Taxonomy-Based Glyph Design—with a Case Study on Visualizing Workflows of Biological Experiments

Path-Based Design Model for Constructing and Exploring Alternative Visualisations

We present a path-based design model and system for designing and creating visualisations. Our model represents a systematic approach to constructing visual representations of data or concepts following a predefined sequence of steps. The initial step involves outlining the overall appearance of the visualisation by creating a skeleton structure, referred to as a flowpath. Subsequently, we specify objects, visual marks, properties, and appearance, storing them in a gene. Lastly, we map data onto the flowpath, ensuring suitable morphisms. Alternative designs are created by exchanging values in the gene. For example, designs that share similar traits, are created by making small incremental changes to the gene. Our design methodology fosters the generation of diverse creative concepts, space-filling visualisations, and traditional formats like bar charts, circular plots and pie charts. Through our implementation we showcase the model in action. As an example application, we integrate the output visualisations onto a smartwatch and visualisation dashboards. In this article we (1) introduce, define and explain the path model and discuss possibilities for its use, (2) present our implementation, results, and evaluation, and (3) demonstrate and evaluate an application of its use on a mobile watch.

RASIPAM: Interactive Pattern Mining of Multivariate Event Sequences in Racket Sports

Experts in racket sports like tennis and badminton use tactical analysis to gain insight into competitors' playing styles. Many data-driven methods apply pattern mining to racket sports data - which is often recorded as multivariate event sequences - to uncover sports tactics. However, tactics obtained in this way are often inconsistent with those deduced by experts through their domain knowledge, which can be confusing to those experts. This work introduces RASIPAM, a RAcket-Sports Interactive PAttern Mining system, which allows experts to incorporate their knowledge into data mining algorithms to discover meaningful tactics interactively. RASIPAM consists of a constraint-based pattern mining algorithm that responds to the analysis demands of experts: Experts provide suggestions for finding tactics in intuitive written language, and these suggestions are translated into constraints to run the algorithm. RASIPAM further introduces a tailored visual interface that allows experts to compare the new tactics with the original ones and decide whether to apply a given adjustment. This interactive workflow iteratively progresses until experts are satisfied with all tactics. We conduct a quantitative experiment to show that our algorithm supports real-time interaction. Two case studies in tennis and in badminton respectively, each involving two domain experts, are conducted to show the effectiveness and usefulness of the system.

Spatial proliferation of African swine fever virus in South Korea

The African swine fever virus (ASFV) was first detected in South Korea on a pig farm in September 2019. Despite active preventive measures to control the spread of ASFV, outbreaks on pig farms and in wild boar have been increasing. In this study, we investigated the spatial contamination area using the minimum convex polygon (MCP) approach, and growth rate using a logistic diffusion model. On the basis of the ASFV outbreak locations recorded from September 17^th, 2019, to May 20^th, 2022, the MCP area for the second week was 618.41 km² and expanded to 37959.67 km² in the final week. The maximum asymptote of the logistic function was considered as the land area of South Korea, and we estimated logistic growth rates of 0.022 km² per week and 0.094 km² per month. Administrative bodies should implement preventive and quarantine measures for infectious diseases. The results of this study will be a reference for epidemiologists, ecologists, and policy makers and contribute to the establishment of appropriate quarantine measures for disease control and management.

To Explore What Isn't There-Glyph-Based Visualization for Analysis of Missing Values

This article contributes a novel visualization method, Missingness Glyph, for analysis and exploration of missing values in data. Missing values are a common challenge in most data generating domains and may cause a range of analysis issues. Missingness in data may indicate potential problems in data collection and pre-processing, or highlight important data characteristics. While the development and improvement of statistical methods for dealing with missing data is a research area in its own right, mainly focussing on replacing missing values with estimated values, considerably less focus has been put on visualization of missing values. Nonetheless, visualization and explorative analysis has great potential to support understanding of missingness in data, and to enable gaining of novel insights into patterns of missingness in a way that statistical methods are unable to. The Missingness Glyph supports identification of relevant missingness patterns in data, and is evaluated and compared to two other visualization methods in context of the missingness patterns. The results are promising and confirms that the Missingness Glyph in several cases perform better than the alternative visualization methods.

