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I analyze the evolution of papers certified by the Graphics Replicability Stamp Initiative (GRSI) to be reproducible, with a specific focus on the subset of publications that address visualization-related topics. With this analysis I show that, while the number of papers is increasing overall and within the visualization field, we still have to improve quite a bit to escape the replication crisis. I base my analysis on the data published by the GRSI as well as publication data for the different venues in visualization and lists of journal papers that have been presented at visualization-focused conferences. I also analyze the differences between the involved journals as well as the percentage of reproducible papers in the different presentation venues. Furthermore, I look at the authors of the publications and, in particular, their affiliation countries to see where most reproducible papers come from. Finally, I discuss potential reasons for the low reproducibility numbers and suggest possible ways to overcome these obstacles. This paper is reproducible itself, with source code and data available from github.com/tobiasisenberg/Visualization-Reproducibility as well as a free paper copy and all supplemental materials at osf.io/mvnbj., Comment: 9 pages plus appendix; 12 figures plus 14 figures in the appendix

We developed and validated an instrument to measure the perceived readability in data visualization: PREVis. Researchers and practitioners can easily use this instrument as part of their evaluations to compare the perceived readability of different visual data representations. Our instrument can complement results from controlled experiments on user task performance or provide additional data during in-depth qualitative work such as design iterations when developing a new technique. Although readability is recognized as an essential quality of data visualizations, so far there has not been a unified definition of the construct in the context of visual representations. As a result, researchers often lack guidance for determining how to ask people to rate their perceived readability of a visualization. To address this issue, we engaged in a rigorous process to develop the first validated instrument targeted at the subjective readability of visual data representations. Our final instrument consists of 11 items across 4 dimensions: understandability, layout clarity, readability of data values, and readability of data patterns. We provide the questionnaire as a document with implementation guidelines on osf.io/9cg8j. Beyond this instrument, we contribute a discussion of how researchers have previously assessed visualization readability, and an analysis of the factors underlying perceived readability in visual data representations., Comment: 11 pages, 35 pages appendix, 5 figures in main paper, additional 94 figures in appendix, paper to appear in IEEE Transactions on Visualization and Computer Graphics

We propose and study a novel cross-reality environment that seamlessly integrates a monoscopic 2D surface (an interactive screen with touch and pen input) with a stereoscopic 3D space (an augmented reality HMD) to jointly host spatial data visualizations. This innovative approach combines the best of two conventional methods of displaying and manipulating spatial 3D data, enabling users to fluidly explore diverse visual forms using tailored interaction techniques. Providing such effective 3D data exploration techniques is pivotal for conveying its intricate spatial structures -- often at multiple spatial or semantic scales -- across various application domains and requiring diverse visual representations for effective visualization. To understand user reactions to our new environment, we began with an elicitation user study, in which we captured their responses and interactions. We observed that users adapted their interaction approaches based on perceived visual representations, with natural transitions in spatial awareness and actions while navigating across the physical surface. Our findings then informed the development of a design space for spatial data exploration in cross-reality. We thus developed cross-reality environments tailored to three distinct domains: for 3D molecular structure data, for 3D point cloud data, and for 3D anatomical data. In particular, we designed interaction techniques that account for the inherent features of interactions in both spaces, facilitating various forms of interaction, including mid-air gestures, touch interactions, pen interactions, and combinations thereof, to enhance the users' sense of presence and engagement. We assessed the usability of our environment with biologists, focusing on its use for domain research. In addition, we evaluated our interaction transition designs with virtual and mixed-reality experts to gather further insights., Comment: 15 pages, 20 figures, IEEE VIS2024

We apply an approach from cognitive linguistics by mapping Conceptual Metaphor Theory (CMT) to the visualization domain to address patterns of visual conceptual metaphors that are often used in science infographics. Metaphors play an essential part in visual communication and are frequently employed to explain complex concepts. However, their use is often based on intuition, rather than following a formal process. At present, we lack tools and language for understanding and describing metaphor use in visualization to the extent where taxonomy and grammar could guide the creation of visual components, e.g., infographics. Our classification of the visual conceptual mappings within scientific representations is based on the breakdown of visual components in existing scientific infographics. We demonstrate the development of this mapping through a detailed analysis of data collected from four domains (biomedicine, climate, space, and anthropology) that represent a diverse range of visual conceptual metaphors used in the visual communication of science. This work allows us to identify patterns of visual conceptual metaphor use within the domains, resolve ambiguities about why specific conceptual metaphors are used, and develop a better overall understanding of visual metaphor use in scientific infographics. Our analysis shows that ontological and orientational conceptual metaphors are the most widely applied to translate complex scientific concepts. To support our findings we developed a visual exploratory tool based on the collected database that places the individual infographics on a spatio-temporal scale and illustrates the breakdown of visual conceptual metaphors., Comment: 11 pages, 8 figures, 1 table, accepted to IEEE VIS 2024 Conference

