37-Issue 3

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https://diglib.eg.org/handle/10.2312/2632394

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Analyzing Residue Surface Proximity to Interpret Molecular Dynamics
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Lichtenberg, Nils; Menges, Raphael; Ageev, Vladimir; George, Ajay Abisheck Paul; Heimer, Pascal; Imhof, Diana; Lawonn, Kai; Jeffrey Heer and Heike Leitte and Timo Ropinski
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.
An Approximate Parallel Vectors Operator for Multiple Vector Fields
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Gerrits, Tim; Rössl, Christian; Theisel, Holger; Jeffrey Heer and Heike Leitte and Timo Ropinski
The Parallel Vectors (PV) Operator extracts the locations of points where two vector fields are parallel. In general, these features are line structures. The PV operator has been used successfully for a variety of problems, which include finding vortex-core lines or extremum lines. We present a new generic feature extraction method for multiple 3D vector fields: The Approximate Parallel Vectors (APV) Operator extracts lines where all fields are approximately parallel. The definition of the APV operator is based on the application of PV for two vector fields that are derived from the given set of fields. The APV operator enables the direct visualization of features of vector field ensembles without processing fields individually and without causing visual clutter. We give a theoretical analysis of the APV operator and demonstrate its utility for a number of ensemble data.
Baseball Timeline: Summarizing Baseball Plays Into a Static Visualization
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Ono, Jorge H. Piazentin; Dietrich, Carlos; Silva, Claudio T.; Jeffrey Heer and Heike Leitte and Timo Ropinski
In sports, Play Diagrams are the standard way to represent and convey information. They are widely used by coaches, managers, journalists and fans in general. There are situations where diagrams may be hard to understand, for example, when several actions are packed in a certain region of the field or there are just too many actions to be transformed in a clear depiction of the play. The representation of how actions develop through time, in particular, may be hardly achieved on such diagrams. The time, and the relationship among the actions of the players through time, is critical on the depiction of complex plays. In this context, we present a study on how player actions may be clearly depicted on 2D diagrams. The study is focused on Baseball plays, a sport where diagrams are heavily used to summarize the actions of the players. We propose a new and simple approach to represent spatiotemporal information in the form of a timeline. We designed our visualization with a requirement driven approach, conducting interviews and fulfilling the needs of baseball experts and expert-fans. We validate our approach by presenting a detailed analysis of baseball plays and conducting interviews with four domain experts.
Bladder Runner: Visual Analytics for the Exploration of RT-Induced Bladder Toxicity in a Cohort Study
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Raidou, Renata Georgia; Casares-Magaz, Oscar; Amirkhanov, Aleksandr; Moiseenko, Vitali; Muren, Ludvig P.; Einck, John P.; Vilanova, Anna; Gröller, Eduard; Jeffrey Heer and Heike Leitte and Timo Ropinski
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.
Core Lines in 3D Second-Order Tensor Fields
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Oster, Timo; Rössl, Christian; Theisel, Holger; Jeffrey Heer and Heike Leitte and Timo Ropinski
Vortices are important features in vector fields that show a swirling behavior around a common core. The concept of a vortex core line describes the center of this swirling behavior. In this work, we examine the extension of this concept to 3D second-order tensor fields. Here, a behavior similar to vortices in vector fields can be observed for trajectories of the eigenvectors. Vortex core lines in vector fields were defined by Sujudi and Haimes to be the locations where stream lines are parallel to an eigenvector of the Jacobian. We show that a similar criterion applied to the eigenvector trajectories of a tensor field yields structurally stable lines that we call tensor core lines. We provide a formal definition of these structures and examine their mathematical properties. We also present a numerical algorithm for extracting tensor core lines in piecewise linear tensor fields. We find all intersections of tensor core lines with the faces of a dataset using a simple and robust root finding algorithm. Applying this algorithm to tensor fields obtained from structural mechanics simulations shows that it is able to effectively detect and visualize regions of rotational or hyperbolic behavior of eigenvector trajectories.
Design Factors for Summary Visualization in Visual Analytics
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Sarikaya, Alper; Gleicher, Michael; Szafir, Danielle Albers; Jeffrey Heer and Heike Leitte and Timo Ropinski
Data summarization allows analysts to explore datasets that may be too complex or too large to visualize in detail. Designers face a number of design and implementation choices when using summarization in visual analytics systems. While these choices influence the utility of the resulting system, there are no clear guidelines for the use of these summarization techniques. In this paper, we codify summarization use in existing systems to identify key factors in the design of summary visualizations. We use quantitative content analysis to systematically survey examples of visual analytics systems and enumerate the use of these design factors in data summarization. Through this analysis, we expose the relationship between design considerations, strategies for data summarization in visualization systems, and how different summarization methods influence the analyses supported by systems. We use these results to synthesize common patterns in real-world use of summary visualizations and highlight open challenges and opportunities that these patterns offer for designing effective systems. This work provides a more principled understanding of design practices for summary visualization and offers insight into underutilized approaches.