GlyphCreator: Towards Example-based Automatic Generation of Circular Glyphs

Circular glyphs are used across disparate fields to represent multidimensional data. However, although these glyphs are extremely effective, creating them is often laborious, even for those with professional design skills. This paper presents GlyphCreator, an interactive tool for the example-based generation of circular glyphs. Given an example circular glyph and multidimensional input data, GlyphCreator promptly generates a list of design candidates, any of which can be edited to satisfy the requirements of a particular representation. To develop GlyphCreator, we first derive a design space of circular glyphs by summarizing relationships between different visual elements. With this design space, we build a circular glyph dataset and develop a deep learning model for glyph parsing. The model can deconstruct a circular glyph bitmap into a series of visual elements. Next, we introduce an interface that helps users bind the input data attributes to visual elements and customize visual styles. We evaluate the parsing model through a quantitative experiment, demonstrate the use of GlyphCreator through two use scenarios, and validate its effectiveness through user interviews.

Generative Design Inspiration for Glyphs with Diatoms

We introduce Diatoms, a technique that generates design inspiration for glyphs by sampling from palettes of mark shapes, encoding channels, and glyph scaffold shapes. Diatoms allows for a degree of randomness while respecting constraints imposed by columns in a data table: their data types and domains as well as semantic associations between columns as specified by the designer. We pair this generative design process with two forms of interactive design externalization that enable comparison and critique of the design alternatives. First, we incorporate a familiar small multiples configuration in which every data point is drawn according to a single glyph design, coupled with the ability to page between alternative glyph designs. Second, we propose a small permutables design gallery, in which a single data point is drawn according to each alternative glyph design, coupled with the ability to page between data points. We demonstrate an implementation of our technique as an extension to Tableau featuring three example palettes, and to better understand how Diatoms could fit into existing design workflows, we conducted interviews and chauffeured demos with 12 designers. Finally, we reflect on our process and the designers' reactions, discussing the potential of our technique in the context of visualization authoring systems. Ultimately, our approach to glyph design and comparison can kickstart and inspire visualization design, allowing for the serendipitous discovery of shape and channel combinations that would have otherwise been overlooked.

Tac-Miner: Visual Tactic Mining for Multiple Table Tennis Matches

In table tennis, tactics specified by three consecutive strokes represent the high-level competition strategies in matches. Effective detection and analysis of tactics can reveal the playing styles of players, as well as their strengths and weaknesses. However, tactical analysis in table tennis is challenging as the analysts can often be overwhelmed by the large quantity and high dimension of the data. Statistical charts have been extensively used by researchers to explore and visualize table tennis data. However, these charts cannot support efficient comparative and correlation analysis of complicated tactic attributes. Besides, existing studies are limited to the analysis of one match. However, one player's strategy can change along with his/her opponents in different matches. Therefore, the data of multiple matches can support a more comprehensive tactical analysis. To address these issues, we introduced a visual analytics system called Tac-Miner to allow analysts to effectively analyze, explore, and compare tactics of multiple matches based on the advanced embedding and dimension reduction algorithms along with an interactive glyph. We evaluate our glyph's usability through a user study and demonstrate the system's usefulness through a case study with insights approved by coaches and domain experts.

Competing Models: Inferring Exploration Patterns and Information Relevance via Bayesian Model Selection

