Uncertainty in phylogenetic tree estimates

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly model the multivariate uncertainty of tree estimates. We consider both the cases where uncertainty information arises extrinsically (through covariate information) and intrinsically (through the tree estimates themselves). The importance of accounting for tree uncertainty in tree space is demonstrated in two case studies. In the first instance, differences between gene trees are small relative to their uncertainties, while in the second, the differences are relatively large. Our main goal is visualization of tree uncertainty, and we demonstrate advantages of our method with respect to reproducibility, speed and preservation of topological differences compared to visualization based on multidimensional scaling. The proposal highlights that phylogenetic trees are estimated in an extremely high-dimensional space, resulting in uncertainty information that cannot be discarded. Most importantly, it is a method that allows biologists to diagnose whether differences between gene trees are biologically meaningful, or due to uncertainty in estimation.Comment: Final version accepted to Journal of Computational and Graphical Statistic

Design Patterns for Situated Visualization in Augmented Reality

Situated visualization has become an increasingly popular research area in the visualization community, fueled by advancements in augmented reality (AR) technology and immersive analytics. Visualizing data in spatial proximity to their physical referents affords new design opportunities and considerations not present in traditional visualization, which researchers are now beginning to explore. However, the AR research community has an extensive history of designing graphics that are displayed in highly physical contexts. In this work, we leverage the richness of AR research and apply it to situated visualization. We derive design patterns which summarize common approaches of visualizing data in situ. The design patterns are based on a survey of 293 papers published in the AR and visualization communities, as well as our own expertise. We discuss design dimensions that help to describe both our patterns and previous work in the literature. This discussion is accompanied by several guidelines which explain how to apply the patterns given the constraints imposed by the real world. We conclude by discussing future research directions that will help establish a complete understanding of the design of situated visualization, including the role of interactivity, tasks, and workflows.Comment: To appear in IEEE VIS 202

A debate dashboard to enhance on-line knowledge sharing

Purpose – Web 2.0 technologies have radically modified the way in which knowledge is created, managed and shared, improving productivity and accelerating innovation processes for the enterprises. These technologies have allowed enterprises to produce knowledge, leverage collective intelligence and build social capital on a scale that was unimaginable a few years ago. In this paper we focus on a particular kind of web-based collaborative platforms known as argument mapping tools and we discuss the main barriers to the adoption of them. Literature has proved that these argument mapping tools provide large and small and medium enterprise with several advantages, but nevertheless, they have low level adoption. In this paper we explore new technological solutions to support the adoption of argument mapping tools. In particular, we propose the design of a Debate Dashboard to provide visual feedback to support online deliberation. These visual feedback aims at compensating the loss of information due to the mediation of the technology. The Debate Dashboard is composed of a set of suitable visualization tools that have been selected on the basis of a literature review of the visualization tools. Design/methodology/approach - We propose a literature review of existing visualization tools. Building on the literature review we selected thirty visualization tools, which have been classified on the basis of the kind of feedback they are able to provide. We identify three classes of feedback: Community feedback (identikit of users), Interaction feedback (about how users interact) and Absorption feedback (about generated content and its organization). We distilled the Debate Dashboard features by building on results of a literature review on Web 2.0 tools for data visualization. As output of literature review we selected six visualization tools. We consider these selected tools as a sort of starting point. Indeed, our aim is the improvement of them through the addition of further features and functions in order to make them more effective in providing feedback. Originality/value – Our paper enriches the debate about computer mediated conversation and visualization tools. We propose a Dashboard prototype to augment collaborative knowledge mapping tools by providing visual feedback on conversations. The Dashboard will provide at the same time three different kinds of feedback about: details of the participants to the conversation, interaction processes and generated content. This will allow the improvement of the benefits and reduce the costs deriving from the use of mapping tools. Moreover, another important novelty is that visualization tools will be integrated to mapping tools, as until now they have been used only to visualize data contained in forums (as Usenet or Slash.dot), chat or email archives Practical implications – The Dashboard provides feedback about participants, interaction processes and generated contents, thus supporting the adoption of mapping tools as technologies able to foster knowledge sharing among remote workers or/and customers and supplier. The integration of Debate Dashboard with common online argument mapping tools aims at enabling the following advantages: 1. Reduction of misunderstanding; 2. Reduction of cognitive effort required to use argument mapping tools; 3. Improvement of the exploration and the analysis of the maps - the Debate Dashboard feedback improves the usability of the object (the map), thus allowing users to pitch into the conversation in the right place

Visualizing Europe's demographic scars with coplots and contour plots

We present two enhancements to existing methods for visualizing vital statistics data. Data from the Human Mortality Database were used and vital statistics from England and Wales are used for illustration. The simpler of these methods involves coplotting mean age of death with its variance, and the more complex of these methods is to present data as a contour plot. The coplot method shows the effect of the 20th century’s epidemiological transitions. The contour plot method allows more complex and subtle age, period and cohort effects to be seen.<p></p> The contour plot shows the effects of broad improvements in public health over the 20th century, including vast reductions in rates of childhood mortality, reduced baseline mortality risks during adulthood and the postponement of higher mortality risks to older ages. They also show the effects of the two world wars and the 1918 influenza pandemic on men of fighting age, women and children. The contour plots also show a cohort effect for people born around 1918, suggesting a possible epigenetic effect of parental exposure to the pandemic which shortened the cohort’s lifespan and which has so far received little attention.<p></p> Although this article focuses on data from England and Wales, the associated online appendices contain equivalent visualizations for almost 50 series of data available on the Human Mortality Database. We expect that further analyses of these visualizations will reveal further insights into global public health.<p></p&gt

The 20th Anniversary Meeting of the Rocky Mountain Virology Association

Due to the COVID-19 pandemic and multiple devastating forest fires, the 2020 meeting of the Rocky Mountain Virology Association was held virtually. The three-day gathering featured talks describing recent advances in virology and prion research. The keynote presentation described the measles virus paradox of immune suppression and life-long immunity. Special invited speakers presented information concerning visualizing antiviral effector cell biology in mucosal tissues, uncovering the T-cell tropism of Epstein-Barr virus type 2, a history and current survey of coronavirus spike proteins, a summary of Zika virus vaccination and immunity, the innate immune response to flavivirus infections, a discussion concerning prion disease as it relates to multiple system atrophy, and clues for discussing virology with the non-virologist. On behalf of the Rocky Mountain Virology Association, this report summarizes selected presentations