DevLan/vispubs huggingface dataset:
Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data
Authors: Jared Jessup, Robert Krüger, Simon Warchol, John Hoffer, Jeremy Muhlich, Cecily C. Ritch, Giorgio Gaglia, Shannon Coy, Yu-An Chen, Jia-Ren Lin, Sandro Santagata, Peter K. Sorger, Hanspeter Pfister
Published at Vis, 2021

Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular information plus cell and tissue morphology using antibody staining. This provides unique insight into disease biology and promises to help with the design of patient-specific therapies. However, a substantial gap remains with respect to visualizing the resulting multivariate image data and effectively supporting pathology workflows in digital environments on screen. We, therefore, developed Scope2Screen, a scalable software system for focus+context exploration and annotation of whole-slide, high-plex, tissue images. Our approach scales to analyzing 100GB images of 109 or more pixels per channel, containing millions of individual cells. A multidisciplinary team of visualization experts, microscopists, and pathologists identified key image exploration and annotation tasks involving finding, magnifying, quantifying, and organizing regions of interest (ROIs) in an intuitive and cohesive manner. Building on a scope-to-screen metaphor, we present interactive lensing techniques that operate at single-cell and tissue levels. Lenses are equipped with task-specific functionality and descriptive statistics, making it possible to analyze image features, cell types, and spatial arrangements (neighborhoods) across image channels and scales. A fast sliding-window search guides users to regions similar to those under the lens; these regions can be analyzed and considered either separately or as part of a larger image collection. A novel snapshot method enables linked lens configurations and image statistics to be saved, restored, and shared with these regions. We validate our designs with domain experts and apply Scope2Screen in two case studies involving lung and colorectal cancers to discover cancer-relevant image features.
Seek for Success: A Visualization Approach for Understanding the Dynamics of Academic Careers
Authors: Yifang Wang 0001, Tai-Quan Peng, Huihua Lu, Haoren Wang, Xiao Xie, Huamin Qu, Yingcai Wu
Published at Vis, 2021

How to achieve academic career success has been a long-standing research question in social science research. With the growing availability of large-scale well-documented academic profiles and career trajectories, scholarly interest in career success has been reinvigorated, which has emerged to be an active research domain called the Science of Science (i.e., SciSci). In this study, we adopt an innovative dynamic perspective to examine how individual and social factors will influence career success over time. We propose ACSeeker, an interactive visual analytics approach to explore the potential factors of success and how the influence of multiple factors changes at different stages of academic careers. We first applied a Multi-factor Impact Analysis framework to estimate the effect of different factors on academic career success over time. We then developed a visual analytics system to understand the dynamic effects interactively. A novel timeline is designed to reveal and compare the factor impacts based on the whole population. A customized career line showing the individual career development is provided to allow a detailed inspection. To validate the effectiveness and usability of ACSeeker, we report two case studies and interviews with a social scientist and general researchers.
Semantic Snapping for Guided Multi-View Visualization Design
Authors: Yngve Sekse Kristiansen, Laura A. Garrison, Stefan Bruckner
Published at Vis, 2021

Visual information displays are typically composed of multiple visualizations that are used to facilitate an understanding of the underlying data. A common example are dashboards, which are frequently used in domains such as finance, process monitoring and business intelligence. However, users may not be aware of existing guidelines and lack expert design knowledge when composing such multi-view visualizations. In this paper, we present semantic snapping, an approach to help non-expert users design effective multi-view visualizations from sets of pre-existing views. When a particular view is placed on a canvas, it is “aligned” with the remaining views-not with respect to its geometric layout, but based on aspects of the visual encoding itself, such as how data dimensions are mapped to channels. Our method uses an on-the-fly procedure to detect and suggest resolutions for conflicting, misleading, or ambiguous designs, as well as to provide suggestions for alternative presentations. With this approach, users can be guided to avoid common pitfalls encountered when composing visualizations. Our provided examples and case studies demonstrate the usefulness and validity of our approach.
Sequen-C: A Multilevel Overview of Temporal Event Sequences
Authors: Jessica Magallanes, Tony Stone, Paul D. Morris, Suzanne Mason, Steven Wood, Maria-Cruz Villa-Uriol
Published at Vis, 2021