Analyzing interaction data provides an opportunity to learn about users, uncover their underlying goals, and create intelligent visualization systems. The first step for intelligent response in visualizations is to enable computers to infer user goals and strategies through observing their interactions with a system. Researchers have proposed multiple techniques to model users, however, their frameworks often depend on the visualization design, interaction space, and dataset. Due to these dependencies, many techniques do not provide a general algorithmic solution to user exploration modeling. In this paper, we construct a series of models based on the dataset and pose user exploration modeling as a Bayesian model selection problem where we maintain a belief over numerous competing models that could explain user interactions. Each of these competing models represent an exploration strategy the user could adopt during a session. The goal of our technique is to make high-level and in-depth inferences about the user by observing their low-level interactions. Although our proposed idea is applicable to various probabilistic model spaces, we demonstrate a specific instance of encoding exploration patterns as competing models to infer information relevance. We validate our technique's ability to infer exploration bias, predict future interactions, and summarize an analytic session using user study datasets. Our results indicate that depending on the application, our method outperforms established baselines for bias detection and future interaction prediction. Finally, we discuss future research directions based on our proposed modeling paradigm and suggest how practitioners can use this method to build intelligent visualization systems that understand users' goals and adapt to improve the exploration process.

Depicting More Information in Enriched Squarified Treemaps with Layered Glyphs

The Treemap is one of the most relevant information visualization (InfoVis) techniques to support the analysis of large hierarchical data structures or data clusters. Despite that, Treemap still presents some challenges for data representation, such as the few options for visual data mappings and the inability to represent zero and negative values. Additionally, visualizing high dimensional data requires many hierarchies, which can impair data visualization. Thus, this paper proposes to add layered glyphs to Treemap’s items to mitigate these issues. Layered glyphs are composed of N partially visible layers, and each layer maps one data dimension to a visual variable. Since the area of the upper layers is always smaller than the bottom ones, the layers can be stacked to compose a multidimensional glyph. To validate this proposal, we conducted a user study to compare three scenarios of visual data mappings for Treemaps: only Glyphs (G), Glyphs and Hierarchy (GH), and only Hierarchy (H). Thirty-six volunteers with a background in InfoVis techniques, organized into three groups of twelve (one group per scenario), performed 8 InfoVis tasks using only one of the proposed scenarios. The results point that scenario GH presented the best accuracy while having a task-solving time similar to scenario H, which suggests that representing more data in Treemaps with layered glyphs enriched the Treemap visualization capabilities without impairing the data readability.

Using Dashboard Networks to Visualize Multiple Patient Histories: A Design Study on Post-Operative Prostate Cancer

In this design study, we present a visualization technique that segments patients' histories instead of treating them as raw event sequences, aggregates the segments using criteria such as the whole history or treatment combinations, and then visualizes the aggregated segments as static dashboards that are arranged in a dashboard network to show longitudinal changes. The static dashboards were developed in nine iterations, to show 15 important attributes from the patients' histories. The final design was evaluated with five non-experts, five visualization experts and four medical experts, who successfully used it to gain an overview of a 2,000 patient dataset, and to make observations about longitudinal changes and differences between two cohorts. The research represents a step-change in the detail of large-scale data that may be successfully visualized using dashboards, and provides guidance about how the approach may be generalized.

KnowledgePearls: Provenance-Based Visualization Retrieval

Storing analytical provenance generates a knowledge base with a large potential for recalling previous results and guiding users in future analyses. However, without extensive manual creation of meta information and annotations by the users, search and retrieval of analysis states can become tedious. We present KnowledgePearls, a solution for efficient retrieval of analysis states that are structured as provenance graphs containing automatically recorded user interactions and visualizations. As a core component, we describe a visual interface for querying and exploring analysis states based on their similarity to a partial definition of a requested analysis state. Depending on the use case, this definition may be provided explicitly by the user by formulating a search query or inferred from given reference states. We explain our approach using the example of efficient retrieval of demographic analyses by Hans Rosling and discuss our implementation for a fast look-up of previous states. Our approach is independent of the underlying visualization framework. We discuss the applicability for visualizations which are based on the declarative grammar Vega and we use a Vega-based implementation of Gapminder as guiding example. We additionally present a biomedical case study to illustrate how KnowledgePearls facilitates the exploration process by recalling states from earlier analyses.