A General Illumination Model for Molecular Visualization
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Casajus, Pedro Hermosilla; Vázquez, Pere-Pau; Vinacua, Àlvar; Ropinski, Timo; Jeffrey Heer and Heike Leitte and Timo Ropinski
Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.
Hierarchical Correlation Clustering in Multiple 2D Scalar Fields
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Liebmann, Tom; Weber, Gunther H.; Scheuermann, Gerik; Jeffrey Heer and Heike Leitte and Timo Ropinski
Sets of multiple scalar fields can be used to model many types of variation in data, such as uncertainty in measurements and simulations or time-dependent behavior of scalar quantities. Many structural properties of such fields can be explained by dependencies between different points in the scalar field. Although these dependencies can be of arbitrary complexity, correlation, i.e., the linear dependency, already provides significant structural information. Existing methods for correlation analysis are usually limited to positive correlation, handle only local dependencies, or use combinatorial approximations to this continuous problem. We present a new approach for computing and visualizing correlated regions in sets of 2-dimensional scalar fields. This paper describes the following three main contributions: (i) An algorithm for hierarchical correlation clustering resulting in a dendrogram, (ii) a generalization of topological landscapes for dendrogram visualization, and (iii) a new method for incorporating negative correlation values in the clustering and visualization. All steps are designed to preserve the special properties of correlation coefficients. The results are visualized in two linked views, one showing the cluster hierarchy as 2D landscape and the other providing a spatial context in the scalar field's domain. Different coloring and texturing schemes coupled with interactive selection support an exploratory data analysis.
Hunting High and Low: Visualising Shifting Correlations in Financial Markets
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Simon, Peter M.; Turkay, Cagatay; Jeffrey Heer and Heike Leitte and Timo Ropinski
The analysis of financial assets' correlations is fundamental to many aspects of finance theory and practice, especially modern portfolio theory and the study of risk. In order to manage investment risk, in-depth analysis of changing correlations is needed, with both high and low correlations between financial assets (and groups thereof) important to identify. In this paper, we propose a visual analytics framework for the interactive analysis of relations and structures in dynamic, high-dimensional correlation data. We conduct a series of interviews and review the financial correlation analysis literature to guide our design. Our solution combines concepts from multi-dimensional scaling, weighted complete graphs and threshold networks to present interactive, animated displays which use proximity as a visual metaphor for correlation and animation stability to encode correlation stability. We devise interaction techniques coupled with context-sensitive auxiliary views to support the analysis of subsets of correlation networks. As part of our contribution, we also present behaviour profiles to help guide future users of our approach. We evaluate our approach by checking the validity of the layouts produced, presenting a number of analysis stories, and through a user study. We observe that our solutions help unravel complex behaviours and resonate well with study participants in addressing their needs in the context of correlation analysis in finance.
Interactive Investigation of Traffic Congestion on Fat-Tree Networks Using TREESCOPE
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Bhatia, Harsh; Jain, Nikhil; Bhatele, Abhinav; Livnat, Yarden; Domke, Jens; Pascucci, Valerio; Bremer, Peer-Timo; Jeffrey Heer and Heike Leitte and Timo Ropinski
Parallel simulation codes often suffer from performance bottlenecks due to network congestion, leaving millions of dollars of investments underutilized. Given a network topology, it is critical to understand how different applications, job placements, routing schemes, etc., are affected by and contribute to network congestion, especially for large and complex networks. Understanding and optimizing communication on large-scale networks is an active area of research. Domain experts often use exploratory tools to develop both intuitive and formal metrics for network health and performance. This paper presents TREESCOPE, an interactive, web-based visualization tool for exploring network traffic on large-scale fat-tree networks. TREESCOPE encodes the network topology using a tailored matrix-based representation and provides detailed visualization of all traffic in the network. We report on the design process of TREESCOPE, which has been received positively by network researchers as well as system administrators. Through case studies of real and simulated data, we demonstrate how TREESCOPE's visual design and interactive support for complex queries on network traffic can provide experts with new insights into the occurrences and causes of congestion in the network.
