Dynamic Risk Perceptions in Times of Avian and Seasonal Influenza Epidemics: A Repeated Cross-Sectional Design.

Infectious diseases pose a serious threat to humans. Therefore, it is crucial to understand how accurately people perceive these risks. However, accuracy can be operationalized differently depending on the standard of comparison. The present study investigated accuracy in risk perceptions for three infectious diseases (avian influenza, seasonal influenza, common cold) using three different standards for accuracy: Social comparison (self vs. others' risk perceptions), general problem level (risk perceptions for diseases with varying threat levels), and dynamic problem level (risk perceptions during epidemics/seasons vs. nonepidemic/off-season times). Four online surveys were conducted using a repeated cross-sectional design. Two surveys were conducted during epidemics/seasons of avian influenza, seasonal influenza, and common cold in 2006 (n = 387) and 2016 (n = 370) and two surveys during nonepidemic/off-season times for the three diseases in 2009 (n = 792) during a swine flu outbreak and in 2018 (n = 422) during no outbreak of zoonotic influenza. While on average participants felt less at risk than others, indicating an optimistic bias, risk perceptions matched the magnitude of risk associated with the three infectious diseases. Importantly, a significant three-way interaction indicated dynamic accuracy in risk perceptions: Participants felt more at risk for seasonal influenza and common cold during influenza and cold seasons, compared with off-season times. However, these dynamic increases were more pronounced in the perceived risk for others than for oneself (optimistic bias). The results emphasize the importance of using multiple approaches to assess accuracy of risk perception as they provided different information on how accurately people gauge their risk when facing infectious diseases.

Where to go: Computational and visual what-if analyses in soccer.

To prepare their teams for upcoming matches, analysts in professional soccer watch and manually annotate up to three matches a day. When annotating matches, domain experts try to identify and improve suboptimal movements based on intuition and professional experience. The high amount of matches needing to be analysed manually result in a tedious and time-consuming process, and results may be subjective. We propose an automatic approach for the realisation of effective region-based what-if analyses in soccer. Our system covers the automatic detection of region-based faulty movement behaviour, as well as the automatic suggestion of possible improved alternative movements. As we show, our approach effectively supports analysts and coaches investigating matches by speeding up previously time-consuming work. We enable domain experts to include their domain knowledge in the analysis process by allowing to interactively adjust suggested improved movement, as well as its implications on region control. We demonstrate the usefulness of our proposed approach via an expert study with three invited domain experts, one being head coach from the first Austrian soccer league. As our results show that experts most often agree with the suggested player movement (83%), our proposed approach enhances the analytical capabilities in soccer and supports a more efficient analysis.

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP.

BACKGROUND: While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. RESULTS: Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics analysis predicted statistically significant target regulons for 15 of the intergenic transcripts; experimental analysis revealed 4-fold or higher differential expression of 46 novel ncRNA in different growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of those, 16 had RIBOseq patterns matching annotated genes in other enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting that such ncRNAs may encode small proteins instead of being solely non-coding. To support that the RIBOseq signals are reflecting translation, we tested the ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded peptide in iron-limiting condition. CONCLUSION: Determination of the RCV is a useful approach for a rapid first-step differentiation between bacterial ncRNAs and small mRNAs. Further, many known ncRNAs may encode proteins as well.

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).

BACKGROUND: Genomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome). RESULTS: Using the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization. CONCLUSIONS: These findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo.

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.

BACKGROUND: Gene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented. RESULTS: RNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the -2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5' rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria. CONCLUSIONS: Since nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli's central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.

SkiVis: Visual Exploration and Route Planning in Ski Resorts.