We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to semi-automatically composite large mesoscale models of complex protein assemblies and complete cellular structures that are based on measured cryo-EM data. The current approaches require manual fitting in three dimensions to start, resulting in approximately aligned structures followed by an automated fine-tuning of the alignment. The DiffFit approach enables domain scientists to fit new structures automatically and visualize the results for inspection and interactive revision. The fitting begins with differentiable three-dimensional (3D) rigid transformations of the protein atom coordinates followed by sampling the density values at the atom coordinates from the target cryo-EM volume. To ensure a meaningful correlation between the sampled densities and the protein structure, we proposed a novel loss function based on a multi-resolution volume-array approach and the exploitation of the negative space. This loss function serves as a critical metric for assessing the fitting quality, ensuring the fitting accuracy and an improved visualization of the results. We assessed the placement quality of DiffFit with several large, realistic datasets and found it to be superior to that of previous methods. We further evaluated our method in two use cases: automating the integration of known composite structures into larger protein complexes and facilitating the fitting of predicted protein domains into volume densities to aid researchers in identifying unknown proteins. We implemented our algorithm as an open-source plugin (github.com/nanovis/DiffFit) in ChimeraX, a leading visualization software in the field. All supplemental materials are available at osf.io/5tx4q., Comment: 16 pages, 7 figures, 3 tables. IEEE VIS 2024

We present and discuss the results of a qualitative analysis of visual representations from images. We labeled each image's essential stimuli, the removal of which would render a visualization uninterpretable. As a result, we derive a typology of 10 visualization types of defined groups. We describe the typology derivation process in which we engaged. The resulting typology and image analysis can serve a number of purposes: enabling researchers to study the evolution of the community and its research output over time, facilitating the categorization of visualization images for the purpose of research and teaching, allowing researchers and practitioners to identify visual design styles to further align the quantification of any visual information processor, be that a person or an algorithm observer, and it facilitates a discussion of standardization in visualization. In addition to the visualization typology from images, we provide a dataset of 6,833 tagged images and an online tool that can be used to explore and analyze the large set of labeled images. The tool and data set enable scholars to closely examine the diverse visual designs used and how they are published and communicated in our community. A pre-registration, a free copy of this paper, and all supplemental materials are available via osf.io/dxjwt., Comment: arXiv admin note: text overlap with arXiv:2209.07533

We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they are interacting. While 3D representations focus on the spatial character of the data or the dedicated 3D data mapping, 2D representations often show abstract data properties and take advantage of the unique benefits of mapping to a plane. Many systems have used unique combinations of both types of data mappings effectively. Yet there are no systematic reviews of the methods in linking 2D and 3D representations. We systematically survey the relationships between 2D and 3D visual representations in major visualization publications -- IEEE VIS, IEEE TVCG, and EuroVis -- from 2012 to 2022. We closely examined 105 papers where 2D and 3D representations are connected visually, interactively, or through animation. These approaches are designed based on their visual environment, the relationships between their visual representations, and their possible layouts. Through our analysis, we introduce a design space as well as provide design guidelines for effectively linking 2D and 3D visual representations.

We investigated data embroidery with black-and-white textures, identifying challenges in the use of textures for machine embroidery based on our own experience. Data embroidery, as a method of physically representing data, offers a unique way to integrate personal data into one's everyday fabric-based objects. Owing to their monochromatic characteristics, black-and-white textures promise to be easy to employ in machine embroidery. We experimented with different textured visualizations designed by experts and, in this paper, we detail our workflow and evaluate the performance and suitability of different textures. We then conducted a survey on vegetable preferences within a family and created a canvas bag as a case study, featuring the embroidered family data to show how embroidered data can be used in practice.

