Abstract We present the first empirical evaluation of techniques for encoding distributions of quantitative edge values within adjacency matrices. In many real‐world networks, edges represent not a single value but a set of measurements. While adjacency matrices preserve structural clarity, their compact cells limit the simultaneous display of multiple values. To address this, we explore edge encodings that represent distributions by two values: a measure of central tendency (mean, median, mode) and a measure of dispersion (standard deviation, variance, IQR). We select four possible encodings for evaluation that prior work has suggested are suitable for the limited space available in matrices: a bivariate color palette, embedded bar charts, and two overlaid‐mark designs mapping the primary attribute to color and the secondary attribute to area or angle. In a preregistered crowdsourced study with 156 participants, we assessed performance of these encodings across eight analytical tasks and collected readability and aesthetic ratings. Results reveal clear performance regimes: area‐based overlaid marks and bar charts achieved the highest overall performance; angle‐based marks show moderate but less stable performance, and bivariate color consistently underperforms these alternatives. These findings clarify how visual channels behave under strict constraints and delineate the strengths and limitations of key design choices for multivariate edge visualization.

Abstract Charts used for persuasion can easily veer into being outright misleading when, for instance, cherry‐picked data is paired with a deceptive caption, as is commonly encountered on social media. The rise of interactive time‐series data explorers for hotly debated topics makes such framing easy to produce and spread. Post‐hoc interventions like fact‐checking often arrive too late and suffer from persistence of belief. Prior work suggests that guardrails, in the form of contextual comparison lines embedded directly into charts, can reduce these effects. We propose and evaluate a practical set of guardrail sampling strategies for implementing such contextual lines in real systems. In a preregistered mixed‐design study with two real‐world scenarios (COVID‐19 and Stocks), participants viewed persuasive charts with different sets of guardrails and reported trust, estimated rank in the dataset, expressed their perceived completeness of context, as well as subjective preference for different tasks. Across scenarios, guardrails improved trust, accuracy of performance judgments, and perceived completeness of context compared to the control. Taken together, the study offers practical guardrail sampling methods, evidence of their contextual benefits, and insights into participants' preferences.

Abstract Decades of advocacy for reproducibility and replication have advanced open, transparent practices in the sciences. However, traditional notions of reproducibility fit poorly with design‐oriented visualization research, where insights emerge through subjective, situated, and iterative work. So how can we ensure rigor and transparency in processes that are inherently unreproducible? To introduce transparency in design‐oriented research, we propose to focus on traceability: surfacing the origin and development of research contributions based on rich sets of artifacts documenting the design process. We investigated traceability through a collaborative autoethnographic reflection that builds on several years of work exploring ways to make design‐oriented research transparent. This exploration includes an experiment to build a tool to support traceability, which we called tRRRacer. The tRRRacer tool provided a testbed for us to operationalize the three tenets of a traceable process: (1) Record abundant, annotated artifacts representative of research activities; (2) Report curated research threads that articulate rationale and evolution of the process, allowing others to (3) Read via interfaces that help retrace claims and assess plausibility. Reflecting on our experiences, we contribute a theorization of traceability and reflections on how we might support it.

Online user studies of visualizations, visual encodings, and interaction techniques are ubiquitous in visualization research. Yet, designing, conducting, and analyzing studies effectively is still a major burden. Although various packages support such user studies, most solutions address only facets of the experiment life cycle, make reproducibility difficult, or do not cater to nuanced study designs or interactions. We introduce reVISit 2, a software framework that supports visualization researchers at all stages of designing and conducting browser-based user studies. ReVISit supports researchers in the design, debug & pilot, data collection, analysis, and dissemination experiment phases by providing both technical affordances (such as replay of participant interactions) and sociotechnical aids (such as a mindfully maintained community of support). It is a proven system that can be (and has been) used in publication-quality studies-which we demonstrate through a series of experimental replications. We reflect on the design of the system via interviews and an analysis of its technical dimensions. Through this work, we seek to elevate the ease with which studies are conducted, improve the reproducibility of studies within our community, and support the construction of advanced interactive studies.

