supporting ports, our algorithm produces fewer edge crossings and bends and yields pleasing results.We also explain and evaluate how layout algorithms can be kept simple by using the concept of intermediate processors to structure them in a modular way. A case study integrating our layout algorithm into UC Berkeley's Ptolemy tool illustrates how KLay Layered can be integrated into Java-based applications.     

基于拉力算法的面向对象程序结构可视化研究

面向对象程序整体结构及其特性的逆向分析和可视化在软件维护、软件重用等过程中起着重要作用。现有的逆向工程工具尽管可以通过对程序代码的静态分析自动获取类模型,但是在自动布图方面仍存在一些明显的问题,特别是难以直观展现类之间的耦合性、聚集效应等程序整体结构的重要特性,从而影响其实际应用。Force-Directed Layout算法能够自然展现复杂结构的耦合关系和聚集现象,因此,将其应用于类图的逆向生成,使其在充分展示程序整体结构的同时,清晰展现类之间的耦合性和聚集效应等结构特征,为软件结构演化分析、缺陷分布分析等提供辅助支持。据此,开发了软件分析与测试工具系列QESat的子工具——基于拉力算法的类图可视化工具QESat/FCD（QualityEasy-Software Analysis and Testing Tools：Force-Directed Class Diagram）,通过实例展示了其在大型类图结构特性方面的展现效果。