Browsing by Subject "Information visualization"

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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
CiSE: a circular spring embedder layout algorithm
(Institute of Electrical and Electronics Engineers, 2013) Dogrusoz, U.; Belviranli, M. E.; Dilek, A.
We present a new algorithm for automatic layout of clustered graphs using a circular style. The algorithm tries to determine optimal location and orientation of individual clusters intrinsically within a modified spring embedder. Heuristics such as reversal of the order of nodes in a cluster and swap of neighboring node pairs in the same cluster are employed intermittently to further relax the spring embedder system, resulting in reduced inter-cluster edge crossings. Unlike other algorithms generating circular drawings, our algorithm does not require the quotient graph to be acyclic, nor does it sacrifice the edge crossing number of individual clusters to improve respective positioning of the clusters. Moreover, it reduces the total area required by a cluster by using the space inside the associated circle. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory, surpassing previous algorithms. The algorithm has also been successfully implemented and made publicly available as part of a compound and clustered graph editing and layout tool named Chisio. © 1995-2012 IEEE.
Open Access
CMGV: a unified framework for complexity management in graph visualization
(2023-08) Zafar, Osama
In today’s era of technological revolution, the sheer volume of data being produced poses a significant challenge for analyzing relational data of such scale, particularly in terms of visual analysis. Graphs provide an effective way of organizing and representing relational data, with nodes representing entities. In contrast, edges representing relationships, a comprehensive and intuitive view of complex large-scale data is created. A well-represented visualization of complex graphs allows users to understand relationships, uncover new insights, and discover hid-den patterns. To this end, we introduce a complexity management framework for effectively analyzing large-scale relational data represented as graphs. Existing methods for managing graph complexity work independently and may lead to in-consistencies and confusion consecutively applied. The Complexity Management Graph Visualization framework (CMGV) presents a novel approach integrating commonly used complexity management techniques while ensuring the preservation of the user’s mental map through a specialized layout algorithm. The frame-work introduces an intuitive Graph Complexity Management Model (CMGM) for both graph representation and complexity management. CMGV supports commonly utilized complexity management tasks, including filtering, hiding, showing, collapsing, and expanding graph elements. Importantly, CMGV is designed to be independent of the rendering method and can be seamlessly integrated with different graph rendering libraries. This is possible through an extension that synchronizes the graph models between the rendering library and CMGM. Our experiments performed on randomly generated graphs verify that CMGV flawlessly performs consecutive graph complexity management operations, leaving the user graph intact, and outperforms existing complexity management solutions in terms of both runtime and generally accepted graph layout criteria. It is fast enough to be used in interactive applications with small to medium-sized graphs.
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
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
A framework for applying the principles of depth perception to information visualization
(Association for Computing Machinery, 2013) Zeynep, C. Y.; Bulbul, A.; Capin, T.
During the visualization of 3D content, using the depth cues selectively to support the design goals and enabling a user to perceive the spatial relationships between the objects are important concerns. In this novel solution, we automate this process by proposing a framework that determines important depth cues for the input scene and the rendering methods to provide these cues. While determining the importance of the cues, we consider the user's tasks and the scene's spatial layout. The importance of each depth cue is calculated using a fuzzy logic-based decision system. Then, suitable rendering methods that provide the important cues are selected by performing a cost-profit analysis on the rendering costs of the methods and their contribution to depth perception. Possible cue conflicts are considered and handled in the system. We also provide formal experimental studies designed for several visualization tasks. A statistical analysis of the experiments verifies the success of our framework. © 2013 ACM.
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
A layout algorithm for undirected compound graphs
(Elsevier, 2009-03-15) Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, Emek
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. © 2008 Elsevier Inc. All rights reserved.
Open Access
Libraries and tools for viewing and editing biological maps in SBGN
(2017-07) Siper, Metin Can
Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats including Systems Biology Graphical Notation (SBGN). E ective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewing and editing tools that support these platforms and other use cases. We propose to develop a modular software architecture to meet this need. This proposed architecture includes reusable web based libraries and easily customizable and embeddable tools developed using these libraries. Our libraries include SBGNViz.js, a Cytoscape.js based library providing a renderer and an API to develop tools visualizing pathway models represented by SBGN Diagrams, and ChiSE.js, an SBGNViz.js based library to visualize and construct pathway models represented in SBGN Diagrams, and miscellaneous Cytoscape.js extensions. Our tools are built using these libraries and include SBGNViz Viewer and Newt, which are sample applications for SBGNViz.js and ChiSE.js, respectively. Newt is being developed to become a rst web based, open source SBGN editor with full support for compound structures such as molecular complexes and compartment, advanced diagramming facilities including grid and alignment guidelines, static and incremental layout, and complexity management of large maps.
