Project A01

Abstract

This paper provides an overview of uncertainty visualization in general, along with specific examples of applications in bioinformatics. Starting from a processing and interaction pipeline of visualization, components are discussed that are relevant for handling and visualizing uncertainty introduced with the original data and at later stages in the pipeline, which shows the importance of making the stages of the pipeline aware of uncertainty and allowing them to propagate uncertainty. We detail concepts and methods for visual mappings of uncertainty, distinguishing between explicit and implict representations of distributions, different ways to show summary statistics, and combined or hybrid visualizations. The basic concepts are illustrated for several examples of graph visualization under uncertainty. Finally, this review paper discusses implications for the visualization of biological data and future research directions.

Abstract

Gaze-based analysis of areas of interest (AOI) is widely used in information visualisation research to understand how people explore visualisations or assess the quality of visualisations concerning key characteristics such as memorability. However, nearby AOIs in visualisations amplify the uncertainty caused by the gaze estimation error, which strongly influences the mapping between gaze samples or fixations and different AOIs. We contribute a novel investigation into gaze uncertainty and quantify its impact on AOI-based analysis on visualisations using two novel metrics: the Flipping Candidate Rate (FCR) and Hit Any AOI Rate (HAAR). Our analysis of 40 real-world visualisations, including human gaze and AOI annotations, shows that uncertainty commonly appears in visualisations, which significantly impacts the analysis conducted in AOI-based studies. Moreover, we analysed four visualisation types and found that bar and scatter plots are commonly designed in a way that causes more uncertainty than line and pie plots in gaze-based analysis.

Abstract

We introduce inverted stippling, a method to mimic an inversion technique used by artists when performing stippling. To this end, we extend Linde-Buzo-Gray (LBG) stippling to multi-class LBG (MLBG) stippling with multiple layers. MLBG stippling couples the layers stochastically to optimize for per-layer and overall blue-noise properties. We propose a stipple-based filling method to generate solid color backgrounds for inverting areas. Our experiments demonstrate the effectiveness of MLBG in terms of reducing overlapping and intensity accuracy. In addition, we showcase MLBG with color stippling and dynamic multi-class blue-noise sampling, which is possible due to its support for temporal coherence.

Abstract

Interactive visualization is a valuable tool for introductory or advanced courses in general relativity as well as for public outreach to provide a deeper understanding of the visual implications due to curved spacetime. In particular, the extreme case of a black hole where the curvature becomes so strong that even light cannot escape, benefits from an interactive visualization where students can investigate the distortion effects by moving objects around. However, the most commonly used technique of four-dimensional general-relativistic ray tracing is still too slow for interactive frame rates. Therefore, we propose an efficient and adaptive polygon rendering method that takes light deflection and light travel time into account. An additional advantage of this method is that it provides a natural demonstration of how multiple images occur and how light travel time affects them. Finally, we present our method using three example scenes: a triangle passing behind a black hole, a sphere orbiting a black hole and an accretion disk with different inclination angles.

Abstract

Predicting and capturing an analyst’s intent behind a selection in a data visualization is valuable in two scenarios: First, a successful prediction of a pattern an analyst intended to select can be used to auto-complete a partial selection which, in turn, can improve the correctness of the selection. Second, knowing the intent behind a selection can be used to improve recall and reproducibility. In this paper, we introduce methods to infer analyst’s intents behind selections in data visualizations, such as scatterplots. We describe intents based on patterns in the data, and identify algorithms that can capture these patterns. Upon an interactive selection, we compare the selected items with the results of a large set of computed patterns, and use various ranking approaches to identify the best pattern for an analyst’s selection. We store annotations and the metadata to reconstruct a selection, such as the type of algorithm and its parameterization, in a provenance graph. We present a prototype system that implements these methods for tabular data and scatterplots. Analysts can select a prediction to auto-complete partial selections and to seamlessly log their intents. We discuss implications of our approach for reproducibility and reuse of analysis workflows. We evaluate our approach in a crowd-sourced study, where we show that auto-completing selection improves accuracy, and that we can accurately capture pattern-based intent.