Building a visual overview of temporal event sequences with an optimal level-of-detail (i.e. simplified but informative) is an ongoing challenge - expecting the user to zoom into every important aspect of the overview can lead to missing insights. We propose a technique to build a multilevel overview of event sequences, whose granularity can be transformed across sequence clusters (vertical level-of-detail) or longitudinally (horizontal level-of-detail), using hierarchical aggregation and a novel cluster data representation Align-Score-Simplify. By default, the overview shows an optimal number of sequence clusters obtained through the average silhouette width metric - then users are able to explore alternative optimal sequence clusterings. The vertical level-of-detail of the overview changes along with the number of clusters, whilst the horizontal level-of-detail refers to the level of summarization applied to each cluster representation. The proposed technique has been implemented into a visualization system called Sequence Cluster Explorer (Sequen-C) that allows multilevel and detail-on-demand exploration through three coordinated views, and the inspection of data attributes at cluster, unique sequence, and individual sequence level. We present two case studies using real-world datasets in the healthcare domain: CUREd and MIMIC-III; which demonstrate how the technique can aid users to obtain a summary of common and deviating pathways, and explore data attributes for selected patterns.
Sibyl: Understanding and Addressing the Usability Challenges of Machine Learning In High-Stakes Decision Making
Authors: Alexandra Zytek, Dongyu Liu, Rhema Vaithianathan, Kalyan Veeramachaneni
Published at Vis, 2021

Machine learning (ML) is being applied to a diverse and ever-growing set of domains. In many cases, domain experts - who often have no expertise in ML or data science - are asked to use ML predictions to make high-stakes decisions. Multiple ML usability challenges can appear as result, such as lack of user trust in the model, inability to reconcile human-ML disagreement, and ethical concerns about oversimplification of complex problems to a single algorithm output. In this paper, we investigate the ML usability challenges that present in the domain of child welfare screening through a series of collaborations with child welfare screeners. Following the iterative design process between the ML scientists, visualization researchers, and domain experts (child screeners), we first identified four key ML challenges and honed in on one promising explainable ML technique to address them (local factor contributions). Then we implemented and evaluated our visual analytics tool, Sibyl, to increase the interpretability and interactivity of local factor contributions. The effectiveness of our tool is demonstrated by two formal user studies with 12 non-expert participants and 13 expert participants respectively. Valuable feedback was collected, from which we composed a list of design implications as a useful guideline for researchers who aim to develop an interpretable and interactive visualization tool for ML prediction models deployed for child welfare screeners and other similar domain experts.
SightBi: Exploring Cross-View Data Relationships with Biclusters
Authors: Maoyuan Sun, Abdul Rahman Shaikh, Hamed Alhoori, Jian Zhao 0010
Published at Vis, 2021

Multiple-view visualization (MV) has been heavily used in visual analysis tools for sensemaking of data in various domains (e.g., bioinformatics, cybersecurity and text analytics). One common task of visual analysis with multiple views is to relate data across different views. For example, to identify threats, an intelligence analyst needs to link people from a social network graph with locations on a crime-map, and then search for and read relevant documents. Currently, exploring cross-view data relationships heavily relies on view-coordination techniques (e.g., brushing and linking), which may require significant user effort on many trial-and-error attempts, such as repetitiously selecting elements in one view, and then observing and following elements highlighted in other views. To address this, we present SightBi, a visual analytics approach for supporting cross-view data relationship explorations. We discuss the design rationale of SightBi in detail, with identified user tasks regarding the use of cross-view data relationships. SightBi formalizes cross-view data relationships as biclusters, computes them from a dataset, and uses a bi-context design that highlights creating stand-alone relationship-views. This helps preserve existing views and offers an overview of cross-view data relationships to guide user exploration. Moreover, SightBi allows users to interactively manage the layout of multiple views by using newly created relationship-views. With a usage scenario, we demonstrate the usefulness of SightBi for sensemaking of cross-view data relationships.
Simultaneous Matrix Orderings for Graph Collections
Authors: Nathan van Beusekom, Wouter Meulemans, Bettina Speckmann
Published at Vis, 2021

Undirected graphs are frequently used to model phenomena that deal with interacting objects, such as social networks, brain activity and communication networks. The topology of an undirected graph $G$ can be captured by an adjacency matrix; this matrix in turn can be visualized directly to give insight into the graph structure. Which visual patterns appear in such a matrix visualization crucially depends on the ordering of its rows and columns. Formally defining the quality of an ordering and then automatically computing a high-quality ordering are both challenging problems; however, effective heuristics exist and are used in practice. Often, graphs do not exist in isolation but as part of a collection of graphs on the same set of vertices, for example, brain scans over time or of different people. To visualize such graph collections, we need a single ordering that works well for all matrices simultaneously. The current state-of-the-art solves this problem by taking a (weighted) union over all graphs and applying existing heuristics. However, this union leads to a loss of information, specifically in those parts of the graphs which are different. We propose a collection-aware approach to avoid this loss of information and apply it to two popular heuristic methods: leaf order and barycenter. The de-facto standard computational quality metrics for matrix ordering capture only block-diagonal patterns (cliques). Instead, we propose to use Moran's $I$, a spatial auto-correlation metric, which captures the full range of established patterns. Moran's $I$ refines previously proposed stress measures. Furthermore, the popular leaf order method heuristically optimizes a similar measure which further supports the use of Moran's $I$ in this context. An ordering that maximizes Moran's $I$ can be computed via solutions to the Traveling Salesperson Problem (TSP); orderings that approximate the optimal ordering can be computed more efficiently, using any of the approximation algorithms for metric TSP. We evaluated our methods for simultaneous orderings on real-world datasets using Moran's $I$ as the quality metric. Our results show that our collection-aware approach matches or improves performance compared to the union approach, depending on the similarity of the graphs in the collection. Specifically, our Moran's $I$-based collection-aware leaf order implementation consistently outperforms other implementations. Our collection-aware implementations carry no significant additional computational costs.
SPEULER: Semantics-preserving Euler Diagrams
Authors: Rebecca Kehlbeck, Jochen Görtler, Yunhai Wang, Oliver Deussen
Published at Vis, 2021

