Visualizing Evolving Trees

Evolving trees arise in many real-life scenarios from computer file systems and dynamic call graphs, to fake news propagation and disease spread. Most layout algorithms for static trees, however, do not work well in an evolving setting (e.g., they are not designed to be stable between time steps). Dynamic graph layout algorithms are better suited to this task, although they often introduce unnecessary edge crossings. With this in mind we propose two methods for visualizing evolving trees that guarantee no edge crossings, while optimizing (1) desired edge length realization, (2) layout compactness, and (3) stability. We evaluate the two new methods, along with four prior approaches (two static and two dynamic), on real-world datasets using quantitative metrics: stress, desired edge length realization, layout compactness, stability, and running time. The new methods are fully functional and available on github

SIGHT - A Tool for Building Multi-Media Structured-Document Interactive Editing and Formatting Applications

SIGHT is a tool for building applications that edit and format multi-media structured documents. The media supported include text, line graphics, handwriting, images and audio. These information media are maintained in a single integrated hierarchical database. The document architecture models documents as trees in which nodes can be shared, i.e., as directed acyclic graphs. For each document there is a logical (or abstract) represention tree and one or more physical (or layout) representation trees. A physical representation is the result of applying the formatter to a logical representation. Both trees are separate but share document content data. The physical representation is displayable and printable, but all editing effectively occurs in the logical representation. Any number of document types can be supported. A document type is defined by the node types it can contain, by how these node types can be hierarchically organized, by what each node type can contain and by the format specifications used in formatting the document. SIGHT provides applications a language to define new document types, a Core Editor, various specialized editors and a formatter. The Core Editor is further subdivided into a generic Tree Editor and a generic Node Editor. Both are not limited by document types but are sensitive to them. The Core Editor is the primary editing system

Top-Down Drawings of Compound Graphs

Bottom-up layout algorithms for compound graphs are suitable for presenting the microscale view of models and are often used in model-driven engineering. However, they have difficulties at the macroscale where maintaining the overview of large models becomes challenging. We propose top-down layout, which utilizes scale to hide low-level details at high zoom levels. The entire high-level view can fit into the viewport and remain readable, while the ability to zoom in to see the details is still maintained. Top-down layout is an abstract high-level layout process that can be used in conjunction with classic layout algorithms to produce visually compelling and readable diagrams of large compound graphs

Visualization of Barrier Tree Sequences Revisited

The increasing complexity of models for prediction of the native spatial structure of RNA molecules requires visualization methods that help to analyze and understand the models and their predictions. This paper improves the visualization method for sequences of barrier trees previously published by the authors. The barrier trees of these sequences are rough topological simplifications of changing folding landscapes – energy landscapes in which kinetic folding takes place. The folding landscapes themselves are generated for RNA molecules where the number of nucleotides increases. Successive landscapes are thus correlated and so are the corresponding barrier trees. The landscape sequence is visualized by an animation of a barrier tree that changes with time. The animation is created by an adaption of the foresight layout with tolerance algorithm for dynamic graph layout problems. Since it is very general, the main ideas for the adaption are presented: construction and layout of a supergraph, and how to build the final animation from its layout. Our previous suggestions for heuristics lead to visually unpleasing results for some datasets and, generally, suffered from a poor usage of available screen space. We will present some new heuristics that improve the readability of the final animation

A layout algorithm for signaling pathways

Cataloged from PDF version of article.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. (C) 2004 Elsevier Inc. All rights reserved

Contours in Visualization

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

Using graphical style and visibility constraints for a meaningful layout in visual programming interfaces

In the expanding field of visual applications, layout design and graphical editing tasks are crucial points. In this paper, we address the incorporation of AI aspects in the visual software design process and the automatic layout and beautification of informational graphics such as visual programs and chart diagrams. Since layout in dynamic settings frequently requires a direct manipulation responsiveness, an incremental redesign of the generated visual material is necessary. Following our previous work on constraint-based multimodal design, we show how powerful constraint processing techniques, such as constraint hierarchies and dynamic constraint satisfaction, can be applied to visual programming environments in order to maintain graphical style and consistency for a meaningful layout. We describe InLay, a system for constraint-based presenting and editing visual programs. Finally, we will have a short look at some extensions with regard to advanced interaction and visualization techniques