432 research outputs found

    Graph Layouts by t‐SNE

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    We propose a new graph layout method based on a modification of the t-distributed Stochastic Neighbor Embedding (t-SNE) dimensionality reduction technique. Although t-SNE is one of the best techniques for visualizing high-dimensional data as 2D scatterplots, t-SNE has not been used in the context of classical graph layout. We propose a new graph layout method, tsNET, based on representing a graph with a distance matrix, which together with a modified t-SNE cost function results in desirable layouts. We evaluate our method by a formal comparison with state-of-the-art methods, both visually and via established quality metrics on a comprehensive benchmark, containing real-world and synthetic graphs. As evidenced by the quality metrics and visual inspection, tsNET produces excellent layouts

    VR-Viz: Visualization system for data visualization in VR

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    Recent years have seen fast growth in big data. The datasets are not only exponentially larger, but also more complex (multi-dimensional). Because of the scale and complexity of these datasets, their visualization poses significant challenges. As a solution, this thesis explores how virtual reality (VR) and 3D visualization can be used to visualize complex and large datasets, and proposes a visualization system for designing visualizations in VR. First, this thesis examines concepts of information visualization, VR, and 3D information visualization. Next, it explores visualization systems for 3D visualization and three examples of information visualization in VR and discusses their successes and short comings. Finally, in order to make VR information visualization accessible to a wider audience, a tool is introduced to simplify the process of designing information visualization in VR for beginners. The tool can also be used as a quick prototyping tool by more advanced users

    Contours in Visualization

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    This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

    Visualizing Set Relations and Cardinalities Using Venn and Euler Diagrams

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    In medicine, genetics, criminology and various other areas, Venn and Euler diagrams are used to visualize data set relations and their cardinalities. The data sets are represented by closed curves and the data set relationships are depicted by the overlaps between these curves. Both the sets and their intersections are easily visible as the closed curves are preattentively processed and form common regions that have a strong perceptual grouping effect. Besides set relations such as intersection, containment and disjointness, the cardinality of the sets and their intersections can also be depicted in the same diagram (referred to as area-proportional) through the size of the curves and their overlaps. Size is a preattentive feature and so similarities, differences and trends are easily identified. Thus, such diagrams facilitate data analysis and reasoning about the sets. However, drawing these diagrams manually is difficult, often impossible, and current automatic drawing methods do not always produce appropriate diagrams. This dissertation presents novel automatic drawing methods for different types of Euler diagrams and a user study of how such diagrams can help probabilistic judgement. The main drawing algorithms are: eulerForce, which uses a force-directed approach to lay out Euler diagrams; eulerAPE, which draws area-proportional Venn diagrams with ellipses. The user study evaluated the effectiveness of area- proportional Euler diagrams, glyph representations, Euler diagrams with glyphs and text+visualization formats for Bayesian reasoning, and a method eulerGlyphs was devised to automatically and accurately draw the assessed visualizations for any Bayesian problem. Additionally, analytic algorithms that instantaneously compute the overlapping areas of three general intersecting ellipses are provided, together with an evaluation of the effectiveness of ellipses in drawing accurate area-proportional Venn diagrams for 3-set data and the characteristics of the data that can be depicted accurately with ellipses

    Enabling collaborative modelling for a multi-site model-driven software development approach for electronic control units.

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    An important aspect of support for distributed work is to enable users at different sites to work collaboratively, across different sites, even different countries but where they may be working on the same artefacts. Where the case is the design of software systems, design models need to be accessible by more than one modeller at a time allowing them to work independently from each other in what can be called a collaborative modelling process supporting parallel evolution. In addition, as such design is a largely creative process users are free to create layouts which appear to better depict their understanding of certain model elements presented in a diagram. That is, that the layout of the model brings meaning which exceed the simple structural or topological connections. However, tools for merging such models tend to do so from a purely structural perspective, thus losing an important aspect of the meaning which was intended to be conveyed by the modeller. This thesis presents a novel approach to model merging which allows the preservation of such layout meaning when merging. It first presents evidence from an industrial study which demonstrates how modellers use layout to convey meanings. An important finding of the study is that diagram layout conveys domain-specific meaning and is important for modellers. This thesis therefore demonstrates the importance of diagram layout in model-based software engineering. It then introduces an approach to merging which allows for the preservation of domain-specific meaning in diagrams of models, and finally describes a prototype tool and core aspects of its implementation
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