Optimal ski route selection is a challenge based on a multitude of factors, such as the steepness, compass direction, or crowdedness. The personal preferences of every skier towards these factors require individual adaptations, which aggravate this task. Current approaches within this domain do not combine automated routing capabilities with user preferences, missing out on the possibility of integrating domain knowledge in the analysis process. We introduce SkiVis, a visual analytics application to interactively explore ski slopes and provide routing recommendations based on user preferences. In collaboration with ski guides and enthusiasts, we elicited requirements and guidelines for such an application and propose different workflows depending on the skiers' familiarity with the resort. In a case study on the resort of Ski Arlberg, we illustrate how to leverage volunteered geographic information to enable a numerical comparison between slopes. We evaluated our approach through a pair-analytics study and demonstrate how it supports skiers in discovering relevant and preference-based ski routes. Besides the tasks investigated in the study, we derive additional use cases from the interviews that showcase the further potential of SkiVis, and contribute directions for further research opportunities.

Comparative Evaluation of Animated Scatter Plot Transitions.

Scatter plots are popular for displaying 2D data, but in practice, many data sets have more than two dimensions. For the analysis of such multivariate data, it is often necessary to switch between scatter plots of different dimension pairs, e.g., in a scatter plot matrix (SPLOM). Alternative approaches include a "grand tour" for an overview of the entire data set or creating artificial axes from dimensionality reduction (DR). A cross-cutting concern in all techniques is the ability of viewers to find correspondence between data points in different views. Previous work proposed animations to preserve the mental map between view changes and to trace points as well as clusters between scatter plots of the same underlying data set. In this article, we evaluate a variety of spline- and rotation-based view transitions in a crowdsourced user study focusing on ecological validity. Using the study results, we assess each animation's suitability for tracing points and clusters across view changes. We evaluate whether the order of horizontal and vertical rotation is relevant for task accuracy. The results show that rotations with an orthographic camera or staged expansion of a depth axis significantly outperform all other animation techniques for the traceability of individual points. Further, we provide a ranking of the animated transition techniques for traceability of individual points. However, we could not find any significant differences for the traceability of clusters. Furthermore, we identified differences by animation direction that could guide further studies to determine potential confounds for these differences. We publish the study data for reuse and provide the animation framework as a D3.js plug-in.

TreEducation: A Visual Education Platform for Teaching Treemap Layout Algorithms.

Treemaps are a powerful tool for representing hierarchical data in a space-efficient manner and are used in various domains, including network security or software development. However, interpreting the topology encoded by nested rectangles can be challenging, particularly compared to tree-structured representations like node-link diagrams or icicle plots. To address this challenge, we introduce TreEducation, a visual education platform designed to improve the visualization literacy skills required for reading treemaps among non-expert users. TreEducation is an online application that combines visualizations, interactions, and gamification elements to facilitate understanding of eight different treemap layout algorithms and enhance students' learning process. We evaluated TreEducation in a classroom setting and a controlled environment. Our results indicate a significant knowledge gain of students training exclusively with TreEducation and the usefulness of competition as a social gamification element included in our competitive quiz.

FS/DS: A Theoretical Framework for the Dual Analysis of Feature Space and Data Space.

With the surge of data-driven analysis techniques, there is a rising demand for enhancing the exploration of large high-dimensional data by enabling interactions for the joint analysis of features (i.e., dimensions). Such a dual analysis of the feature space and data space is characterized by three components, (1) a view visualizing feature summaries, (2) a view that visualizes the data records, and (3) a bidirectional linking of both plots triggered by human interaction in one of both visualizations, e.g., Linking & Brushing. Dual analysis approaches span many domains, e.g., medicine, crime analysis, and biology. The proposed solutions encapsulate various techniques, such as feature selection or statistical analysis. However, each approach establishes a new definition of dual analysis. To address this gap, we systematically reviewed published dual analysis methods to investigate and formalize the key elements, such as the techniques used to visualize the feature space and data space, as well as the interaction between both spaces. From the information elicited during our review, we propose a unified theoretical framework for dual analysis, encompassing all existing approaches extending the field. We apply our proposed formalization describing the interactions between each component and relate them to the addressed tasks. Additionally, we categorize the existing approaches using our framework and derive future research directions to advance dual analysis by including state-of-the-art visual analysis techniques to improve data exploration.