Abstract

We present an approach for visual analysis of high-dimensional measurement data with varying sampling rates in the context of an experimental post-surgery study performed on a porcine surrogate model. The study aimed at identifying parameters suitable for diagnosing and prognosticating the volume state-a crucial and difficult task in intensive care medicine. In intensive care, most assessments not only depend on a single measurement but a plethora of mixed measurements over time. Even for trained experts, efficient and accurate analysis of such multivariate time-dependent data remains a challenging task. We present a linked-view post hoc visual analysis application that reduces data complexity by combining projection-based time curves for overview with small multiples for details on demand. Our approach supports not only the analysis of individual patients but also the analysis of ensembles by adapting existing techniques using non-parametric statistics. We evaluated the effectiveness and acceptance of our application through expert feedback with domain scientists from the surgical department using real-world data: the results show that our approach allows for detailed analysis of changes in patient state while also summarizing the temporal development of the overall condition. Furthermore, the medical experts believe that our method can be transferred from medical research to the clinical context, for example, to identify the early onset of a sepsis.

Abstract

We present a novel variant of parallel coordinates plots (PCPs) in which we show clusters in 2D subspaces of multivariate data and emphasize flow between them. We achieve this by duplicating and stacking individual axes vertically. On a high level, our clusterflow layout shows how data points move from one cluster to another in different subspaces. We achieve cluster-based bundling and limit plot growth through the reduction of available vertical space for each duplicated axis. Although we introduce space between clusters, we preserve the readability of intra-cluster correlations by starting and ending with the original slopes from regular PCPs and drawing Hermite spline segments in between. Moreover, our rendering technique enables the visualization of small and large data sets alike. Cluster-flow PCPs can even propagate the uncertainty inherent to fuzzy clustering through the layout and rendering stages of our pipeline. Our layout algorithm is based on A*. It achieves an optimal result with regard to a novel set of cost functions that allow us to arrange axes horizontally (dimension ordering) and vertically (cluster ordering).

Abstract

Among the many changes brought about by the COVID-19 pandemic, one of the most pressing for scientific research concerns user testing. For the researchers who conduct studies with human participants, the requirements for social distancing have created a need for reflecting on methodologies that previously seemed relatively straightforward. It has become clear from the emerging literature on the topic and from first-hand experiences of researchers that the restrictions due to the pandemic affect every aspect of the research pipeline. The current paper offers an initial reflection on user-based research, drawing on the authors' own experiences and on the results of a survey that was conducted among researchers in different disciplines, primarily psychology, human-computer interaction (HCI), and visualization communities. While this sampling of researchers is by no means comprehensive, the multi-disciplinary approach and the consideration of different aspects of the research pipeline allow us to examine current and future challenges for user-based research. Through an exploration of these issues, this paper also invites others in the VIS-as well as in the wider-research community, to reflect on and discuss the ways in which the current crisis might also present new and previously unexplored opportunities.

Abstract

Rectangular treemaps visualize hierarchical numerical data by recursively partitioning an input rectangle into smaller rectangles whose areas match the data. Numerical data often has uncertainty associated with it. To visualize uncertainty in a rectangular treemap, we identify two conflicting key requirements: (i) to assess the data value of a node in the hierarchy, the area of its rectangle should directly match its data value, and (ii) to facilitate comparison between data and uncertainty, uncertainty should be encoded using the same visual variable as the data, that is, area. We present Uncertainty Treemaps, which meet both requirements simultaneously by introducing the concept of hierarchical uncertainty masks. First, we define a new cost function that measures the quality of Uncertainty Treemaps. Then, we show how to adapt existing treemapping algorithms to support uncertainty masks. Finally, we demonstrate the usefulness and quality of our technique through an expert review and a computational experiment on real-world datasets.

