Bladder Runner: Visual Analytics for the Exploration of RT‐Induced Bladder Toxicity in a Cohort Study

We present the Bladder Runner, a novel tool to enable detailed visual exploration and analysis of the impact of bladder shape variation on the accuracy of dose delivery, during the course of prostate cancer radiotherapy (RT). Our tool enables the investigation of individual patients and cohorts through the entire treatment process, and it can give indications of RT‐induced complications for the patient. In prostate cancer RT treatment, despite the design of an initial plan prior to dose administration, bladder toxicity remains very common. The main reason is that the dose is delivered in multiple fractions over a period of weeks, during which, the anatomical variation of the bladder – due to differences in urinary filling – causes deviations between planned and delivered doses. Clinical researchers want to correlate bladder shape variations to dose deviations and toxicity risk through cohort studies, to understand which specific bladder shape characteristics are more prone to side effects. This is currently done with Dose‐Volume Histograms (DVHs), which provide limited, qualitative insight. The effect of bladder variation on dose delivery and the resulting toxicity cannot be currently examined with the DVHs. To address this need, we designed and implemented the Bladder Runner, which incorporates visualization strategies in a highly interactive environment with multiple linked views. Individual patients can be explored and analyzed through the entire treatment period, while inter‐patient and temporal exploration, analysis and comparison are also supported. We demonstrate the applicability of our presented tool with a usage scenario, employing a dataset of 29 patients followed through the course of the treatment, across 13 time points. We conducted an evaluation with three clinical researchers working on the investigation of RT‐induced bladder toxicity. All participants agreed that Bladder Runner provides better understanding and new opportunities for the exploration and analysis of the involved cohort data.     

Dynamic Visibility‐Driven Molecular Surfaces

Molecular surface representations are an important tool for the visual analysis of molecular structure and function. In this paper, we present a novel method for the visualization of dynamic molecular surfaces based on the Gaussian model. In contrast to previous approaches, our technique does not rely on the construction of intermediate representations such as grids or triangulated surfaces. Instead, it operates entirely in image space, which enables us to exploit visibility information to efficiently skip unnecessary computations. With this visibility‐driven approach, we can visualize dynamic high‐quality surfaces for molecules consisting of millions of atoms. Our approach requires no preprocessing, allows for the interactive adjustment of all properties and parameters, and is significantly faster than previous approaches, while providing superior quality.     

IGM‐Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context

We introduce IGM‐Vis, a novel astrophysics visualization and data analysis application for investigating galaxies and the gas that surrounds them in context with their larger scale environment, the Cosmic Web. Environment is an important factor in the evolution of galaxies from actively forming stars to quiescent states with little, if any, discernible star formation activity. The gaseous halos of galaxies (the circumgalactic medium, or CGM) play a critical role in their evolution, because the gas necessary to fuel star formation and any gas expelled from widely observed galactic winds must encounter this interface region between galaxies and the intergalactic medium (IGM). We present a taxonomy of tasks typically employed in IGM/CGM studies informed by a survey of astrophysicists at various career levels, and demonstrate how these tasks are facilitated via the use of our visualization software. Finally, we evaluate the effectiveness of IGM‐Vis through two in‐depth use cases that depict real‐world analysis sessions that use IGM/CGM data.     

Bird's‐Eye ‐ Large‐Scale Visual Analytics of City Dynamics using Social Location Data

The analysis of behavioral city dynamics, such as temporal patterns of visited places and citizens' mobility routines, is an essential task for urban and transportation planning. Social media applications such as Foursquare and Twitter provide access to large‐scale and up‐to‐date dynamic movement data that not only help to understand the social life and pulse of a city but also to maintain and improve urban infrastructure. However, the fast growth rate of this data poses challenges for conventional methods to provide up‐to‐date, flexible analysis. Therefore, planning authorities barely consider it. We present a system and design study to leverage social media data that assist urban and transportation planners to achieve better monitoring and analysis of city dynamics such as visited places and mobility patterns in large metropolitan areas. We conducted a goal‐and‐task analysis with urban planning experts. To address these goals, we designed a system with a scalable data monitoring back‐end and an interactive visual analytics interface. The monitoring component uses intelligent pre‐aggregation to allow dynamic queries in near real‐time. The visual analytics interface leverages unsupervised learning to reveal clusters, routines, and unusual behavior in massive data, allowing to understand patterns in time and space. We evaluated our approach based on a qualitative user study with urban planning experts which demonstrates that intuitive integration of advanced analytical tools with visual interfaces is pivotal in making behavioral city dynamics accessible to practitioners. Our interviews also revealed areas for future research.     