Investigating the Sketchplan: A Novel Way of Identifying Tactical Behavior in Massive Soccer Datasets.

Coaches and analysts prepare for upcoming matches by identifying common patterns in the positioning and movement of the competing teams in specific situations. Existing approaches in this domain typically rely on manual video analysis and formation discussion using whiteboards; or expert systems that rely on state-of-the-art video and trajectory visualization techniques and advanced user interaction. We bridge the gap between these approaches by contributing a light-weight, simplified interaction and visualization system, which we conceptualized in an iterative design study with the coaching team of a European first league soccer team. Our approach is walk-up usable by all domain stakeholders, and at the same time, can leverage advanced data retrieval and analysis techniques: a virtual magnetic tactic-board. Users place and move digital magnets on a virtual tactic-board, and these interactions get translated to spatio-temporal queries, used to retrieve relevant situations from massive team movement data. Despite such seemingly imprecise query input, our approach is highly usable, supports quick user exploration, and retrieval of relevant results via query relaxation. Appropriate simplified result visualization supports in-depth analyses to explore team behavior, such as formation detection, movement analysis, and what-if analysis. We evaluated our approach with several experts from European first league soccer clubs. The results show that our approach makes the complex analytical processes needed for the identification of tactical behavior directly accessible to domain experts for the first time, demonstrating our support of coaches in preparation for future encounters.

Multiscale Visualization: A Structured Literature Analysis.

Multiscale visualizations are typically used to analyze multiscale processes and data in various application domains, such as the visual exploration of hierarchical genome structures in molecular biology. However, creating such multiscale visualizations remains challenging due to the plethora of existing work and the expression ambiguity in visualization research. Up to today, there has been little work to compare and categorize multiscale visualizations to understand their design practices. In this article, we present a structured literature analysis to provide an overview of common design practices in multiscale visualization research. We systematically reviewed and categorized 122 published journal or conference articles between 1995 and 2020. We organized the reviewed articles in a taxonomy that reveals common design factors. Researchers and practitioners can use our taxonomy to explore existing work to create new multiscale navigation and visualization techniques. Based on the reviewed articles, we examine research trends and highlight open research challenges.

Visual Comparison of Networks in VR.

Networks are an important means for the representation and analysis of data in a variety of research and application areas. While there are many efficient methods to create layouts for networks to support their visual analysis, approaches for the comparison of networks are still underexplored. Especially when it comes to the comparison of weighted networks, which is an important task in several areas, such as biology and biomedicine, there is a lack of efficient visualization approaches. With the availability of affordable high-quality virtual reality (VR) devices, such as head-mounted displays (HMDs), the research field of immersive analytics emerged and showed great potential for using the new technology for visual data exploration. However, the use of immersive technology for the comparison of networks is still underexplored. With this work, we explore how weighted networks can be visually compared in an immersive VR environment and investigate how visual representations can benefit from the extended 3D design space. For this purpose, we develop different encodings for 3D node-link diagrams supporting the visualization of two networks within a single representation and evaluate them in a pilot user study. We incorporate the results into a more extensive user study comparing node-link representations with matrix representations encoding two networks simultaneously. The data and tasks designed for our experiments are similar to those occurring in real-world scenarios. Our evaluation shows significantly better results for the node-link representations, which is contrary to comparable 2D experiments and indicates a high potential for using VR for the visual comparison of networks.

Task-Based Visual Interactive Modeling: Decision Trees and Rule-Based Classifiers.