We propose three novel spatial data selection techniques for particle data in VR visualization environments. They are designed to be target- and context-aware and be suitable for a wide range of data features and complex scenarios. Each technique is designed to be adjusted to particular selection intents: the selection of consecutive dense regions, the selection of filament-like structures, and the selection of clusters -- with all of them facilitating post-selection threshold adjustment. These techniques allow users to precisely select those regions of space for further exploration -- with simple and approximate 3D pointing, brushing, or drawing input -- using flexible point- or path-based input and without being limited by 3D occlusions, non-homogeneous feature density, or complex data shapes. These new techniques are evaluated in a controlled experiment and compared with the Baseline method, a region-based 3D painting selection. Our results indicate that our techniques are effective in handling a wide range of scenarios and allow users to select data based on their comprehension of crucial features. Furthermore, we analyze the attributes, requirements, and strategies of our spatial selection methods and compare them with existing state-of-the-art selection methods to handle diverse data features and situations. Based on this analysis we provide guidelines for choosing the most suitable 3D spatial selection techniques based on the interaction environment, the given data characteristics, or the need for interactive post-selection threshold adjustment.

We investigate the use of 2D black-and-white textures for the visualization of categorical data and contribute a summary of texture attributes, and the results of three experiments that elicited design strategies as well as aesthetic and effectiveness measures. Black-and-white textures are useful, for instance, as a visual channel for categorical data on low-color displays, in 2D/3D print, to achieve the aesthetic of historic visualizations, or to retain the color hue channel for other visual mappings. We specifically study how to use what we call geometric and iconic textures. Geometric textures use patterns of repeated abstract geometric shapes, while iconic textures use repeated icons that may stand for data categories. We parameterized both types of textures and developed a tool for designers to create textures on simple charts by adjusting texture parameters. 30 visualization experts used our tool and designed 66 textured bar charts, pie charts, and maps. We then had 150 participants rate these designs for aesthetics. Finally, with the top-rated geometric and iconic textures, our perceptual assessment experiment with 150 participants revealed that textured charts perform about equally well as non-textured charts, and that there are some differences depending on the type of chart.

We present a new way to merge any two point distribution approaches using distance fields. Our new process allows us to produce digital stippling that fills areas with stipple dots without visual artifacts as well as includes clear linear features without fussiness. Our merging thus benefits from past work that can optimize for either goal individually, yet typically by sacrificing the other. The new possibility of combining any two distributions using different distance field functions and their parameters also allows us to produce a vast range of stippling styles, which we demonstrate as well., Comment: 41 pages, 42 figures

We present and discuss the results of a two-year qualitative analysis of images published in IEEE Visualization (VIS) papers. Specifically, we derive a typology of 13 visualization image types, coded to distinguish visualizations and several image characteristics. The categorization process required much more time and was more difficult than we initially thought. The resulting typology and image analysis may serve a number of purposes: to study the evolution of the community and its research output over time, to facilitate the categorization of visualization images for the purpose of teaching, to identify visual designs for evaluation purposes, or to enable progress towards standardization in visualization. In addition to the typology and image characterization, we provide a dataset of 6,833 tagged images and an online tool that can be used to explore and analyze the large set of tagged images. We thus facilitate a discussion of the diverse visualizations used and how they are published and communicated in our community.

We developed and validated a rating scale to assess the aesthetic pleasure (or beauty) of a visual data representation: the BeauVis scale. With our work we offer researchers and practitioners a simple instrument to compare the visual appearance of different visualizations, unrelated to data or context of use. Our rating scale can, for example, be used to accompany results from controlled experiments or be used as informative data points during in-depth qualitative studies. Given the lack of an aesthetic pleasure scale dedicated to visualizations, researchers have mostly chosen their own terms to study or compare the aesthetic pleasure of visualizations. Yet, many terms are possible and currently no clear guidance on their effectiveness regarding the judgment of aesthetic pleasure exists. To solve this problem, we engaged in a multi-step research process to develop the first validated rating scale specifically for judging the aesthetic pleasure of a visualization (osf.io/fxs76). Our final BeauVis scale consists of five items, "enjoyable," "likable," "pleasing," "nice," and "appealing." Beyond this scale itself, we contribute (a) a systematic review of the terms used in past research to capture aesthetics, (b) an investigation with visualization experts who suggested terms to use for judging the aesthetic pleasure of a visualization, and (c) a confirmatory survey in which we used our terms to study the aesthetic pleasure of a set of 3 visualizations.