ShutterApp: Spatio‐temporal Exposure Control for Videos

A camera's shutter controls the incoming light that is reaching the camera sensor. Different shutters lead to wildly different results, and are often used as a tool in movies for artistic purpose, e.g., they can indirectly control the effect of motion blur. However, a physical camera is limited to a single shutter setting at any given moment. ShutterApp enables users to define spatio‐temporally‐varying virtual shutters that go beyond the options available in real‐world camera systems. A user provides a sparse set of annotations that define shutter functions at selected locations in key frames. From this input, our solution defines shutter functions for each pixel of the video sequence using a suitable interpolation technique, which are then employed to derive the output video. Our solution performs in real‐time on commodity hardware. Hereby, users can explore different options interactively, leading to a new level of expressiveness without having to rely on specialized hardware or laborious editing.     

Exploratory Stage Lighting Design using Visual Objectives

Lighting is a critical element of theater. A lighting designer is responsible for drawing the audience's attention to a specific part of the stage, setting time of day, creating a mood, and conveying emotions. Designers often begin the lighting design process by collecting reference visual imagery that captures different aspects of their artistic intent. Then, they experiment with various lighting options to determine which ideas work best on stage. However, modern stages contain tens to hundreds of lights, and setting each light source's parameters individually to realize an idea is both tedious and requires expert skill. In this paper, we describe an exploratory lighting design tool based on feedback from professional designers. The system extracts abstract visual objectives from reference imagery and applies them to target regions of the stage. Our system can rapidly generate plausible design candidates that embody the visual objectives through a Gibbs sampling method, and present them as a design gallery for rapid exploration and iterative refinement. We demonstrate that the resulting system allows lighting designers of all skill levels to quickly create and communicate complex designs, even for scenes containing many color‐changing lights.     

Generating Color Scribble Images using Multi‐layered Monochromatic Strokes Dithering

Color scribbling is a unique form of illustration where artists use compact, overlapping, and monochromatic scribbles at microscopic scale to create astonishing colorful images at macroscopic scale. The creation process is skill‐demanded and time‐consuming, which typically involves drawing monochromatic scribbles layer‐by‐layer to depict true‐color subjects using a limited color palette delicately. In this work, we present a novel computational framework for automatic generation of color scribble images from arbitrary raster images. The core contribution of our work lies in a novel color dithering model tailor‐made for synthesizing a smooth color appearance using multiple layers of overlapped monochromatic strokes. Specifically, our system reconstructs the appearance of the input image by (i) generating layers of monochromatic scribbles based on a limited color palette derived from input image, and (ii) optimizing the drawing sequence among layers to minimize the visual color dissimilarity between dithered image and original image as well as the color banding artifacts. We demonstrate the effectiveness and robustness of our algorithm with various convincing results synthesized from a variety of input images with different stroke patterns. The experimental study further shows that our approach faithfully captures the scribble style and the color presentation at respectively microscopic and macroscopic scales, which is otherwise difficult for state‐of‐the‐art methods.     