Visual analytics enables the coupling of machine learning models and humans in a tightly integrated workflow, addressing various analysis tasks. Each task poses distinct demands to analysts and decision-makers. In this survey, we focus on one canonical technique for rule-based classification, namely decision tree classifiers. We provide an overview of available visualizations for decision trees with a focus on how visualizations differ with respect to 16 tasks. Further, we investigate the types of visual designs employed, and the quality measures presented. We find that (i) interactive visual analytics systems for classifier development offer a variety of visual designs, (ii) utilization tasks are sparsely covered, (iii) beyond classifier development, node-link diagrams are omnipresent, (iv) even systems designed for machine learning experts rarely feature visual representations of quality measures other than accuracy. In conclusion, we see a potential for integrating algorithmic techniques, mathematical quality measures, and tailored interactive visualizations to enable human experts to utilize their knowledge more effectively.

Why Visualize? Untangling a Large Network of Arguments.

Visualization has been deemed a useful technique by researchers and practitioners, alike, leaving a trail of arguments behind that reason why visualization works. In addition, examples of misleading usages of visualizations in information communication have occasionally been pointed out. Thus, to contribute to the fundamental understanding of our discipline, we require a comprehensive collection of arguments on "why visualize?" (or "why not?"), untangling the rationale behind positive and negative viewpoints. In this paper, we report a theoretical study to understand the underlying reasons of various arguments; their relationships (e.g., built-on, and conflict); and their respective dependencies on tasks, users, and data. We curated an argumentative network based on a collection of arguments from various fields, including information visualization, cognitive science, psychology, statistics, philosophy, and others. Our work proposes several categorizations for the arguments, and makes their relations explicit. We contribute the first comprehensive and systematic theoretical study of the arguments on visualization. Thereby, we provide a roadmap towards building a foundation for visualization theory and empirical research as well as for practical application in the critique and design of visualizations. In addition, we provide our argumentation network and argument collection online at https://whyvis.dbvis.de, supported by an interactive visualization.

Visual Analytics for Temporal Hypergraph Model Exploration.

Many processes, from gene interaction in biology to computer networks to social media, can be modeled more precisely as temporal hypergraphs than by regular graphs. This is because hypergraphs generalize graphs by extending edges to connect any number of vertices, allowing complex relationships to be described more accurately and predict their behavior over time. However, the interactive exploration and seamless refinement of such hypergraph-based prediction models still pose a major challenge. We contribute Hyper-Matrix, a novel visual analytics technique that addresses this challenge through a tight coupling between machine-learning and interactive visualizations. In particular, the technique incorporates a geometric deep learning model as a blueprint for problem-specific models while integrating visualizations for graph-based and category-based data with a novel combination of interactions for an effective user-driven exploration of hypergraph models. To eliminate demanding context switches and ensure scalability, our matrix-based visualization provides drill-down capabilities across multiple levels of semantic zoom, from an overview of model predictions down to the content. We facilitate a focused analysis of relevant connections and groups based on interactive user-steering for filtering and search tasks, a dynamically modifiable partition hierarchy, various matrix reordering techniques, and interactive model feedback. We evaluate our technique in a case study and through formative evaluation with law enforcement experts using real-world internet forum communication data. The results show that our approach surpasses existing solutions in terms of scalability and applicability, enables the incorporation of domain knowledge, and allows for fast search-space traversal. With the proposed technique, we pave the way for the visual analytics of temporal hypergraphs in a wide variety of domains.

MultiSegVA: Using Visual Analytics to Segment Biologging Time Series on Multiple Scales.

Segmenting biologging time series of animals on multiple temporal scales is an essential step that requires complex techniques with careful parameterization and possibly cross-domain expertise. Yet, there is a lack of visual-interactive tools that strongly support such multi-scale segmentation. To close this gap, we present our MultiSegVA platform for interactively defining segmentation techniques and parameters on multiple temporal scales. MultiSegVA primarily contributes tailored, visual-interactive means and visual analytics paradigms for segmenting unlabeled time series on multiple scales. Further, to flexibly compose the multi-scale segmentation, the platform contributes a new visual query language that links a variety of segmentation techniques. To illustrate our approach, we present a domain-oriented set of segmentation techniques derived in collaboration with movement ecologists. We demonstrate the applicability and usefulness of MultiSegVA in two real-world use cases from movement ecology, related to behavior analysis after environment-aware segmentation, and after progressive clustering. Expert feedback from movement ecologists shows the effectiveness of tailored visual-interactive means and visual analytics paradigms at segmenting multi-scale data, enabling them to perform semantically meaningful analyses. A third use case demonstrates that MultiSegVA is generalizable to other domains.