Creating comprehensible visualizations of highly overlapping set-typed data is a challenging task due to its complexity. To facilitate insights into set connectivity and to leverage semantic relations between intersections, we propose a fast two-step layout technique for Euler diagrams that are both well-matched and well-formed. Our method conforms to established form guidelines for Euler diagrams regarding semantics, aesthetics, and readability. First, we establish an initial ordering of the data, which we then use to incrementally create a planar, connected, and monotone dual graph representation. In the next step, the graph is transformed into a circular layout that maintains the semantics and yields simple Euler diagrams with smooth curves. When the data cannot be represented by simple diagrams, our algorithm always falls back to a solution that is not well-formed but still well-matched, whereas previous methods often fail to produce expected results. We show the usefulness of our method for visualizing set-typed data using examples from text analysis and infographics. Furthermore, we discuss the characteristics of our approach and evaluate our method against state-of-the-art methods.
STNet: An End-to-End Generative Framework for Synthesizing Spatiotemporal Super-Resolution Volumes
Authors: Jun Han 0010, Hao Zheng 0006, Danny Ziyi Chen, Chaoli Wang 0001
Published at Vis, 2021

We present STNet, an end-to-end generative framework that synthesizes spatiotemporal super-resolution volumes with high fidelity for time-varying data. STNet includes two modules: a generator and a spatiotemporal discriminator. The input to the generator is two low-resolution volumes at both ends, and the output is the intermediate and the two-ending spatiotemporal super-resolution volumes. The spatiotemporal discriminator, leveraging convolutional long short-term memory, accepts a spatiotemporal super-resolution sequence as input and predicts a conditional score for each volume based on its spatial (the volume itself) and temporal (the previous volumes) information. We propose an unsupervised pre-training stage using cycle loss to improve the generalization of STNet. Once trained, STNet can generate spatiotemporal super-resolution volumes from low-resolution ones, offering scientists an option to save data storage (i.e., sparsely sampling the simulation output in both spatial and temporal dimensions). We compare STNet with the baseline bicubic+linear interpolation, two deep learning solutions ($\mathsf{SSR}+\mathsf{TSF}$, STD), and a state-of-the-art tensor compression solution (TTHRESH) to show the effectiveness of STNet.
STRATISFIMAL LAYOUT: A modular optimization model for laying out layered node-link network visualizations
Authors: Sara Di Bartolomeo, Mirek Riedewald, Wolfgang Gatterbauer, Cody Dunne
Published at Vis, 2021

Node-link visualizations are a familiar and powerful tool for displaying the relationships in a network. The readability of these visualizations highly depends on the spatial layout used for the nodes. In this paper, we focus on computing layered layouts, in which nodes are aligned on a set of parallel axes to better expose hierarchical or sequential relationships. Heuristic-based layouts are widely used as they scale well to larger networks and usually create readable, albeit sub-optimal, visualizations. We instead use a layout optimization model that prioritizes optimality - as compared to scalability - because an optimal solution not only represents the best attainable result, but can also serve as a baseline to evaluate the effectiveness of layout heuristics. We take an important step towards powerful and flexible network visualization by proposing Stratisfimal Layout, a modular integer-linear-programming formulation that can consider several important readability criteria simultaneously — crossing reduction, edge bendiness, and nested and multi-layer groups. The layout can be adapted to diverse use cases through its modularity. Individual features can be enabled and customized depending on the application. We provide open-source and documented implementations of the layout, both for web-based and desktop visualizations. As a proof-of-concept, we apply it to the problem of visualizing complicated SQL queries, which have features that we believe cannot be addressed by existing layout optimization models. We also include a benchmark network generator and the results of an empirical evaluation to assess the performance trade-offs of our design choices. A full version of this paper with all appendices, data, and source code is available at osf.io/qdyt9 with live examples at https://visdunneright.github.io/stratisfimal/.
TacticFlow: Visual Analytics of Ever-Changing Tactics in Racket Sports
Authors: Jiang Wu, Dongyu Liu, Ziyang Guo, Qingyang Xu, Yingcai Wu
Published at Vis, 2021