We investigate whether tactile charts support comprehension and learning of complex visualizations for blind and low-vision (BLV) individuals and contribute four tactile chart designs and an interview study. Visualizations are powerful tools for conveying data, yet BLV individuals typically can rely only on assistive technologies-primarily alternative texts-to access this information. Prior research shows the importance of mental models of chart types for interpreting these descriptions, yet BLV individuals have no means to build such a mental model based on images of visualizations. Tactile charts show promise to fill this gap in supporting the process of building mental models. Yet studies on tactile data representations mostly focus on simple chart types, and it is unclear whether they are also appropriate for more complex charts as would be found in scientific publications. Working with two BLV researchers, we designed 3D-printed tactile template charts with exploration instructions for four advanced chart types: UpSet plots, violin plots, clustered heatmaps, and faceted line charts. We then conducted an interview study with 12 BLV participants comparing whether using our tactile templates improves mental models and understanding of charts and whether this understanding translates to novel datasets experienced through alt texts. Thematic analysis shows that tactile models support chart type understanding and are the preferred learning method by BLV individuals. We also report participants' opinions on tactile chart design and their role in BLV education.

Data-driven decision making has become a popular practice in science, industry, and public policy. Yet data alone, as an imperfect and partial representation of reality, is often insufficient to make good analysis decisions. Knowledge about the context of a dataset, its strengths and weaknesses, and its applicability for certain tasks is essential. Analysts are often not only familiar with the data itself, but also have data hunches about their analysis subject. In this work, we present an interview study with analysts from a wide range of domains and with varied expertise and experience, inquiring about the role of contextual knowledge. We provide insights into how data is insufficient in analysts' workflows and how they incorporate other sources of knowledge into their analysis. We analyzed how knowledge of data shaped their analysis outcome. Based on the results, we suggest design opportunities to better and more robustly consider both knowledge and data in analysis processes.

Abstract Data visualizations are typically not accessible to blind and low‐vision (BLV) users. Automatically generating text descriptions offers an enticing mechanism for democratizing access to the information held in complex scientific charts, yet appropriate procedures for generating those texts remain elusive. Pursuing this issue, we study a single complex chart form: UpSet plots. UpSet Plots are a common way to analyze set data, an area largely unexplored by prior accessibility literature. By analyzing the patterns present in real‐world examples, we develop a system for automatically captioning any UpSet plot. We evaluated the utility of our captions via semi‐structured interviews with (N=11) BLV users and found that BLV users find them informative. In extensions, we find that sighted users can use our texts similarly to UpSet plots and that they are better than naive LLM usage.

Exploratory data science is an iterative process of obtaining, cleaning, profiling, analyzing, and interpreting data. This cyclical way of working creates challenges within the linear structure of computational notebooks, leading to issues with code quality, recall, and reproducibility. To remedy this, we present Loops, a set of visual support techniques for iterative and exploratory data analysis in computational notebooks. Loops leverages provenance information to visualize the impact of changes made within a notebook. In visualizations of the notebook provenance, we trace the evolution of the notebook over time and highlight differences between versions. Loops visualizes the provenance of code, markdown, tables, visualizations, and images and their respective differences. Analysts can explore these differences in detail in a separate view. Loops not only makes the analysis process transparent but also supports analysts in their data science work by showing the effects of changes and facilitating comparison of multiple versions. We demonstrate our approach's utility and potential impact in two use cases and feedback from notebook users from various backgrounds. This paper and all supplemental materials are available at https://osf.io/79eyn.