Maps and Globes in Virtual Reality
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Yang, Yalong; Jenny, Bernhard; Dwyer, Tim; Marriott, Kim; Chen, Haohui; Cordeil, Maxime; Jeffrey Heer and Heike Leitte and Timo Ropinski
This paper explores different ways to render world-wide geographic maps in virtual reality (VR). We compare: (a) a 3D exocentric globe, where the user's viewpoint is outside the globe; (b) a flat map (rendered to a plane in VR); (c) an egocentric 3D globe, with the viewpoint inside the globe; and (d) a curved map, created by projecting the map onto a section of a sphere which curves around the user. In all four visualisations the geographic centre can be smoothly adjusted with a standard handheld VR controller and the user, through a head-tracked headset, can physically move around the visualisation. For distance comparison exocentric globe is more accurate than egocentric globe and flat map. For area comparison more time is required with exocentric and egocentric globes than with flat and curved maps. For direction estimation, the exocentric globe is more accurate and faster than the other visual presentations. Our study participants had a weak preference for the exocentric globe. Generally the curved map had benefits over the flat map. In almost all cases the egocentric globe was found to be the least effective visualisation. Overall, our results provide support for the use of exocentric globes for geographic visualisation in mixed-reality.
Rendering and Extracting Extremal Features in 3D Fields
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Kindlmann, Gordon L.; Chiw, Charisee; Huynh, Tri; Gyulassy, Attila; Reppy, John; Bremer, Peer-Timo; Jeffrey Heer and Heike Leitte and Timo Ropinski
Visualizing and extracting three-dimensional features is important for many computational science applications, each with their own feature definitions and data types. While some are simple to state and implement (e.g. isosurfaces), others require more complicated mathematics (e.g. multiple derivatives, curvature, eigenvectors, etc.). Correctly implementing mathematical definitions is difficult, so experimenting with new features requires substantial investments. Furthermore, traditional interpolants rarely support the necessary derivatives, and approximations can reduce numerical stability. Our new approach directly translates mathematical notation into practical visualization and feature extraction, with minimal mental and implementation overhead. Using a mathematically expressive domain-specific language, Diderot, we compute direct volume renderings and particlebased feature samplings for a range of mathematical features. Non-expert users can experiment with feature definitions without any exposure to meshes, interpolants, derivative computation, etc. We demonstrate high-quality results on notoriously difficult features, such as ridges and vortex cores, using working code simple enough to be presented in its entirety.
SetCoLa: High-Level Constraints for Graph Layout
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Hoffswell, Jane; Borning, Alan; Heer, Jeffrey; Jeffrey Heer and Heike Leitte and Timo Ropinski
Constraints enable flexible graph layout by combining the ease of automatic layout with customizations for a particular domain. However, constraint-based layout often requires many individual constraints defined over specific nodes and node pairs. In addition to the effort of writing and maintaining a large number of similar constraints, such constraints are specific to the particular graph and thus cannot generalize to other graphs in the same domain. To facilitate the specification of customized and generalizable constraint layouts, we contribute SetCoLa: a domain-specific language for specifying high-level constraints relative to properties of the backing data. Users identify node sets based on data or graph properties and apply high-level constraints within each set. Applying constraints to node sets rather than individual nodes reduces specification effort and facilitates reapplication of customized layouts across distinct graphs. We demonstrate the conciseness, generalizability, and expressiveness of SetCoLa on a series of real-world examples from ecological networks, biological systems, and social networks.
Towards Easy Comparison of Local Businesses Using Online Reviews
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Wang, Yong; Haleem, Hammad; Shi, Conglei; Wu, Yanhong; Zhao, Xun; Fu, Siwei; Qu, Huamin; Jeffrey Heer and Heike Leitte and Timo Ropinski
With the rapid development of e-commerce, there is an increasing number of online review websites, such as Yelp, to help customers make better purchase decisions. Viewing online reviews, including the rating score and text comments by other customers, and conducting a comparison between different businesses are the key to making an optimal decision. However, due to the massive amount of online reviews, the potential difference of user rating standards, and the significant variance of review time, length, details and quality, it is difficult for customers to achieve a quick and comprehensive comparison. In this paper, we present E-Comp, a carefully-designed visual analytics system based on online reviews, to help customers compare local businesses at different levels of details. More specifically, intuitive glyphs overlaid on maps are designed for quick candidate selection. Grouped Sankey diagram visualizing the rating difference by common customers is chosen for more reliable comparison of two businesses. Augmented word cloud showing adjective-noun word pairs, combined with a temporal view, is proposed to facilitate in-depth comparison of businesses in terms of different time periods, rating scores and features. The effectiveness and usability of E-Comp are demonstrated through a case study and in-depth user interviews.