Event sequence mining is often used to summarize patterns from hundreds of sequences but faces special challenges when handling racket sports data. In racket sports (e.g., tennis and badminton), a player hitting the ball is considered a multivariate event consisting of multiple attributes (e.g., hit technique and ball position). A rally (i.e., a series of consecutive hits beginning with one player serving the ball and ending with one player winning a point) thereby can be viewed as a multivariate event sequence. Mining frequent patterns and depicting how patterns change over time is instructive and meaningful to players who want to learn more short-term competitive strategies (i.e., tactics) that encompass multiple hits. However, players in racket sports usually change their tactics rapidly according to the opponent's reaction, resulting in ever-changing tactic progression. In this work, we introduce a tailored visualization system built on a novel multivariate sequence pattern mining algorithm to facilitate explorative identification and analysis of various tactics and tactic progression. The algorithm can mine multiple non-overlapping multivariate patterns from hundreds of sequences effectively. Based on the mined results, we propose a glyph-based Sankey diagram to visualize the ever-changing tactic progression and support interactive data exploration. Through two case studies with four domain experts in tennis and badminton, we demonstrate that our system can effectively obtain insights about tactic progression in most racket sports. We further discuss the strengths and the limitations of our system based on domain experts' feedback.
THALIS: Human-Machine Analysis of Longitudinal Symptoms in Cancer Therapy
Authors: Carla Floricel, Nafiul Nipu, Mikayla Biggs, Andrew Wentzel, Guadalupe Canahuate, Lisanne van Dijk, Abdallah Sherif Radwan Mohamed, Clifton D. Fuller, G. Elisabeta Marai
Published at Vis, 2021

Although cancer patients survive years after oncologic therapy, they are plagued with long-lasting or permanent residual symptoms, whose severity, rate of development, and resolution after treatment vary largely between survivors. The analysis and interpretation of symptoms is complicated by their partial co-occurrence, variability across populations and across time, and, in the case of cancers that use radiotherapy, by further symptom dependency on the tumor location and prescribed treatment. We describe THALIS, an environment for visual analysis and knowledge discovery from cancer therapy symptom data, developed in close collaboration with oncology experts. Our approach leverages unsupervised machine learning methodology over cohorts of patients, and, in conjunction with custom visual encodings and interactions, provides context for new patients based on patients with similar diagnostic features and symptom evolution. We evaluate this approach on data collected from a cohort of head and neck cancer patients. Feedback from our clinician collaborators indicates that THALIS supports knowledge discovery beyond the limits of machines or humans alone, and that it serves as a valuable tool in both the clinic and symptom research.
The Weighted Average Illusion: Biases in Perceived Mean Position in Scatterplots
Authors: Matt-Heun Hong, Jessica K. Witt, Danielle Albers Szafir
Published at Vis, 2021

Scatterplots can encode a third dimension by using additional channels like size or color (e.g. bubble charts). We explore a potential misinterpretation of trivariate scatterplots, which we call the weighted average illusion, where locations of larger and darker points are given more weight toward x- and y-mean estimates. This systematic bias is sensitive to a designer's choice of size or lightness ranges mapped onto the data. In this paper, we quantify this bias against varying size/lightness ranges and data correlations. We discuss possible explanations for its cause by measuring attention given to individual data points using a vision science technique called the centroid method. Our work illustrates how ensemble processing mechanisms and mental shortcuts can significantly distort visual summaries of data, and can lead to misjudgments like the demonstrated weighted average illusion.
ThreadStates: State-based Visual Analysis of Disease Progression
Authors: Qianwen Wang, Tali Mazor, Theresa Harbig, Ethan Cerami, Nils Gehlenborg
Published at Vis, 2021

A growing number of longitudinal cohort studies are generating data with extensive patient observations across multiple timepoints. Such data offers promising opportunities to better understand the progression of diseases. However, these observations are usually treated as general events in existing visual analysis tools. As a result, their capabilities in modeling disease progression are not fully utilized. To fill this gap, we designed and implemented ThreadStates, an interactive visual analytics tool for the exploration of longitudinal patient cohort data. The focus of ThreadStates is to identify the states of disease progression by learning from observation data in a human-in-the-loop manner. We propose a novel Glyph Matrix design and combine it with a scatter plot to enable seamless identification, observation, and refinement of states. The disease progression patterns are then revealed in terms of state transitions using Sankey-based visualizations. We employ sequence clustering techniques to find patient groups with distinctive progression patterns, and to reveal the association between disease progression and patient-level features. The design and development were driven by a requirement analysis and iteratively refined based on feedback from domain experts over the course of a 10-month design study. Case studies and expert interviews demonstrate that ThreadStates can successively summarize disease states, reveal disease progression, and compare patient groups.