Topic Tomographies (TopTom): a visual approach to distill information from media streams

In this paper we present Top Tom, a digital platform whose goal is to provide analytical and visual solutions for the exploration of a dynamic corpus of user‐generated messages and media articles, with the aim of i) distilling the information from thousands of documents in a low‐dimensional space of explainable topics, ii) cluster them in a hierarchical fashion while allowing to drill down to details and stories as constituents of the topics, iii) spotting trends and anomalies. Top Tom implements a batch processing pipeline able to run both in near‐real time with time stamped data from streaming sources and on historical data with a temporal dimension in a cold start mode. The resulting output unfolds along three main axes: time, volume and semantic similarity (i.e. topic hierarchical aggregation). To allow the browsing of data in a multiscale fashion and the identification of anomalous behaviors, three visual metaphors were adopted from biological and medical fields to design visualizations, i.e. the flowing of particles in a coherent stream, tomographic cross sectioning and contrast‐like analysis of biological tissues. The platform interface is composed by three main visualizations with coherent and smooth navigation interactions: calendar view, flow view, and temporal cut view. The integration of these three visual models with the multiscale analytic pipeline proposes a novel system for the identification and exploration of topics from unstructured texts. We evaluated the system using a collection of documents about the emerging opioid epidemics in the United States.     

Analyzing Residue Surface Proximity to Interpret Molecular Dynamics

The surface of a molecule holds important information about the interaction behavior with other molecules. In dynamic folding or docking processes, residues of amino acids with different properties change their position within the molecule over time. The atoms of the residues that are accessible to the solvent can directly contribute to binding interactions, while residues buried within the molecular structure contribute to the stability of the molecule. Understanding patterns and causality of structural changes is important for experts in the pharmaceutical domain, e.g., in the process of drug design. We apply an iterative computation of the Solvent Accessible Surface in order to extract virtual layers of a molecule. The extraction allows to track the movement of residues in the body of the molecule, with respect to the distance of the residue to the surface or the core during dynamics simulations. We visualize the obtained layer information for the complete time span of the molecular dynamics simulation as a 2D‐map and for individual time‐steps as a 3D‐representation of the molecule. The data acquisition has been implemented alongside with further analysis functionality in a prototypical application, which is available to the public domain. We underline the feasibility of our approach with a study from the pharmaceutical domain, where our approach has been used for novel insights into the folding behavior of μ‐conotoxins.     

A Color‐Pair Based Approach for Accurate Color Harmony Estimation

Harmonious color combinations can stimulate positive user emotional responses. However, a widely open research question is: how can we establish a robust and accurate color harmony measure for the public and professional designers to identify the harmony level of a color theme or color set. Building upon the key discovery that color pairs play an important role in harmony estimation, in this paper we present a novel color‐pair based estimation model to accurately measure the color harmony. It first takes a two‐layer maximum likelihood estimation (MLE) based method to compute an initial prediction of color harmony by statistically modeling the pair‐wise color preferences from existing datasets. Then, the initial scores are refined through a back‐propagation neural network (BPNN) with a variety of color features extracted in different color spaces, so that an accurate harmony estimation can be obtained at the end. Our extensive experiments, including performance comparisons of harmony estimation applications, show the advantages of our method in comparison with the state of the art methods.     

Applying Visual Analytics to Physically Based Rendering

Physically based rendering is a well‐understood technique to produce realistic‐looking images. However, different algorithms exist for efficiency reasons, which work well in certain cases but fail or produce rendering artefacts in others. Few tools allow a user to gain insight into the algorithmic processes. In this work, we present such a tool, which combines techniques from information visualization and visual analytics with physically based rendering. It consists of an interactive parallel coordinates plot, with a built‐in sampling‐based data reduction technique to visualize the attributes associated with each light sample. Two‐dimensional (2D) and three‐dimensional (3D) heat maps depict any desired property of the rendering process. An interactively rendered 3D view of the scene displays animated light paths based on the user's selection to gain further insight into the rendering process. The provided interactivity enables the user to guide the rendering process for more efficiency. To show its usefulness, we present several applications based on our tool. This includes differential light transport visualization to optimize light setup in a scene, finding the causes of and resolving rendering artefacts, such as fireflies, as well as a path length contribution histogram to evaluate the efficiency of different Monte Carlo estimators.     