VirtualDesk: A Comfortable and Efficient Immersive Information Visualization Approach
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Filho, Jorge A. Wagner; Freitas, Carla M.D.S.; Nedel, Luciana; Jeffrey Heer and Heike Leitte and Timo Ropinski
3D representations are potentially useful under many circumstances, but suffer from long known perception and interaction challenges. Current immersive technologies, which combine stereoscopic displays and natural interaction, are being progressively seen as an opportunity to tackle this issue, but new guidelines and studies are still needed, especially regarding information visualization. Many proposed approaches are impractical for actual usage, resulting in user discomfort or requiring too much time or space. In this work, we implement and evaluate an alternative data exploration metaphor where the user remains seated and viewpoint change is only realisable through physical movements. All manipulation is done directly by natural mid-air gestures, with the data being rendered at arm's reach. The virtual reproduction of the analyst's desk aims to increase immersion and enable tangible interaction with controls and two dimensional associated information. A comparative user study was carried out against a desktop-based equivalent, exploring a set of 9 perception and interaction tasks based on previous literature and a multidimensional projection use case. We demonstrate that our prototype setup, named VirtualDesk, presents excellent results regarding user comfort and immersion, and performs equally or better in all analytical tasks, while adding minimal or no time overhead and amplifying user subjective perceptions of efficiency and engagement. Results are also contrasted to a previous experiment employing artificial flying navigation, with significant observed improvements.
Visual Analysis of Protein-ligand Interactions
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Vázquez, Pere-Pau; Casajus, Pedro Hermosilla; Guallar, Victor; Estrada, Jorge; Vinacua, Àlvar; Jeffrey Heer and Heike Leitte and Timo Ropinski
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.
Visualizing Expanded Query Results
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Mazurek, Michael; Waldner, Manuela; Jeffrey Heer and Heike Leitte and Timo Ropinski
When performing queries in web search engines, users often face difficulties choosing appropriate query terms. Search engines therefore usually suggest a list of expanded versions of the user query to disambiguate it or to resolve potential term mismatches. However, it has been shown that users find it difficult to choose an expanded query from such a list. In this paper, we describe the adoption of set-based text visualization techniques to visualize how query expansions enrich the result space of a given user query and how the result sets relate to each other. Our system uses a linguistic approach to expand queries and topic modeling to extract the most informative terms from the results of these queries. In a user study, we compare a common text list of query expansion suggestions to three set-based text visualization techniques adopted for visualizing expanded query results - namely, Compact Euler Diagrams, Parallel Tag Clouds, and a List View - to resolve ambiguous queries using interactive query expansion. Our results show that text visualization techniques do not increase retrieval efficiency, precision, or recall. Overall, users rate Parallel Tag Clouds visualizing key terms of the expanded query space lowest. Based on the results, we derive recommendations for visualizations of query expansion results, text visualization techniques in general, and discuss alternative use cases of set-based text visualization techniques in the context of web search.
Visualizing Multidimensional Data with Order Statistics
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Raj, Mukund; Whitaker, Ross T.; Jeffrey Heer and Heike Leitte and Timo Ropinski
Multidimensional data sets are common in many domains, and dimensionality reduction methods that determine a lower dimensional embedding are widely used for visualizing such data sets. This paper presents a novel method to project data onto a lower dimensional space by taking into account the order statistics of the individual data points, which are quantified by their depth or centrality in the overall set. Thus, in addition to conveying relative distances in the data, the proposed method also preserves the order statistics, which are often lost or misrepresented by existing visualization methods. The proposed method entails a modification of the optimization objective of conventional multidimensional scaling (MDS) by introducing a term that penalizes discrepancies between centrality structures in the original space and the embedding. We also introduce two strategies for visualizing lower dimensional embeddings of multidimensional data that takes advantage of the coherent representation of centrality provided by the proposed projection method. We demonstrate the effectiveness of our visualization with comparisons on different kinds of multidimensional data, including categorical and multimodal, from a variety of domains such as botany and health care.
Visualizing the Phase Space of Heterogeneous Inertial Particles in 2D Flows
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Rojo, Irene Baeza; Gross, Markus; Günther, Tobias; Jeffrey Heer and Heike Leitte and Timo Ropinski
In many scientific disciplines, the motion of finite-sized objects in fluid flows plays an important role, such as in brownout engineering, sediment transport, oceanology or meteorology. These finite-sized objects are called inertial particles and, in contrast to traditional tracer particles, their motion depends on their current position, their own particle velocity, the time and their size. Thus, the visualization of their motion becomes a high-dimensional problem that entails computational and perceptual challenges. So far, no visualization explored and visualized the particle trajectories under variation of all seeding parameters. In this paper, we propose three coordinated views that visualize the different aspects of the high-dimensional space in which the particles live. We visualize the evolution of particles over time, showing that particles travel different distances in the same time, depending on their size. The second view provides a clear illustration of the trajectories of different particle sizes and allows the user to easily identify differences due to particle size. Finally, we embed the trajectories in the space-velocity domain and visualize their distance to an attracting manifold using ribbons. In all views, we support interactive linking and brushing, and provide abstraction through density volumes that are shown by direct volume rendering and isosurface slabs. Using our method, users gain deeper insights into the dynamics of inertial particles in 2D fluids, including size-dependent separation, preferential clustering and attraction. We demonstrate the effectiveness of our method in multiple steady and unsteady 2D flows.

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