How do cancer cells grow, divide, proliferate, and die? How do drugs influence these processes? These are difficult questions that we can attempt to answer with a combination of time-series microscopy experiments, classification algorithms, and data visualization. However, collecting this type of data and applying algorithms to segment and track cells and construct lineages of proliferation is error-prone; and identifying the errors can be challenging since it often requires cross-checking multiple data types. Similarly, analyzing and communicating the results necessitates synthesizing different data types into a single narrative. State-of-the-art visualization methods for such data use independent line charts, tree diagrams, and images in separate views. However, this spatial separation requires the viewer of these charts to combine the relevant pieces of data in memory. To simplify this challenging task, we describe design principles for weaving cell images, time-series data, and tree data into a cohesive visualization. Our design principles are based on choosing a primary data type that drives the layout and integrates the other data types into that layout. We then introduce Aardvark, a system that uses these principles to implement novel visualization techniques. Based on Aardvark, we demonstrate the utility of each of these approaches for discovery, communication, and data debugging in a series of case studies.

Attempting to make sense of a phenomenon or crisis, social media users often share data visualizations and interpretations that can be erroneous or misleading. Prior work has studied how data visualizations can mislead, but do misleading visualizations reach a broad social media audience? And if so, do users amplify or challenge misleading interpretations? To answer these questions, we conducted a mixed-methods analysis of the public’s engagement with data visualization posts about COVID-19 on Twitter. Compared to posts with accurate visual insights, our results show that posts with misleading visualizations garner more replies in which the audiences point out nuanced fallacies and caveats in data interpretations. Based on the results of our thematic analysis of engagement, we identify and discuss important opportunities and limitations to effectively leveraging crowdsourced assessments to address data-driven misinformation.

Abstract Computational notebooks, such as Jupyter, support rich data visualization. However, even when visualizations in notebooks are interactive, they are a dead end: Interactive data manipulations, such as selections, applying labels, filters, categorizations, or fixes to column or cell values, could be efficiently applied in interactive visual components, but interactive components typically cannot manipulate Python data structures. Furthermore, actions performed in interactive plots are lost as soon as the cell is re‐run, prohibiting reusability and reproducibility. To remedy this problem, we introduce Persist, a family of techniques to (a) capture interaction provenance, enabling the persistence of interactions, and (b) map interactions to data manipulations that can be applied to dataframes. We implement our approach as a JupyterLab extension that supports tracking interactions in Vega‐Altair plots and in a data table view. Persist can re‐execute interaction provenance when a notebook or a cell is re‐executed, enabling reproducibility and re‐use. We evaluate Persist in a user study targeting data manipulations with 11 participants skilled in Python and Pandas, comparing it to traditional code‐based approaches. Participants were consistently faster and were able to correctly complete more tasks with Persist.

A common research process in visualization is for visualization researchers to collaborate with domain experts to solve particular applied data problems. While there is existing guidance and expertise around how to structure collaborations to strengthen research contributions, there is comparatively little guidance on how to navigate the implications of, and power produced through the socio-technical entanglements of collaborations. In this paper, we qualitatively analyze reflective interviews of past participants of collaborations from multiple perspectives: visualization graduate students, visualization professors, and domain collaborators. We juxtapose the perspectives of these individuals, revealing tensions about the tools that are built and the relationships that are formed — a complex web of competing motivations. Through the lens of matters of care, we interpret this web, concluding with considerations that both trouble and necessitate reformation of current patterns around collaborative work in visualization design studies to promote more equitable, useful, and care-ful outcomes.

Data visualizations can empower an audience to make informed decisions. At the same time, deceptive representations of data can lead to inaccurate interpretations while still providing an illusion of data-driven insights. Existing research on misleading visualizations primarily focuses on examples of charts and techniques previously reported to be deceptive. These approaches do not necessarily describe how charts mislead the general population in practice. We instead present an analysis of data visualizations found in a real-world discourse of a significant global event—Twitter posts with visualizations related to the COVID-19 pandemic. Our work shows that, contrary to conventional wisdom, violations of visualization design guidelines are not the dominant way people mislead with charts. Specifically, they do not disproportionately lead to reasoning errors in posters’ arguments. Through a series of examples, we present common reasoning errors and discuss how even faithfully plotted data visualizations can be used to support misinformation.

