Querying and creating visualizations by analogy

While there have been advances in visualization systems, particularly in multi-view visualizations and visual exploration, the process of building visualizations remains a major bottleneck in data exploration. We show that provenance metadata collected during the creation of pipelines can be reused to suggest similar content in related visualizations and guide semi-automated changes. We introduce the idea of query-by-example in the context of an ensemble of visualizations, and the use of analogies as first-class operations in a system to guide scalable interactions. We describe an implementation of these techniques in VisTrails, a publicly-available, open-source system.     

Graphs in Scientific Visualization: A Survey

Graphs represent general node‐link diagrams and have long been utilized in scientific visualization for data organization and management. However, using graphs as a visual representation and interface for navigating and exploring scientific data sets has a much shorter history, yet the amount of work along this direction is clearly on the rise in recent years. In this paper, we take a holistic perspective and survey graph‐based representations and techniques for scientific visualization. Specifically, we classify these representations and techniques into four categories, namely partition‐wise, relationship‐wise, structure‐wise and provenance‐wise. We survey related publications in each category, explaining the roles of graphs in related work and highlighting their similarities and differences. At the end, we reexamine these related publications following the graph‐based visualization pipeline. We also point out research trends and remaining challenges in graph‐based representations and techniques for scientific visualization.     

Automatic Animation for Time‐Varying Data Visualization

This paper presents a digital storytelling approach that generates automatic animations for time‐varying data visualization. Our approach simulates the composition and transition of storytelling techniques and synthesizes animations to describe various event features. Specifically, we analyze information related to a given event and abstract it as an event graph, which represents data features as nodes and event relationships as links. This graph embeds a tree‐like hierarchical structure which encodes data features at different scales. Next, narrative structures are built by exploring starting nodes and suitable search strategies in this graph. Different stages of narrative structures are considered in our automatic rendering parameter decision process to generate animations as digital stories. We integrate this animation generation approach into an interactive exploration process of time‐varying data, so that more comprehensive information can be provided in a timely fashion. We demonstrate with a storm surge application that our approach allows semantic visualization of time‐varying data and easy animation generation for users without special knowledge about the underlying visualization techniques.     

Topology‐based Visualization of Transformation Pathways in Complex Chemical Systems

Studying transformation in a chemical system by considering its energy as a function of coordinates of the system's components provides insight and changes our understanding of this process. Currently, a lack of effective visualization techniques for high‐dimensional energy functions limits chemists to plot energy with respect to one or two coordinates at a time. In some complex systems, developing a comprehensive understanding requires new visualization techniques that show relationships between all coordinates at the same time. We propose a new visualization technique that combines concepts from topological analysis, multi‐dimensional scaling, and graph layout to enable the analysis of energy functions for a wide range of molecular structures. We demonstrate our technique by studying the energy function of a dimer of formic and acetic acids and a LTA zeolite structure, in which we consider diffusion of methane.     

Context Aware Terrain Visualization for Wayfinding and Navigation

To assist wayfinding and navigation, the display of maps and driving directions on mobile devices is nowadays commonplace. While existing system can naturally exploit GPS information to facilitate orientation, the inherently limited screen space is often perceived as a drawback compared to traditional street maps as it constrains the perception of contextual information. Moreover, occlusion issues add to this problem if the environment is shown from the popular egocentric perspective. In this paper we describe an interactive visualization system that addresses these problems by reallocating the available screen space. At the heart of our system are three novel visualization techniques: First, we propose a non‐standard perspective that allows to blend between the familiar pedestrian perspective and a standard map depiction with reduced occlusion. Second, we derive an efficient deformation technique that allows an interactive allocation of screen space to areas of interest like e.g. nearby touristic attractions. Finally, a path adaptive isometric perspective is proposed that reveals otherwise hidden facades in top‐down views. We describe efficient implementations of all techniques and exemplify our interactive system on real world urban models.     

