Browsing by Subject "Graph layout"

Now showing 1 - 12 of 12

Open Access
Algorithms for layout of disconnected graphs
(Elsevier, 2000) Doğrusöz, Uğur
We present efficient algorithms for the layout of disconnected objects in a graph (isolated nodes and components) for a specified aspect ratio. These linear and near-linear algorithms are based on alternate-bisection and two-dimensional packing methodologies. In addition, the parameters that affect the performance of these algorithms as well as the circumstances under which the two methodologies perform well are analyzed.
Open Access
Automated layout of process description maps drawn in systems biology graphical notation = Systems biology graphical notation kullanılarak çizilen proses diyagramlarının otomatik yerleştirilmesi
(2014) Genç, Begüm
Evolving technology has increased the focus on genomics. The combination of today’s advanced studies with decades of molecular biology research yield in huge amount of pathway data. These models can be used to improve high-throughput data analysis by linking correlation to the causation, shedding light on many complex diseases. In order to prevent ambiguity and ensure regularity of the research, a need for using a standard notation has emerged. Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modellers and computer scientists with the intention of enabling scientists to represent networks, including models of cellular processes, in a standard, unambiguous way. SBGN is formed of three languages: process, entity relationship and activity flow. This research is focused on its process diagram branch. Automated layout is commonly used to clearly visualize the information represented by graphs. Considering the fact that, biological pathways includes nested structures (e.g., nucleoplasms), we have made use of a force-directed automatic layout algorithm called Compound Spring Embedder (CoSE), which supports the compound graph structures. On top of this layout structure, we have developed a specialized layout algorithm called SBGN-PD layout. SBGN-PD layout enhancements mainly include properly tiling of complex members and disconnected molecules, placement of product and substrate edges on the opposite sides of a process node without disturbing the force-directed structure of the algorithm.
Open Access
Chisio : a visual framework for compound graph editing and layout
(2007) Küçükkeçeci, Cihan
Graphs are data models, widely used in many areas from networking to biology to computer science. Visualization, interactive editing ability and layout of graphs are critical issues when analyzing the underlying relational information. There are many commercial and non-commercial graph visualization tools. However, overall support for compound or hierarchically organized graph representations is very limited. We introduce a new open-source editing and layout framework named Chisio for compound graphs. Chisio is developed as a free, easy-to-use and powerful academic graph visualization tool, supporting various automatic layout algorithms. It is written in Java and based on Eclipse’s Graphical Editing Framework (GEF). Chisio can be used as a finished generic compound graph editor with standard graph editing facilities such as zoom, scroll, add or remove graph objects, move, and resize. Object property and layout options dialogs are provided to modify existing graph object properties and layout options, respectively. In addition, printing or saving the current drawing as a static image and persistent storage facilities are supported. Saved graphs or GraphML formatted files created by other tools can be loaded into Chisio. Furthermore, a highlight mechanism is provided to emphasize subgraphs of users interest. The framework has an architecture suitable for easy customization of the tool for end-users’ specific needs as well. Also Chisio offers several layout styles from the basic spring embedder to hierarchical layout to compound spring embedder to circular layout. Furthermore, new algorithms are straightforward to add, making Chisio an ideal test environment for layout algorithm developers.
Open Access
A compound graph layout algorithm with support for ports
(2020-10) Okka, Alihan
Information visualization is a eld of study that aims to represent abstract data in an aesthetically pleasing and easy to comprehend visual manner. Various approaches and standards have been created to reinforce the discovery of unstructured insights that are limited to human cognition via visual depictions. Complex systems and processes are often modelled as graphs since it would be di cult to describe in text. A type of visualization, graph drawing, addresses the notion of creating geometric representations of graphs. There are plentiful research directed to designing automatic layout algorithms for visualizing graphs. Nevertheless, a limited number of studies utilize ports, which are dedicated connection points on the locations where edge ends link to their incident nodes. We propose a new automatic layout algorithm named CoSEP supporting port constraints on compound nodes used for nested levels of abstractions in data. The CoSEP algorithm is based on a force-directed algorithm, Compound Spring Embedder (CoSE). Additional heuristics and force types are introduced on top of existing physical model. Using CoSE's layout structure as a baseline enables CoSEP to handle non-uniform node sizes, arbitrary levels of nesting, and intergraph edges that may span multiple levels of nesting. Our experiments show that CoSEP signi cantly improves the quality of the layouts for compound graphs with port constraints with respect to commonly accepted graph drawing criteria, while running in at most a few seconds, suitable for use in interactive applications for small to medium sized graphs. The CoSEP algorithm is implemented in JavaScript as a Cytoscape.js extension, and the sources along with a demo are available on the associated GitHub repository.