Abstract

We propose a technique to represent two-dimensional data using stipples. While stippling is often regarded as an illustrative method, we argue that it is worth investigating its suitability for the visualization domain. For this purpose, we generalize the Linde-Buzo-Gray stippling algorithm for information visualization purposes to encode continuous and discrete 2D data. Our proposed modifications provide more control over the resulting distribution of stipples for encoding additional information into the representation, such as contours. We show different approaches to depict contours in stipple drawings based on locally adjusting the stipple distribution. Combining stipple-based gradients and contours allows for simultaneous assessment of the overall structure of the data while preserving important local details. We discuss the applicability of our technique using datasets from different domains and conduct observation-validating studies to assess the perception of stippled representations

Abstract

Selecting a good aspect ratio is crucial for effective 2D diagrams. There are several aspect ratio selection methods for function plots and line charts, but only few can handle general, discrete diagrams such as 2D scatter plots. However, these methods either lack a perceptual foundation or heavily rely on intermediate isoline representations, which depend on choosing the right isovalues and are time-consuming to compute. This paper introduces a general image-based approach for selecting aspect ratios for a wide variety of 2D diagrams, ranging from scatter plots and density function plots to line charts. Our approach is derived from Federer's co-area formula and a line integral representation that enable us to directly construct image-based versions of existing selection methods using density fields. In contrast to previous methods, our approach bypasses isoline computation, so it is faster to compute, while following the perceptual foundation to select aspect ratios. Furthermore, this approach is complemented by an anisotropic kernel density estimation to construct density fields, allowing us to more faithfully characterize data patterns, such as the subgroups in scatterplots or dense regions in time series. We demonstrate the effectiveness of our approach by quantitatively comparing to previous methods and revisiting a prior user study. Finally, we present extensions for ROI banking, multi-scale banking, and the application to image data.

Abstract

The IEEE SciVis 2019 Contest targets the visual analysis of structure formation in the cosmic evolution of the universe from when the universe was five million years old up to now. In our submission, we analyze high-dimensional data to get an overview, then investigate the impact of Active Galactic Nuclei (AGNs) using various visualization techniques, for instance, an adapted filament filtering method for detailed analysis and particle flow in the vicinity of filaments. Based on feedback from domain scientists on these initial visualizations, we also analyzed X-ray emissions and star formation areas. The conversion of star-forming gas to stars and the resulting increasing molecular weight of the particles could be observed.

Abstract

Foveal vision is located in the center of the field of view with a rich impression of detail and color, whereas peripheral visionoccurs on the side with more fuzzy and colorless perception. This visual acuity fall-off can be used to achieve higher frame ratesby adapting rendering quality to the human visual system. Volume raycasting has unique characteristics, preventing a directtransfer of many traditional foveated rendering techniques. We present an approach that utilizes the visual acuity fall-off toaccelerate volume rendering based on Linde-Buzo-Gray sampling and natural neighbor interpolation. First, we measure gazeusing a stationary 1200 Hz eye-tracking system. Then, we adapt our sampling and reconstruction strategy to that gaze. Finally,we apply a temporal smoothing filter to attenuate undersampling artifacts since peripheral vision is particularly sensitive tocontrast changes and movement. Our approach substantially improves rendering performance with barely perceptible changes invisual quality. We demonstrate the usefulness of our approach through performance measurements on various data se

Abstract

We present a framework for rapid prototyping of pervasive visual deficiency simulation in the context of graphical interfaces, virtual reality, and augmented reality. Our framework facilitates the emulation of various visual deficiencies for a wide range of applications, which allows users with normal vision to experience combinations of conditions such as myopia, hyperopia, presbyopia, cataract, nyctalopia, protanopia, deuteranopia, tritanopia, and achromatopsia. Our framework provides an infrastructure to encourage researchers to evaluate visualization and other display techniques regarding visual deficiencies, and opens up the field of visual disease simulation to a broader audience. The benefits of our framework are easy integration, configuration, fast prototyping, and portability to new emerging hardware. To demonstrate the applicability of our framework, we showcase a desktop application and an Android application that transform commodity hardware into glasses for visual deficiency simulation. We expect that this work promotes a greater understanding of visual impairments, leads to better product design for the visually impaired, and forms a basis for research to compensate for these impairments as everyday help