We present document domain randomization (DDR), the first successful transfer of convolutional neural networks (CNNs) trained only on graphically rendered pseudo-paper pages to real-world document segmentation. DDR renders pseudo-document pages by modeling randomized textual and non-textual contents of interest, with user-defined layout and font styles to support joint learning of fine-grained classes. We demonstrate competitive results using our DDR approach to extract nine document classes from the benchmark CS-150 and papers published in two domains, namely annual meetings of Association for Computational Linguistics (ACL) and IEEE Visualization (VIS). We compare DDR to conditions of style mismatch, fewer or more noisy samples that are more easily obtained in the real world. We show that high-fidelity semantic information is not necessary to label semantic classes but style mismatch between train and test can lower model accuracy. Using smaller training samples had a slightly detrimental effect. Finally, network models still achieved high test accuracy when correct labels are diluted towards confusing labels; this behavior hold across several classes., Comment: Main paper to appear in ICDAR 2021 (16th International Conference on Document Analysis and Recognition). This version contains additional materials. The associated test data is hosted on IEEE Data Port: http://doi.org/10.21227/326q-bf39

We present the VIS30K dataset, a collection of 29,689 images that represents 30 years of figures and tables from each track of the IEEE Visualization conference series (Vis, SciVis, InfoVis, VAST). VIS30K's comprehensive coverage of the scientific literature in visualization not only reflects the progress of the field but also enables researchers to study the evolution of the state-of-the-art and to find relevant work based on graphical content. We describe the dataset and our semi-automatic collection process, which couples convolutional neural networks (CNN) with curation. Extracting figures and tables semi-automatically allows us to verify that no images are overlooked or extracted erroneously. To improve quality further, we engaged in a peer-search process for high-quality figures from early IEEE Visualization papers. With the resulting data, we also contribute VISImageNavigator (VIN, visimagenavigator.github.io), a web-based tool that facilitates searching and exploring VIS30K by author names, paper keywords, title and abstract, and years., Comment: 12 pages

We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods instead of the rigid traditional production pipeline. Our method is motivated by the rapid evolution of interactive scientific visualization, which shows great potential in science dissemination. Without some form of explanation or guidance, however, novices and lay-persons often find it difficult to gain insights from the visualization itself. We integrate such knowledge using the verbal channel and provide it along an engaging visual presentation. To realize the synthesis of a molecumentary, we provide technical solutions along two major production steps: 1) preparing a story structure and 2) turning the story into a concrete narrative. In the first step, information about the model from heterogeneous sources is compiled into a story graph. Local knowledge is combined with remote sources to complete the story graph and enrich the final result. In the second step, a narrative, i.e., story elements presented in sequence, is synthesized using the story graph. We present a method for traversing the story graph and generating a virtual tour, using automated camera and visualization transitions. Texts written by domain experts are turned into verbal representations using text-to-speech functionality and provided as a commentary. Using the described framework we synthesize automatic fly-throughs with descriptions that mimic a manually authored documentary. Furthermore, we demonstrate a second scenario: guiding the documentary narrative by a textual input.

In this article we revisit the concept of abstraction as it is used in visualization and put it on a solid formal footing. While the term \emph{abstraction} is utilized in many scientific disciplines, arts, as well as everyday life, visualization inherits the notion of data abstraction or class abstraction from computer science, topological abstraction from mathematics, and visual abstraction from arts. All these notions have a lot in common, yet there is a major discrepancy in the terminology and basic understanding about visual abstraction in the context of visualization. We thus root the notion of abstraction in the philosophy of science, clarify the basic terminology, and provide crisp definitions of visual abstraction as a process. Furthermore, we clarify how it relates to similar terms often used interchangeably in the field of visualization. Visual abstraction is characterized by a conceptual space where this process exists, by the purpose it should serve, and by the perceptual and cognitive qualities of the beholder. These characteristics can be used to control the process of visual abstraction to produce effective and informative visual representations.

We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.

We study user preference between allocentric and egocentric 3D manipulation on mobile devices, in a configuration where the motion of the device is applied to an object displayed on the device itself. We first evaluate this preference for translations and for rotations alone, then for full 6-DOF manipulation. We also investigate the role of contextual cues by performing this experiment in different 3D scenes. Finally, we look at the specific influence of each manipulation axis. Our results provide guidelines to help interface designers select an appropriate default mapping in this locally coupled configuration.

Approximate computing (AC) is an emerging paradigm for energy-efficient computation. The basic idea of AC is to sacrifice high precision for low energy by allowing for hardware which only carries out "approximately correct" calculations. For software verification, this challenges the validity of verification results for programs run on approximate hardware. In this paper, we present a novel approach to examine program correctness in the context of approximate computing. In contrast to all existing approaches, we start with a standard program verification and compute the allowed tolerances for AC hardware from that verification run. More precisely, we derive a set of constraints which - when met by the AC hardware - guarantees the verification result to carry over to AC. Our approach is based on the framework of abstract interpretation. On the practical side, we furthermore (1) show how to extract tolerance constraints from verification runs employing predicate abstraction as an instance of abstract interpretation, and (2) show how to check such constraints on hardware designs. We exemplify our technique on example C programs and a number of recently proposed approximate adders.