Open Access
Connectivity models for optoelectronic computing systems
(Springer, Berlin, Heidelberg, 2000-05) Özaktaş, Haldun M.; Rolim, J.
Rent’s rule and related concepts of connectivity such as dimensionality, line-length distributions, and separators have found great use in fundamental studies of different interconnection media, including superconductors and optics, as well as the study of optoelectronic computing systems. In this paper generalizations for systems for which the Rent exponent is not constant throughout the interconnection hierarchy are provided. The origin of Rent’s rule is stressed as resulting from the embedding of a high-dimensional information flow graph to two- or three-dimensional physical space. The applicability of these traditionally solid-wire-based concepts to free-space optically interconnected systems is discussed.
Open Access
CoSEP: a compound spring embedder layout algorithm with support for ports
(Sage Publications, 2021-07-01) Okka, Alihan; Doğrusöz, Uğur; Balcı, Hasan
This paper describes a new automatic layout algorithm named CoSEP for compound graphs with port constraints. The algorithm works by extending the physical model of a previous algorithm named CoSE by defining additional force types and heuristics for constraining edges to connect to certain user-defined locations on end nodes. Similar to its predecessor, CoSEP also accounts for non-uniform node dimensions and arbitrary levels of nesting via compound nodes. Our experiments show that CoSEP significantly improves the quality of the layouts for compound graphs with port constraints with respect to commonly accepted graph drawing criteria while running reasonably fast, suitable for use in interactive applications for small to medium-sized (up to 500 nodes) graphs. A complete JavaScript implementation of CoSEP as a Cytoscape.js extension along with a demo page is freely available at https://github.com/iVis-at-Bilkent/cytoscape.js-cosep.
Open Access
Extending constrained hierarchical layout for drawing UML activity diagrams
(2002) Yüksel, H. Mehmet
While modeling an object-oriented software, a visual language called Unified Modeling Language (UML) may be used. UML is a language and notation for specification, construction, visualization, and documentation of models of software systems. It consists of a variety of diagrams including class diagrams and activity diagrams. Graph layout has become an important area of research in Computer Science for the last couple of decades. There is a wide range of applications for graph layout including data structures, databases, software engineering, VLSI technology, electrical engineering, production planning, chemistry, and biology. Diagrams are more effective means of expressing relational information and automatic graph layout makes them to be more comprehensible. In other words, with graph layout techniques, the readability and the comprehensibility of the graphs increases and the complexity is reduced. UML diagrams are no exception. In this thesis, we present graph layout algorithms for UML activity diagrams based on constrained hierarchical layout. We use an existing implementation of constrained hierarchical layout to draw UML activity diagrams. We analyze and present the results of these new layout algorithms.
Open Access
Fast compound graph layout with constraint support
(2022-08) Balcı, Hasan
Visual analysis of relational data becomes more challenging in today's world as the amount of data increases exponentially. Effective visual display of such data is therefore a key requirement to simplify the analysis process. Compound graphs present a practical structure for both representing the relational data with varying levels of groupings or abstractions and managing its complexity. In addition, a good automatic layout of these graphs lets users understand relationships, uncover new insights and find important patterns hidden in the data. To this end, we introduce a new layout algorithm named fCoSE (fast Compound Spring Embedder) for compound graphs with support for user-specified placement constraints. fCoSE combines the speed of spectral layout with the aesthetics and quality of force-directed layout while satisfying specified constraints and properly displaying compound structures. The algorithm first generates a draft layout with the help of a spectral approach, then enforces placement constraints by using newly introduced heuristics and finally polishes the layout via a force-directed layout algorithm modified to maintain enforced constraints. Our experiments performed on both real-life and randomly generated graphs verify that fCoSE outperforms its competitors in terms of both speed and generally accepted graph layout criteria and is fast enough to be used in interactive applications with small to medium-sized graphs.