Abstract

We present a novel type of circular treemap, where we intentionally allocate extra space for additional visual variables. With this extended visual design space, we encode hierarchically structured data along with their uncertainties in a combined diagram. We introduce a hierarchical and force-based circle-packing algorithm to compute Bubble Treemaps, where each node is visualized using nested contour arcs. Bubble Treemaps do not require any color or shading, which offers additional design choices. We explore uncertainty visualization as an application of our treemaps using standard error and Monte Carlo-based statistical models. To this end, we discuss how uncertainty propagates within hierarchies. Furthermore, we show the effectiveness of our visualization using three different examples: the package structure of Flare, the S&P 500 index, and the US consumer expenditure survey

Abstract

Even if you have spent some time reading about machine learning, chances are that you have never heard of Gaussian processes. And if you have, rehearsing the basics is always a good way to refresh your memory. With this blog post we want to give an introduction to Gaussian processes and make the mathematical intuition behind them more approachable. Gaussian processes are a powerful tool in the machine learning toolbox. They allow us to make predictions about our data by incorporating prior knowledge. Their most obvious area of application is fitting a function to the data. This is called regression and is used, for example, in robotics or time series forecasting. But Gaussian processes are not limited to regression — they can also be extended to classification and clustering tasks. For a given set of training points, there are potentially infinitely many functions that fit the data. Gaussian processes offer an elegant solution to this problem by assigning a probability to each of these functions. The mean of this probability distribution then represents the most probable characterization of the data. Furthermore, using a probabilistic approach allows us to incorporate the confidence of the prediction into the regression result. We will first explore the mathematical foundation that Gaussian processes are built on — we invite you to follow along using the interactive figures and hands-on examples. They help to explain the impact of individual components, and show the flexibility of Gaussian processes. After following this article we hope that you will have a visual intuition on how Gaussian processes work and how you can configure them for different types of data.

Abstract

We present a technique that conveys the uncertainty in the secondary structure of proteins-an abstraction model based on atomic coordinates. While protein data inherently contains uncertainty due to the acquisition method or the simulation algorithm, we argue that it is also worth investigating uncertainty induced by analysis algorithms that precede visualization. Our technique helps researchers investigate differences between multiple secondary structure assignment methods. We modify established algorithms for fuzzy classification and introduce a discrepancy-based approach to project an ensemble of sequences to a single importance-weighted sequence. In 2D, we depict the aggregated secondary structure assignments based on the per-residue deviation in a collapsible sequence diagram. In 3D, we extend the ribbon diagram using visual variables such as transparency, wave form, frequency, or amplitude to facilitate qualitative analysis of uncertainty. We evaluated the effectiveness and acceptance of our technique through expert reviews using two example applications: the combined assignment against established algorithms and time-dependent structural changes originating from simulated protein dynamics.

Abstract

We present a comparison between autoencoders and variational autoencoders. For this, we describe their architecture and explain the respective advantages. To gain a deeper insight into the encoding and decoding process, we visualize the distribution of values in latent space for both models. While autoencoders are commonly used for compression, variational autoencoders typically act as generative models. We provide an interactive visualization to explore their differences. By manually modifying the latent activations, the user can directly observe the impact of different latent values on the generated output. In addition, we provide an information theoretic view on the compressive properties of autoencoders.

Abstract

We propose a tree visualization technique for comparison of structures and attributes across multiple hierarchies. Many software systems are structured hierarchically by design. For example, developers subdivide source code into libraries, modules, and functions. This design propagates to software configuration and business processes, rendering software hierarchies even more important. Often these structural elements are attributed with reference counts, code quality metrics, and the like. Throughout the entire software life cycle, these hierarchies are reviewed, integrated, debugged, and changed many times by different people so that the identity of a structural element and its attributes is not clearly traceable. We argue that pairwise comparison of similar trees is a tedious task due to the lack of overview, especially when applied to a large number of hierarchies. Therefore, we strive to visualize multiple similar trees as a whole by merging them into one supertree. To merge structures and combine attributes from different trees, we leverage the Jaccard similarity and solve a matching problem while keeping track of the origin of a structure element and its attributes. Our visualization approach allows users to inspect these supertrees using node-link diagrams and indented tree plots. The nodes in these plots depict aggregated attributes and, using word-sized line plots, detailed data. We demonstrate the usefulness of our method by exploring the evolution of software repositories and debugging data processing pipelines using provenance data.