A User‐based Visual Analytics Workflow for Exploratory Model Analysis

Many visual analytics systems allow users to interact with machine learning models towards the goals of data exploration and insight generation on a given dataset. However, in some situations, insights may be less important than the production of an accurate predictive model for future use. In that case, users are more interested in generating of diverse and robust predictive models, verifying their performance on holdout data, and selecting the most suitable model for their usage scenario. In this paper, we consider the concept of Exploratory Model Analysis (EMA), which is defined as the process of discovering and selecting relevant models that can be used to make predictions on a data source. We delineate the differences between EMA and the well‐known term exploratory data analysis in terms of the desired outcome of the analytic process: insights into the data or a set of deployable models. The contributions of this work are a visual analytics system workflow for EMA, a user study, and two use cases validating the effectiveness of the workflow. We found that our system workflow enabled users to generate complex models, to assess them for various qualities, and to select the most relevant model for their task.     

Visualization of 4D Vector Field Topology

In this paper, we present an approach to the topological analysis of four‐dimensional vector fields. In analogy to traditional 2D and 3D vector field topology, we provide a classification and visual representation of critical points, together with a technique for extracting their invariant manifolds. For effective exploration of the resulting four‐dimensional structures, we present a 4D camera that provides concise representation by exploiting projection degeneracies, and a 4D clipping approach that avoids self‐intersection in the 3D projection. We exemplify the properties and the utility of our approach using specific synthetic cases.     

Visual Analysis of protein‐ligand interactions

The analysis of protein‐ligand interactions is complex because of the many factors at play. Most current methods for visual analysis provide this information in the form of simple 2D plots, which, besides being quite space hungry, often encode a low number of different properties. In this paper we present a system for compact 2D visualization of molecular simulations. It purposely omits most spatial information and presents physical information associated to single molecular components and their pairwise interactions through a set of 2D InfoVis tools with coordinated views, suitable interaction, and focus+context techniques to analyze large amounts of data. The system provides a wide range of motifs for elements such as protein secondary structures or hydrogen bond networks, and a set of tools for their interactive inspection, both for a single simulation and for comparing two different simulations. As a result, the analysis of protein‐ligand interactions of Molecular Simulation trajectories is greatly facilitated.     

State‐of‐the‐art in Multi‐Light Image Collections for Surface Visualization and Analysis

Multi‐Light Image Collections (MLICs), i.e., stacks of photos of a scene acquired with a fixed viewpoint and a varying surface illumination, provide large amounts of visual and geometric information. In this survey, we provide an up‐to‐date integrative view of MLICs as a mean to gain insight on objects through the analysis and visualization of the acquired data. After a general overview of MLICs capturing and storage, we focus on the main approaches to produce representations usable for visualization and analysis. In this context, we first discuss methods for direct exploration of the raw data. We then summarize approaches that strive to emphasize shape and material details by fusing all acquisitions in a single enhanced image. Subsequently, we focus on approaches that produce relightable images through intermediate representations. This can be done both by fitting various analytic forms of the light transform function, or by locally estimating the parameters of physically plausible models of shape and reflectance and using them for visualization and analysis. We finally review techniques that improve object understanding by using illustrative approaches to enhance relightable models, or by extracting features and derived maps. We also review how these methods are applied in several, main application domains, and what are the available tools to perform MLIC visualization and analysis. We finally point out relevant research issues, analyze research trends, and offer guidelines for practical applications.     

Adaptive Temporal Sampling for Volumetric Path Tracing of Medical Data

Monte‐Carlo path tracing techniques can generate stunning visualizations of medical volumetric data. In a clinical context, such renderings turned out to be valuable for communication, education, and diagnosis. Because a large number of computationally expensive lighting samples is required to converge to a smooth result, progressive rendering is the only option for interactive settings: Low‐sampled, noisy images are shown while the user explores the data, and as soon as the camera is at rest the view is progressively refined. During interaction, the visual quality is low, which strongly impedes the user's experience. Even worse, when a data set is explored in virtual reality, the camera is never at rest, leading to constantly low image quality and strong flickering. In this work we present an approach to bring volumetric Monte‐Carlo path tracing to the interactive domain by reusing samples over time. To this end, we transfer the idea of temporal antialiasing from surface rendering to volume rendering. We show how to reproject volumetric ray samples even though they cannot be pinned to a particular 3D position, present an improved weighting scheme that makes longer history trails possible, and define an error accumulation method that downweights less appropriate older samples. Furthermore, we exploit reprojection information to adaptively determine the number of newly generated path tracing samples for each individual pixel. Our approach is designed for static, medical data with both volumetric and surface‐like structures. It achieves good‐quality volumetric Monte‐Carlo renderings with only little noise, and is also usable in a VR context.     