AVOCADO: Visualization of Workflow–Derived Data Provenance for Reproducible Biomedical Research

A major challenge in data‐driven biomedical research lies in the collection and representation of data provenance information to ensure that findings are reproducibile. In order to communicate and reproduce multi‐step analysis workflows executed on datasets that contain data for dozens or hundreds of samples, it is crucial to be able to visualize the provenance graph at different levels of aggregation. Most existing approaches are based on node‐link diagrams, which do not scale to the complexity of typical data provenance graphs. In our proposed approach, we reduce the complexity of the graph using hierarchical and motif‐based aggregation. Based on user action and graph attributes, a modular degree‐of‐interest (DoI) function is applied to expand parts of the graph that are relevant to the user. This interest‐driven adaptive approach to provenance visualization allows users to review and communicate complex multi‐step analyses, which can be based on hundreds of files that are processed by numerous workflows. We have integrated our approach into an analysis platform that captures extensive data provenance information, and demonstrate its effectiveness by means of a biomedical usage scenario.     

State‐of‐the‐Art in GPU‐Based Large‐Scale Volume Visualization

This survey gives an overview of the current state of the art in GPU techniques for interactive large‐scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga‐, tera‐ and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out‐of‐core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e. ‘output‐sensitive’ algorithms and system designs. This leads to recent output‐sensitive approaches that are ‘ray‐guided’, ‘visualization‐driven’ or ‘display‐aware’. In this survey, we focus on these characteristics and propose a new categorization of GPU‐based large‐scale volume visualization techniques based on the notions of actual output‐resolution visibility and the current working set of volume bricks—the current subset of data that is minimally required to produce an output image of the desired display resolution. Furthermore, we discuss the differences and similarities of different rendering and data traversal strategies in volume rendering by putting them into a common context—the notion of address translation. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we present in this survey.     

A Visualization‐Based Analysis System for Urban Search & Rescue Mission Planning Support

We propose a visualization system for incident commanders (ICs) in urban search and rescue scenarios that supports path planning in post‐disaster structures. Utilizing point cloud data acquired from unmanned robots, we provide methods for the assessment of automatically generated paths. As data uncertainty and a priori unknown information make fully automated systems impractical, we present the IC with a set of viable access paths, based on varying risk factors, in a 3D environment combined with visual analysis tools enabling informed decision making and trade‐offs. Based on these decisions, a responder is guided along the path by the IC, who can interactively annotate and reevaluate the acquired point cloud and generated paths to react to the dynamics of the situation. We describe visualization design considerations for our system and decision support systems in general, technical realizations of the visualization components, and discuss the results of two qualitative expert evaluation; one online study with nine search and rescue experts and an eye‐tracking study in which four experts used the system on an application case.     

Analysis of Decadal Climate Predictions with User‐guided Hierarchical Ensemble Clustering

In order to gain probabilistic results, ensemble simulation techniques are increasingly applied in the weather and climate sciences (as well as in various other scientific disciplines). In many cases, however, only mean results or other abstracted quantities such as percentiles are used for further analyses and dissemination of the data. In this work, we aim at a more detailed visualization of the temporal development of the whole ensemble that takes the variability of all single members into account. We propose a visual analytics tool that allows an effective analysis process based on a hierarchical clustering of the time‐dependent scalar fields. The system includes a flow chart that shows the ensemble members' cluster affiliation over time, reflecting the whole cluster hierarchy. The latter one can be dynamically explored using a visualization derived from a dendrogram. As an aid in linking the different views, we have developed an adaptive coloring scheme that takes into account cluster similarity and the containment relationships. Finally, standard visualizations of the involved field data (cluster means, ground truth data, etc.) are also incorporated. We include results of our work on real‐world datasets to showcase the utility of our approach.     