We evaluate the performance and usability of mouse-based, touch-based, and tangible interaction for manipulating objects in a 3D virtual environment. This comparison is a step toward a better understanding of the limitations and benefits of these existing interaction techniques, with the ultimate goal of facilitating the integration of different 3D data exploration environments into a single interaction continuum. For this purpose we analyze participants' performance in 3D manipulation using a docking task. We measured completion times, docking precision, as well as subjective criteria such as fatigue, workload, and preference. Our results show that the three input modalities provide similar levels of precision but require different interaction times. We also discuss our qualitative observations as well as people's preferences and put our findings into context of the practical application domain of 3D data analysis environments.

We examine a class of techniques for 3D object manipulation on mobile devices, in which the device's physical motion is applied to 3D objects displayed on the device itself. This "local coupling" between input and display creates specific challenges compared to manipulation techniques designed for monitor-based or immersive virtual environments. Our work focuses specifically on the mapping between device motion and object motion. We review existing manipulation techniques and introduce a formal description of the main mappings under a common notation. Based on this notation, we analyze these mappings and their properties in order to answer crucial usability questions. We first investigate how the 3D objects should move on the screen, since the screen also moves with the mobile device during manipulation. We then investigate the effects of a limited range of manipulation and present a number of solutions to overcome this constraint. This work provides a theoretical framework to better understand the properties of locally-coupled 3D manipulation mappings based on mobile device motion.

We present a new approach to achieve tangible object manipulation with a single, fully portable and self-contained device. Our solution is based on the concept of a "tangible volume". We turn a tangible object into a handheld fish-tank display. The tangible volume represents a volume of space that can be freely manipulated within a virtual scene. This volume can be positioned onto virtual objects to directly grasp them, and to manipulate them in 3D space. We investigate this concept through two user studies. The first study evaluates the intuitiveness of using a tangible volume for grasping and manipulating virtual objects. The second study evaluates the effects of the limited field of view on spatial awareness. Finally, we present a generalization of this concept to other forms of interaction through the surface of the volume.

We present a flexible illustrative line style model for the visualization of streamline data. Our model partitions view-oriented line strips into parallel bands whose basic visual properties can be controlled independently. We thus extend previous line stylization techniques specifically for visualization purposes by allowing the parametrization of these bands based on the local line data attributes. Moreover, our approach supports emphasis and abstraction by introducing line style transfer functions that map local line attribute values to complete line styles. With a flexible GPU implementation of this line style model we enable the interactive exploration of visual representations of streamlines. We demonstrate the effectiveness of our model by applying it to 3D flow field datasets., Comment: Extended version of a short paper at Pacific Graphics 2011 (http://dx.doi.org/10.2312/PE/PG/PG2011short/105-110)

Proof-carrying hardware (PCH) is an approach to achieving safety of dynamically reconfigurable hardware, transferring the idea of proof-carrying code to the hardware domain. Current PCH approaches are, however, either limited to combinational and bounded unfoldings of sequential circuits, or only provide semi-automatic proof generation. We propose a new approach to PCH which employs IC3 as proof generator, making automatic PCH applicable to sequential circuits in their full generality. We demonstrate feasibility of our approach by showing that proof validation is several orders of magnitude faster than original proof generation while (most often) generating smaller proofs than current PCHs.

We present the results of a comprehensive analysis of visualization paper keywords supplied for 4366 papers submitted to five main visualization conferences. We describe main keywords, topic areas, and 10-year historic trends from two datasets: (1) the standardized PCS taxonomy keywords in use for paper submissions for IEEE InfoVis, IEEE Vis-SciVis, IEEE VAST, EuroVis, and IEEE PacificVis since 2009 and (2) the author-chosen keywords for papers published in the IEEE Visualization conference series (now called IEEE VIS) since 2004. Our analysis of research topics in visualization can serve as a starting point to (a) help create a common vocabulary to improve communication among different visualization sub-groups, (b) facilitate the process of understanding differences and commonalities of the various research sub-fields in visualization, (c) provide an understanding of emerging new research trends, (d) facilitate the crucial step of finding the right reviewers for research submissions, and (e) it can eventually lead to a comprehensive taxonomy of visualization research. One additional tangible outcome of our work is an application that allows visualization researchers to easily browse the 2600+ keywords used for IEEE VIS papers during the past 10 years, aiming at more informed and, hence, more effective keyword selections for future visualization publications.