A stable graph layout algorithm for processes

Process mining enables organizations to analyze data about their (business) processes. Visualization is key to gaining insight into these processes and the associated data. Process visualization requires a high‐quality graph layout that intuitively represents the semantics of the process. Process analysis additionally requires interactive filtering to explore the process data and process graph. The ideal process visualization therefore provides a high‐quality, intuitive layout and preserves the mental map of the user during the visual exploration. The current industry standard used for process visualization does not satisfy either of these requirements. In this paper, we propose a novel layout algorithm for processes based on the Sugiyama framework. Our approach consists of novel ranking and order constraint algorithms and a novel crossing minimization algorithm. These algorithms make use of the process data to compute stable, high‐quality layouts. In addition, we use phased animation to further improve mental map preservation. Quantitative and qualitative evaluations show that our approach computes layouts of higher quality and preserves the mental map better than the industry standard. Additionally, our approach is substantially faster, especially for graphs with more than 250 edges.     

An Interactive Visualization System for Large Sets of Phase Space Trajectories

We introduce a visual analysis system with GPU acceleration techniques for large sets of trajectories from complex dynamical systems. The approach is based on an interactive Boolean combination of subsets into a Focus+Context phase‐space visualization. We achieve high performance through efficient bitwise algorithms utilizing runtime generated GPU shaders and kernels. This enables a higher level of interactivity for visualizing the large multivariate trajectory data. We explain how our design meets a set of carefully considered analysis requirements, provide performance results, and demonstrate utility through case studies with many‐particle simulation data from two application areas.     

Robust Reference Frame Extraction from Unsteady 2D Vector Fields with Convolutional Neural Networks

Robust feature extraction is an integral part of scientific visualization. In unsteady vector field analysis, researchers recently directed their attention towards the computation of near‐steady reference frames for vortex extraction, which is a numerically challenging endeavor. In this paper, we utilize a convolutional neural network to combine two steps of the visualization pipeline in an end‐to‐end manner: the filtering and the feature extraction. We use neural networks for the extraction of a steady reference frame for a given unsteady 2D vector field. By conditioning the neural network to noisy inputs and resampling artifacts, we obtain numerically stabler results than existing optimization‐based approaches. Supervised deep learning typically requires a large amount of training data. Thus, our second contribution is the creation of a vector field benchmark data set, which is generally useful for any local deep learning‐based feature extraction. Based on Vatistas velocity profile, we formulate a parametric vector field mixture model that we parameterize based on numerically‐computed example vector fields in near‐steady reference frames. Given the parametric model, we can efficiently synthesize thousands of vector fields that serve as input to our deep learning architecture. The proposed network is evaluated on an unseen numerical fluid flow simulation.     

Analytic Spectral Integration of Birefringence‐Induced Iridescence

Optical phenomena that are only observable in optically anisotropic materials are generally ignored in the computer graphics. However, such optical effects are not restricted to exotic materials and can also be observed with common translucent objects when optical anisotropy is induced, e.g. via mechanical stress. Furthermore accurate prediction and reproduction of those optical effects has important practical applications. We provide a short but complete analysis of the relevant electromagnetic theory of light propagation in optically anisotropic media and derive the full set of formulations required to render birefringent materials. We then present a novel method for spectral integration of refraction and reflection in an anisotropic slab. Our approach allows fast and robust rendering of birefringence‐induced iridescence in a physically faithful manner and is applicable to both real‐time and offline rendering.