Open Access
A multi-graph approach to complexity management in interactive graph visualization
(Pergamon Press, 2006-02) Dogrusoz, U.; Genc, B.
In this paper we describe a new, multi-graph approach for development of a comprehensive set of complexity management techniques for interactive graph visualization tools. This framework facilitates efficient implementation of management of multiple associated graphs with navigation links and nesting of graphs as well as ghosting, folding and hiding of unwanted graph elements. The theoretical analyses show that the involved data structures and operations on them are quite efficient, and an implementation in a graph drawing tool has proven to be successful. © 2005 Elsevier Ltd. All rights reserved.
Open Access
An orthogonal layout algorithm for small compound graphs
(2021-09) Zaman, Mubashira
Information visualization is the study of diﬀerent approaches that aid in the visualization and examination of data. Among the broad variety of diﬀerent op-tions and techniques available in this ﬁeld is “Graph Drawing”, which is regarded as the algorithmic foundation of relational information or graph visualization. Graph drawing fuses graph theory and visualization for presenting data as geo-metric shapes and for laying them out in a 2-D or 3-D space. There exist many diﬀerent types of automatic graph layouts. One such layout is the orthogonal graph layout in which edges are made up of horizontal and vertical segments. A specialized version of graphs called compound graphs are used to represent grouping or clustering of graph objects. Many orthogonal layout approaches have been presented for simple graphs but there is considerably less research available for orthogonal layout algorithms for compound graphs. In this thesis, we present C-TSM, which takes the already existing Topology-Shape-Metrics (TSM) approach and extends it to cater to 4-degree small compound graphs with uniform node sizes. First, compound graphs are converted to simple graphs and then the TSM approach is applied to it. The resulting output is compacted again in a post-processing step and then the graph is converted back to a compound graph. The results of performance tests on our algorithm show that C-TSM works considerably well on small-sized graphs and gives the output in up to a few seconds. This algorithm has been implemented in Javascript and Python and is available as a Cytoscape.js extension. The source code and a demo application are available on a GitHub repository.
Open Access
Realistic rendering and animation of a multi-layered human body model
(IEEE, 2006) Yeşil, Mehmet Şahin; Güdükbay, Uğur
A framework for realistic rendering of a multi-layered human body model is proposed in this paper. The human model is composed of three layers: skeleton, muscle, and skin. The skeleton layer, represented by a set of joints and bones, controls the animation of the human body using inverse kinematics. Muscles are represented with action lines that are defined by a set of control points. An action line applies the force produced by a muscle on the bones and on the skin mesh. The skin layer is modeled as a 3D mesh and deformed during animation by binding the skin layer to both the skeleton and muscle layers. The skin is deformed by a two-step algorithm according to the current state of the skeleton and muscle layers. Performance experiments show that it is possible to obtain real-time frame rates for a moderately complex human model containing approximately 33,000 triangles on the skin layer. © 2006 IEEE.
Open Access
Visuall: a quickly customizable library for jumpstarting visual graph analysis components
(2021-09) Canbaz, Yusuf Sait
Graph visualization is an area of information visualization, where relational data is depicted in the form of nodes (objects) and edges (links). Many people or organizations utilize graph visualization for insightful analysis and interpretation of relational data. In graph visualization, primary challenges include complexity management, eﬃcient database querying, and customization for speciﬁc domains. Visuall aims to solve these problems by providing a generic, highly customizable, and easily conﬁgurable software component for building web-based visual graph analysis tools. Essential functionalities needed by such visual analysis components include manually or automatically setting the layout of graph elements, support for nested or hierarchical drawings, eﬃcient querying of the database or client-side data, emphasizing or highlighting graph elements of interest, customization of visuals and styles, clustering, calculating graph-theoretical properties, and time-based ﬁltering of graph elements. Although Visuall provides all these functionalities out of the box for jumpstarting, customization of software for domain-speciﬁc needs is still unavoidable. Such software changes might result in complications due to unstructured code and code ignoring the invariants assumed by the orig-inal development team. To prevent these and to facilitate easily maintainable customization, Visuall provides a modular architecture. Furthermore, the devel-opers straightforwardly upgrade the software so long as the Visuall developers and the users developing visual analysis components based on Visuall maintain the provided architecture. We tested our database queries on a database that contains about half a million graph elements. We also examined our client-side operations up to a thousand graph elements. In both client-side and database operations, we observe that operations take at most several seconds, making Visuall convenient for interactive exploration and analysis of networks.