Open Access
fCoSE: A fast compound graph layout algorithm with constraint support
(IEEE, 2021-07-07) Balcı, Hasan; Doğrusöz, Uğur
Visual analysis of relational information is vital in most real-life analytics applications. Automatic layout is a key requirement for effective visual display of such information. This paper introduces a new layout algorithm named fCoSE for compound graphs showing varying levels of groupings or abstractions with support for user-specified placement constraints. fCoSE builds on a previous compound spring embedder layout algorithm and makes use of the spectral graph drawing technique for producing a quick draft layout, followed by phases where constraints are enforced and compound structures are properly shown while polishing the layout with respect to commonly accepted graph layout criteria. Experimental evaluation verifies that fCoSE produces quality layouts and is fast enough for interactive applications with small to medium-sized graphs by combining the speed of spectral graph drawing technique with the quality of force-directed layout algorithms while satisfying specified constraints and properly displaying compound structures. An implementation of fCoSE along with documentation and a demo page is freely available on GitHub.
Open Access
HySE: a spring embedder approach for layout of hybrid graphs
(2023-09) Islam, Hamza
In recent times, the growth of data has been exponential, making the visual analysis of relational data progressively complex. Presenting such data in a visually appealing manner can help simplify the analysis process. Hybrid graphs, comprising a central directed or hierarchical part and interconnected undirected components, offer a practical structure for representing relational data with varying levels of abstraction while managing its complexity. To comprehend the relationships in data, discover insights, and get important patterns, a well-optimized graph layout for such graphs is needed. In response, we present HySE (Hybrid Spring Embedder), a novel graph layout algorithm tailored for hybrid graphs. HySE makes use of a holistic approach based on the popular spring embedder to achieve the aesthetics and quality of an optimized force-directed layout, not only on the undirected part of the graph but also on the hierarchy while maintaining the cohesion between both directed and undirected elements of the graph. The layout algorithm assumes the rank information of directed graph elements is already calculated with one of the popular approaches. Then, it finds appropriate initial positions and uses a force-directed layout technique to integrate the undirected parts into the layout, applying spring forces to model the edges, and repulsive electric forces for the nodes. Iteratively, HySE converges to an equilibrium state with minimized energy, resulting in visually pleasing and interpretable layouts for intricate hybrid graphs. Experiments performed on graphs, generated randomly through a well-designed process, validate that HySE performs as well as the state-of-the-art algorithms in terms of quality. It also matches the speed of well-established algorithms as well in small-to-medium-sized graphs.
Open Access
A layout algorithm for signaling pathways
(Elsevier, 2006-01-20) Genç, Burkay; Doğrusöz, Uğur
Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named Patika, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. Patika version 1.0 beta is available upon request at http://www.patika.org. © 2004 Elsevier Inc. All rights reserved.
Open Access
VISIBIOweb : a web-based visualization and layout service for biological pathways
(2009) Dilek, Alptuğ
A biological pathway is a representation of biological reactions between molecules in a living cell. At present, there are hundreds of Internet-accessible databases storing biological pathway data. Exchanging, handling, and storing this data are crucial in terms of both providing understandability and allowing further enhancements on the gathered data. As a result of this necessity, many biological models were developed to cluster the data in a meaningful manner under a semantically reasonable hierarchy. As the amount and complexity of the data increases, visualization of pathways becomes inevitable. Graphs are inherently suitable for modeling pathways. The task of creating a visual representation for pathways dynamically requires methods from the area of graph visualization. As a result, many software systems, which can interpret the pathway data with a graph structure and visualize the constructed graph, emerged. However, many of these software systems are insufficient due to poor complexity handling of the underlying model, lack of visual standardization or long installation steps. In this thesis, we introduce VISIBIOweb, a new open-source and web-based visualization service for biological pathway models stored in BioPAX (Biological Pathways Exchange Language) format. VISIBIOweb runs on Apache Tomcat server and is implemented in Java based on Eclipse GEF (Graphical Editing Framework). Google Maps API is used on the client side as the core component to visualize the representation constructed on the server. VISIBIOweb supports basic graph viewing functionalities such as zooming, scrolling, and selection of graph objects. The inspector window is provided to view the properties of the selected graph object. Once the view for the uploaded biological model is created, it can be stored as a static image. The biological models can also be persisted and embedded within other web sites just like Google Maps. The layout information of the constructed graph is also provided in an XML-based format. The introduction of such a format is a good starting point to develop an official layout extension for BioPAX format.