The Role of Interactive Visualization in Fostering Trust in AI.

The increasing use of artificial intelligence (AI) technologies across application domains has prompted our society to pay closer attention to AI's trustworthiness, fairness, interpretability, and accountability. In order to foster trust in AI, it is important to consider the potential of interactive visualization, and how such visualizations help build trust in AI systems. This manifesto discusses the relevance of interactive visualizations and makes the following four claims: i) trust is not a technical problem, ii) trust is dynamic, iii) visualization cannot address all aspects of trust, and iv) visualization is crucial for human agency in AI.

Virtual Reality Potentiates Emotion and Task Effects of Alpha/Beta Brain Oscillations.

The progress of technology has increased research on neuropsychological emotion and attention with virtual reality (VR). However, direct comparisons between conventional two-dimensional (2D) and VR stimulations are lacking. Thus, the present study compared electroencephalography (EEG) correlates of explicit task and implicit emotional attention between 2D and VR stimulation. Participants (n = 16) viewed angry and neutral faces with equal size and distance in both 2D and VR, while they were asked to count one of the two facial expressions. For the main effects of emotion (angry vs. neutral) and task (target vs. nontarget), established event related potentials (ERP), namely the late positive potential (LPP) and the target P300, were replicated. VR stimulation compared to 2D led to overall bigger ERPs but did not interact with emotion or task effects. In the frequency domain, alpha/beta-activity was larger in VR compared to 2D stimulation already in the baseline period. Of note, while alpha/beta event related desynchronization (ERD) for emotion and task conditions were seen in both VR and 2D stimulation, these effects were significantly stronger in VR than in 2D. These results suggest that enhanced immersion with the stimulus materials enabled by VR technology can potentiate induced brain oscillation effects to implicit emotion and explicit task effects.

Perspectives on the 2 × 2 Matrix: Solving Semantically Distinct Problems Based on a Shared Structure of Binary Contingencies.

Cognition is both empowered and limited by representations. The matrix lens model explicates tasks that are based on frequency counts, conditional probabilities, and binary contingencies in a general fashion. Based on a structural analysis of such tasks, the model links several problems and semantic domains and provides a new perspective on representational accounts of cognition that recognizes representational isomorphs as opportunities, rather than as problems. The shared structural construct of a 2 × 2 matrix supports a set of generic tasks and semantic mappings that provide a unifying framework for understanding problems and defining scientific measures. Our model's key explanatory mechanism is the adoption of particular perspectives on a 2 × 2 matrix that categorizes the frequency counts of cases by some condition, treatment, risk, or outcome factor. By the selective steps of filtering, framing, and focusing on specific aspects, the measures used in various semantic domains negotiate distinct trade-offs between abstraction and specialization. As a consequence, the transparent communication of such measures must explicate the perspectives encapsulated in their derivation. To demonstrate the explanatory scope of our model, we use it to clarify theoretical debates on biases and facilitation effects in Bayesian reasoning and to integrate the scientific measures from various semantic domains within a unifying framework. A better understanding of problem structures, representational transparency, and the role of perspectives in the scientific process yields both theoretical insights and practical applications.

Teaching Clustering Algorithms With EduClust: Experience Report and Future Directions.

We share our experiences teaching university students about clustering algorithms using EduClust, an online visualization we developed. EduClust supports professors in preparing teaching material and students in visually and interactively exploring cluster steps and the effects of changing clustering parameters. We used EduClust for two years in our computer science lectures on clustering algorithms and share our experience integrating the online application in a data science curriculum. We also point to opportunities for future development.