A Systematic Review of Experimental Studies on Data Glyphs

We systematically reviewed 64 user-study papers on data glyphs to help researchers and practitioners gain an informed understanding of tradeoffs in the glyph design space. The glyphs we consider are individual representations of multi-dimensional data points, often meant to be shown in small-multiple settings. Over the past 60 years many different glyph designs were proposed and many of these designs have been subjected to perceptual or comparative evaluations. Yet, a systematic overview of the types of glyphs and design variations tested, the tasks under which they were analyzed, or even the study goals and results does not yet exist. In this paper we provide such an overview by systematically sampling and tabulating the literature on data glyph studies, listing their designs, questions, data, and tasks. In addition we present a concise overview of the types of glyphs and their design characteristics analyzed by researchers in the past, and a synthesis of the study results. Based on our meta analysis of all results we further contribute a set of design implications and a discussion on open research directions.

Glyph Visualization: A Fail-Safe Design Scheme Based on Quasi-Hamming Distances

In many spatial and temporal visualization applications, glyphs provide an effective means for encoding multivariate data. However, because glyphs are typically small, they are vulnerable to various perceptual errors. This article introduces the concept of a quasi-Hamming distance in the context of glyph design and examines the feasibility of estimating the quasi-Hamming distance between a pair of glyphs and the minimal Hamming distance for a glyph set. The authors demonstrate the design concept by developing a file-system event visualization that can depict the activities of multiple users.

3D hybrid modelling of vascular network formation

We develop an off-lattice, agent-based model to describe vasculogenesis, the de novo formation of blood vessels from endothelial progenitor cells during development. The endothelial cells that comprise our vessel network are viewed as linearly elastic spheres that move in response to the forces they experience. We distinguish two types of endothelial cells: vessel elements are contained within the network and tip cells are located at the ends of vessels. Tip cells move in response to mechanical forces caused by interactions with neighbouring vessel elements and the local tissue environment, chemotactic forces and a persistence force which accounts for their tendency to continue moving in the same direction. Vessel elements are subject to similar mechanical forces but are insensitive to chemotaxis. An angular persistence force representing interactions with the local tissue is introduced to stabilise buckling instabilities caused by cell proliferation. Only vessel elements proliferate, at rates which depend on their degree of stretch: elongated elements have increased rates of proliferation, and compressed elements have reduced rates. Following division, the fate of the new cell depends on the local mechanical environment: the probability of forming a new sprout is increased if the parent vessel is highly compressed and the probability of being incorporated into the parent vessel increased if the parent is stretched. Simulation results reveal that our hybrid model can reproduce the key qualitative features of vasculogenesis. Extensive parameter sensitivity analyses show that significant changes in network size and morphology are induced by varying the chemotactic sensitivity of tip cells, and the sensitivities of the proliferation rate and the sprouting probability to mechanical stretch. Varying the chemotactic sensitivity directly influences the directionality of the networks. The degree of branching, and thereby the density of the networks, is influenced by the sprouting probability. Glyphs that simultaneously depict several network properties are introduced to show how these and other network quantities change over time and also as model parameters vary. We also show how equivalent glyphs constructed from in vivo data could be used to discriminate between normal and tumour vasculature and, in the longer term, for model validation. We conclude that our biomechanical hybrid model can generate vascular networks that are qualitatively similar to those generated from in vitro and in vivo experiments.

Characterizing Provenance in Visualization and Data Analysis: An Organizational Framework of Provenance Types and Purposes

While the primary goal of visual analytics research is to improve the quality of insights and findings, a substantial amount of research in provenance has focused on the history of changes and advances throughout the analysis process. The term, provenance, has been used in a variety of ways to describe different types of records and histories related to visualization. The existing body of provenance research has grown to a point where the consolidation of design knowledge requires cross-referencing a variety of projects and studies spanning multiple domain areas. We present an organizational framework of the different types of provenance information and purposes for why they are desired in the field of visual analytics. Our organization is intended to serve as a framework to help researchers specify types of provenance and coordinate design knowledge across projects. We also discuss the relationships between these factors and the methods used to capture provenance information. In addition, our organization can be used to guide the selection of evaluation methodology and the comparison of study outcomes in provenance research.