Abstract

We present a novel uncertain network visualization technique based on node-link diagrams. Nodes expand spatially in our probabilistic graph layout, depending on the underlying probability distributions of edges. The visualization is created by computing a two-dimensional graph embedding that combines samples from the probabilistic graph. A Monte Carlo process is used to decompose a probabilistic graph into its possible instances and to continue with our graph layout technique. Splatting and edge bundling are used to visualize point clouds and network topology. The results provide insights into probability distributions for the entire network-not only for individual nodes and edges. We validate our approach using three data sets that represent a wide range of network types: synthetic data, protein-protein interactions from the STRING database, and travel times extracted from Google Maps. Our approach reveals general limitations of the force-directed layout and allows the user to recognize that some nodes of the graph are at a specific position just by chance.

Abstract

Analysis of software performance typically takes into account clock cycles and memory consumption at each sampling point in time. Although this is a valid strategy, we argue that it is also worth investigating data and control flow structures, as observed using memory traces and call stacks, because of their importance for performance engineering. In this work, we present a visual approach to memory profiling that supports analysis of memory layout, access patterns, and aliasing in correlation to program execution. Our method leverages language-agnostic dynamic code instrumentation to minimize the impact of tracing on performance, i.e., the application remains usable on commodity hardware. The profiled data is then clustered and visualized using a density-based scatter plot. If debug symbols are available, the scatter plot is augmented by a flame graph to ease linking to the high-level source code. Our visualization helps software engineers to identify runtime behavior by relating memory addresses to instruction execution. We demonstrate our approach using a set of examples revealing different memory access patterns and discuss their influence on software performance.

Abstract

Analysis and visualization of eye movement data from eye-tracking studies typically take into account gazes, fixations, and saccades of both eyes filtered and fused into a combined eye. Although this is a valid strategy, we argue that it is also worth investigating low-level eye-tracking data prior to high-level analysis, because today’s eye-tracking systems measure and infer data from both eyes separately. In this work, we present an approach that supports visual analysis and cleansing of low-level time-varying data for eye-tracking experiments. The visualization helps researchers get insights into the quality of the data in terms of its uncertainty, or reliability. We discuss uncertainty originating from eye tracking, and how to reveal it for visualization, using a comparative approach for disagreement between plots, and a density-based approach for accuracy in volume rendering. Finally, we illustrate the usefulness of our approach by applying it to eye movement data recorded with two state-of-the-art eye trackers.

Abstract

We present a visual analytics approach to support the workload management process for z/OS mainframes at IBM. This process typically requires the analysis of records consisting of 100 to 150 performance-related metrics, sampled over time. We aim at replacing the previous spreadsheet-based workflow with an easier, faster, and more scalable one regarding measurement periods and collected performance metrics. To achieve this goal, we collaborate with a developer embedded at IBM in a formative process. Based on that experience, we discuss the application background and formulate requirements to support decision making based on performance data for large-scale systems. Our visual approach helps analysts find outliers, patterns, and relations between performance metrics by data exploration through various visualizations. We demonstrate the usefulness and applicability of line plots, scatter plots, scatter plot matrices, parallel coordinates, and correlation matrices for workload management. Finally, we evaluate our approach in a qualitative user study with IBM domain experts.

Abstract

We facilitate the comparative visual analysis of eye tracking data from multiple participants with a visualization that represents the temporal changes of viewing behavior. Common approaches to visually analyze eye tracking data either occlude or ignore the underlying visual stimulus, impairing the interpretation of displayed measures. We introduce fixation-image charts: a new technique to display the temporal changes of fixations in the context of the stimulus without visual overlap between participants. Fixation durations, the distance and direction of saccades between consecutive fixations, as well as the stimulus context can be interpreted in one visual representation. Our technique is not limited to static stimuli, but can be applied to dynamic stimuli as well. Using fixation metrics and the visual similarity of stimulus regions, we complement our visualization technique with an interactive filter concept that allows for the identification of interesting fixation sequences without the time-consuming annotation of areas of interest. We demonstrate how our technique can be applied to different types of stimuli to perform a range of analysis tasks. Furthermore, we discuss advantages and shortcomings derived from a preliminary user study.