Visualizing Strain Anisotropy in Mantle Flow Fields

The evolution of strain and development of material anisotropy in models of the Earth’s mantle flow convey important information about how to interpret the geometric relationship between observation of seismic anisotropy and the actual mantle flow field. By combining feature extraction techniques such as path line integration and tensor accumulation, we compute time‐varying strain vector fields that build the foundation for a number of feature extraction and visualization techniques. The proposed field segmentation, clustering, histograms and multi‐volume visualization techniques facilitate an intuitive understanding of three‐dimensional strain in such flow fields, overcoming limitations of previous methods such as 2‐D line plots and slicing. We present applications of our approach to an artificial time varying flow data set and a real world example of stationary flow in a subduction zone and discuss the challenges of processing these geophysical data sets as well as the insights gained.     

Understanding provenance black boxes

Current provenance stores associated with workflow management systems (WfMSs) capture enough coarse-grained information to describe which datasets were used and which processes were run. While this information is enough to rebuild a workflow run, it is not enough to facilitate user understanding. Because the data is manipulated via a series of black boxes, it is often impossible for a human to understand what happened to the data. In this work, we highlight the missing information that can assist user understanding. Unfortunately, provenance information is already very complex and difficult for a user to comprehend, which can be exacerbated by adding the extra information needed for deeper blackbox understanding. In order to alleviate this, we develop a model of provenance answers that follow a “roll up”, “drill down” strategy. We evaluate these techniques to determine if users have better understanding of provenance information. We show how this information can be captured by workflow management systems, and that the structures and information needed for this model are a negligible addition to standard provenance stores. Finally, we implement these techniques in a real provenance system, and evaluate implementation feasibility.     

Map‐based Visualizations Increase Recall Accuracy of Data

We investigate the memorability of data represented in two different visualization designs. In contrast to recent studies that examine which types of visual information make visualizations memorable, we examine the effect of different visualizations on time and accuracy of recall of the displayed data, minutes and days after interaction with the visualizations. In particular, we describe the results of an evaluation comparing the memorability of two different visualizations of the same relational data: node‐link diagrams and map‐based visualization. We find significant differences in the accuracy of the tasks performed, and these differences persist days after the original exposure to the visualizations. Specifically, participants in the study recalled the data better when exposed to map‐based visualizations as opposed to node‐link diagrams. We discuss the scope of the study and its limitations, possible implications, and future directions.     

科学工作流溯源表示和查询技术综述

溯源管理是科学工作流系统的核心功能之一。科学工作流语境下的溯源,可分为工作流定义溯源和工作流执行溯源,分别描述工作流定义和执行阶段的元数据、过程依赖及数据演化。本文重点关注工作流定义溯源和执行溯源的表示及查询技术,并阐释针对科学工作流领域内独有问题,如"黑盒"问题、依赖区分问题以及细粒度溯源等问题的解决方案。文中还将介绍现存的一些面向科学工作流的溯源系统,并提出对溯源技术未来的展望。     

A Survey on Multimodal Medical Data Visualization

Multi‐modal data of the complex human anatomy contain a wealth of information. To visualize and explore such data, techniques for emphasizing important structures and controlling visibility are essential. Such fused overview visualizations guide physicians to suspicious regions to be analysed in detail, e.g. with slice‐based viewing. We give an overview of state of the art in multi‐modal medical data visualization techniques. Multi‐modal medical data consist of multiple scans of the same subject using various acquisition methods, often combining multiple complimentary types of information. Three‐dimensional visualization techniques for multi‐modal medical data can be used in diagnosis, treatment planning, doctor–patient communication as well as interdisciplinary communication. Over the years, multiple techniques have been developed in order to cope with the various associated challenges and present the relevant information from multiple sources in an insightful way. We present an overview of these techniques and analyse the specific challenges that arise in multi‐modal data visualization and how recent works aimed to solve these, often using smart visibility techniques. We provide a taxonomy of these multi‐modal visualization applications based on the modalities used and the visualization techniques employed. Additionally, we identify unsolved problems as potential future research directions.     