PathwayMatrix: visualizing binary relationships between proteins in biological pathways

Background

Molecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules.

Results

In this paper, we introduce PathwayMatrix, a visualization tool that presents the binary relations between proteins in the pathway via the use of an interactive adjacency matrix. We provide filtering, lensing, clustering, and brushing and linking capabilities in order to present relevant details about proteins within a pathway.

Conclusions

We evaluated PathwayMatrix by conducting a series of in-depth interviews with domain experts who provided positive feedback, leading us to believe that our visualization technique could be helpful for the larger community of researchers utilizing pathway visualizations. PathwayMatrix is freely available at https://github.com/CreativeCodingLab/PathwayMatrix.

Glyph-Based Video Visualization for Semen Analysis

The existing efforts in computer assisted semen analysis have been focused on high speed imaging and automated image analysis of sperm motility. This results in a large amount of data, and it is extremely challenging for both clinical scientists and researchers to interpret, compare and correlate the multidimensional and time-varying measurements captured from video data. In this work, we use glyphs to encode a collection of numerical measurements taken at a regular interval and to summarize spatio-temporal motion characteristics using static visual representations. The design of the glyphs addresses the needs for (a) encoding some 20 variables using separable visual channels, (b) supporting scientific observation of the interrelationships between different measurements and comparison between different sperm cells and their flagella, and (c) facilitating the learning of the encoding scheme by making use of appropriate visual abstractions and metaphors. As a case study, we focus this work on video visualization for computer-aided semen analysis, which has a broad impact on both biological sciences and medical healthcare. We demonstrate that glyph-based visualization can serve as a means of external memorization of video data as well as an overview of a large set of spatiotemporal measurements. It enables domain scientists to make scientific observation in a cost-effective manner by reducing the burden of viewing videos repeatedly, while providing them with a new visual representation for conveying semen statistics.

Visualizing Cardiovascular Magnetic Resonance (CMR) imagery: challenges and opportunities

Cardiovascular Magnetic Resonance (CMR) imaging is an essential technique for measuring regional myocardial function. However, it is a time-consuming and cognitively demanding task to interpret, identify and compare various motion characteristics based on watching CMR imagery. In this work, we focus on the problems of visualising imagery resulting from 2D myocardial tagging in CMR. In particular we provide an overview of the current state of the art of relevant visualization techniques, and a discussion on why the problem is difficult from a perceptual perspective. Finally, we introduce a proof-of-concept multilayered visualization user interface for visualizing CMR data using multiple derived attributes encoded into multivariate glyphs. An initial evaluation of the system by clinicians suggested a great potential for this visualisation technology to become a clinical practice in the future.

Information visualisation for science and policy: engaging users and avoiding bias

Visualisations and graphics are fundamental to studying complex subject matter. However, beyond acknowledging this value, scientists and science-policy programmes rarely consider how visualisations can enable discovery, create engaging and robust reporting, or support online resources. Producing accessible and unbiased visualisations from complicated, uncertain data requires expertise and knowledge from science, policy, computing, and design. However, visualisation is rarely found in our scientific training, organisations, or collaborations. As new policy programmes develop [e.g., the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES)], we need information visualisation to permeate increasingly both the work of scientists and science policy. The alternative is increased potential for missed discoveries, miscommunications, and, at worst, creating a bias towards the research that is easiest to display.

Visual compression of workflow visualizations with automated detection of macro motifs

This paper is concerned with the creation of 'macros' in workflow visualization as a support tool to increase the efficiency of data curation tasks. We propose computation of candidate macros based on their usage in large collections of workflows in data repositories. We describe an efficient algorithm for extracting macro motifs from workflow graphs. We discovered that the state transition information, used to identify macro candidates, characterizes the structural pattern of the macro and can be harnessed as part of the visual design of the corresponding macro glyph. This facilitates partial automation and consistency in glyph design applicable to a large set of macro glyphs. We tested this approach against a repository of biological data holding some 9,670 workflows and found that the algorithmically generated candidate macros are in keeping with domain expert expectations.