Abstract

We argue that there is a need for substantially more research on the use of generative data models in the validation and evaluation of visualization techniques. For example, user studies will require the display of representative and uncon-founded visual stimuli, while algorithms will need functional coverage and assessable benchmarks. However, data is often collected in a semi-automatic fashion or entirely hand-picked, which obscures the view of generality, impairs availability, and potentially violates privacy. There are some sub-domains of visualization that use synthetic data in the sense of generative data models, whereas others work with real-world-based data sets and simulations. Depending on the visualization domain, many generative data models are "side projects" as part of an ad-hoc validation of a techniques paper and thus neither reusable nor general-purpose. We review existing work on popular data collections and generative data models in visualization to discuss the opportunities and consequences for technique validation, evaluation, and experiment design. We distill handling and future directions, and discuss how we can engineer generative data models and how visualization research could benefit from more and better use of generative data models.

Abstract

This book discusses research, methods, and recent developments in the interdisciplinary field that spans research in visualization, eye tracking, human-computer interaction, and psychology. It presents extended versions of papers from the First Workshop on Eye Tracking and Visualization (ETVIS), which was organized as a workshop of the IEEE VIS Conference 2015. Topics include visualization and visual analytics of eye-tracking data, metrics and cognitive models, eye-tracking experiments in the context of visualization interfaces, and eye tracking in 3D and immersive environments. The extended ETVIS papers are complemented by a chapter offering an overview of visualization approaches for analyzing eye-tracking data and a chapter that discusses electrooculography (EOG) as an alternative of acquiring information about eye movements. Covering scientific visualization, information visualization, and visual analytics, this book is a valuable resource for eye-tracking researchers within the visualization community.

Abstract

Investigating user behavior involves abstracting low-level events to higher-level concepts. This requires an analyst to study individual user activities, assign codes which categorize behavior, and develop a consistent classification scheme. To better support this reasoning process of an analyst, we suggest a novel visual analytics approach which integrates rich user data including transcripts, videos, eye movement data, and interaction logs. Word-sized visualizations embedded into a tabular representation provide a space-efficient and detailed overview of user activities. An analyst assigns codes, grouped into code categories, as part of an interactive process. Filtering and searching helps to select specific activities and focus an analysis. A comparison visualization summarizes results of coding and reveals relationships between codes. Editing features support efficient assignment, refinement, and aggregation of codes. We demonstrate the practical applicability and usefulness of our approach in a case study and describe expert feedback.

Abstract

The application of eye tracking for the evaluation of humans’ viewing behavior is a common approach in psy-chological research. So far, the use of this technique for the evaluation of visual analytics and visualization isless prominent. We investigate recent scientific publications from the main visualization and visual analyticsconferences and journals, as well as related research fields that include an evaluation by eye tracking.Furthermore, we provide an overview of evaluation goals that can be achieved by eye tracking and state-of-the-art analysis techniques for eye tracking data. Ideally, visual analytics leads to a mixed-initiative cognitivesystem where the mechanism of distribution is the interaction of the user with the visualization environment.Therefore, we also include a discussion of cognitive approaches and models to include the user in the evalua-tion process. Based on our review of the current use of eye tracking evaluation in our field and the cognitivetheory, we propose directions for future research on evaluation methodology, leading to the grand challengeof developing an evaluation approach to the mixed-initiative cognitive system of visual analytics.

Abstract

Analysis and visualization of eye movement data from eye tracking studies typically take into account gazes, fixations,and saccades of both eyes filtered and fused into a combined eye. Although this is a valid strategy, we argue that it is also worthinvestigating low-level eye tracking data prior to high-level analysis, since today’s eye tracking systems measure and infer data fromboth eyes separately. In this work, we present an approach that supports visual analysis and cleansing of low-level time-varying datafor a wide range of eye tracking experiments. The visualization helps researchers get insights into the quality in terms of uncertainty—not only for both eyes in combination but each eye individually. Furthermore, we discuss uncertainty originating from eye tracking,how to reveal it for visualization and illustrate its usefulness using our approach by applying it to eye movement data formerly recordedwith a Tobii T60XL stationary eye tracker using a prototypical implementation.