Ontology engineering in provenance enablement for the National Climate Assessment

The National Climate Assessment of the U.S. Global Change Research Program (USGCRP) analyzes and presents the impacts of climate change on the United States. The provenance information in the assessment is important because the assessment findings are of great public and academic concern and are used in policy and decision-making. By applying a use case-driven iterative methodology, we developed information models and ontology to represent the content structure of the recent National Climate Assessment draft report and its associated provenance information. We tested the ontology by using it in pilot systems serving information about instances of chapters, scientific findings, figures, tables, images, datasets, references, people, and organizations, etc. in the draft report, as well as interrelationships among those instances. The results successfully help users trace provenance in the draft report, such as finding all the journal articles from which a figure in the report was derived. The provenance information in our work was maintained in the context of the “Web of Data”. In addition to the pilot systems we developed, other tools and services are also able to retrieve and utilize the provenance information. Our work is part of a Global Change Information System coordinated by the USGCRP that will eventually cover provenance information for the entire scope of global change research. Such a system will greatly increase understanding, credibility and trust in the global change research and foster reproducibility of scientific results and conclusions.     

Compact visualization of Java program execution

The context of this work is a practical, open‐source visualization system, called JIVE, that supports two forms of runtime visualizations of Java programs – object diagrams and sequence diagrams. They capture, respectively, the current execution state and execution history of a Java program. These diagrams are similar to those found in the UML for specifying design–time decisions. In our work, we construct these diagrams at execution time, thereby ensuring continuity of notation from design to execution. In so doing, a few extensions to the UML notation are proposed in order to better represent runtime behavior. As sequence diagrams can become long and unwieldy, we present techniques for their compact representation. A key result in this paper is a novel labeling scheme based upon regular expressions to compactly represent long sequences and an O(r²) algorithm for computing these labels, where r is the length of the input sequence, based upon the concept of ‘tandem repeats’ in a sequence. Horizontal compaction greatly helps minimize the extent of white space in sequence diagrams by the elimination of object lifelines and also by grouping lifelines together. We propose a novel extension to the sequence diagram to deal with out‐of‐model calls when the lifelines of certain classes of objects are filtered out of the visualization, but method calls may occur between in‐model and out‐of‐model calls. The paper also presents compaction techniques for multi‐threaded Java execution with different forms of synchronization. Finally, we present experimental results from compacting the runtime visualizations of a variety of Java programs and execution trace sizes in order to demonstrate the practicality and efficacy of our techniques. Copyright © 2016 John Wiley & Sons, Ltd.     

Ethnographic notes on visualization practices in tissue engineering research

Visual information is central to several of the scientific disciplines. This paper studies how scientists working in a multidisciplinary field produce scientific evidence through building and manipulating scientific visualizations. Using ethnographic methods, we studied visualization practices of eight scientists working in the domain of tissue engineering research. Tissue engineering is an upcoming field of research that deals with replacing or regenerating human cells, tissues, or organs to restore or establish normal function. We spent 3 months in the field, where we recorded laboratory sessions of these scientists and used semi-structured interviews to get an insight into their visualization practices. From our results, we elicit two themes characterizing their visualization practices: multiplicity and physicality. In this article, we provide several examples of scientists’ visualization practices to describe these two themes and show that multimodality of such practices plays an important role in scientific visualization.     

Visual Supercomputing: Technologies, Applications and Challenges

If we were to have a Grid infrastructure for visualization, what technologies would be needed to build such an infrastructure, what kind of applications would benefit from it, and what challenges are we facing in order to accomplish this goal? In this survey paper, we make use of the term ‘visual supercomputing’ to encapsulate a subject domain concerning the infrastructural technology for visualization. We consider a broad range of scientific and technological advances in computer graphics and visualization, which are relevant to visual supercomputing. We identify the state‐of‐the‐art technologies that have prepared us for building such an infrastructure. We examine a collection of applications that would benefit enormously from such an infrastructure, and discuss their technical requirements. We propose a set of challenges that may guide our strategic efforts in the coming years.