Abstract How do we ensure the veracity of science? The act of manipulating or fabricating scientific data has led to many high‐profile fraud cases and retractions. Detecting manipulated data, however, is a challenging and time‐consuming endeavor. Automated detection methods are limited due to the diversity of data types and manipulation techniques. Furthermore, patterns automatically flagged as suspicious can have reasonable explanations. Instead, we propose a nuanced approach where experts analyze tabular datasets, e.g., as part of the peer‐review process, using a guided, interactive visualization approach. In this paper, we present an analysis of how manipulated datasets are created and the artifacts these techniques generate. Based on these findings, we propose a suite of visualization methods to surface potential irregularities. We have implemented these methods in Ferret, a visualization tool for data forensics work. Ferret makes potential data issues salient and provides guidance on spotting signs of tampering and differentiating them from truthful data.

The trouble with data is that it frequently provides only an imperfect representation of a phenomenon of interest. Experts who are familiar with their datasets will often make implicit, mental corrections when analyzing a dataset, or will be cautious not to be overly confident about their findings if caveats are present. However, personal knowledge about the caveats of a dataset is typically not incorporated in a structured way, which is problematic if others who lack that knowledge interpret the data. In this work, we define such analysts' knowledge about datasets as data hunches. We differentiate data hunches from uncertainty and discuss types of hunches. We then explore ways of recording data hunches, and, based on a prototypical design, develop recommendations for designing visualizations that support data hunches. We conclude by discussing various challenges associated with data hunches, including the potential for harm and challenges for trust and privacy. We envision that data hunches will empower analysts to externalize their knowledge, facilitate collaboration and communication, and support the ability to learn from others' data hunches.

Data science is the practice of deriving insight from data, enabled by modeling, computational methods, interactive visual analysis, and domain-driven problem solving. Data science draws from methodology developed in such fields as applied mathematics, statistics, machine learning, data mining, data management, visualization, and HCI. It drives discoveries in business, economy, biology, medicine, environmental science, the physical sciences, the humanities and social sciences, and beyond. Machine learning and data mining and visualization are integral parts of data science, and essential to enable sophisticated analysis of data. Nevertheless, both research areas are currently still rather separated and investigated by different communities rather independently. The goal of this workshop is to bring researchers from both communities together in order to discuss common interests, to talk about practical issues in application-related projects, and to identify open research problems. This summary gives a brief overview of the ACM KDD Workshop on Visualization in Data Science (VDS at ACM KDD and IEEE VIS), which will take place virtually on Aug 14-18, 2022 (Held in conjunction with KDD'22). The workshop website is available at http://www.visualdatascience.org/2022/

Abstract Interactive visual analysis has many advantages, but an important disadvantage is that analysis processes and workflows cannot be easily stored and reused. This is in contrast to code‐based analysis workflows, which can simply be run on updated datasets, and adapted when necessary. In this paper, we introduce methods to capture workflows in interactive visualization systems for different interactions such as selections, filters, categorizing/grouping, labeling, and aggregation. These workflows can then be applied to updated datasets, making interactive visualization sessions reusable. We demonstrate this specification using an interactive visualization system that tracks interaction provenance, and allows generating workflows from the recorded actions. The system can then be used to compare different versions of datasets and apply workflows to them. Finally, we introduce a Python library that can load workflows and apply it to updated datasets directly in a computational notebook, providing a seamless bridge between computational workflows and interactive visualization tools.

Which drug is most promising for a cancer patient? A new microscopy-based approach for measuring the mass of individual cancer cells treated with different drugs promises to answer this question in only a few hours. However, the analysis pipeline for extracting data from these images is still far from complete automation: human intervention is necessary for quality control for preprocessing steps such as segmentation, adjusting filters, removing noise, and analyzing the result. To address this workflow, we developed Loon, a visualization tool for analyzing drug screening data based on quantitative phase microscopy imaging. Loon visualizes both derived data such as growth rates and imaging data. Since the images are collected automatically at a large scale, manual inspection of images and segmentations is infeasible. However, reviewing representative samples of cells is essential, both for quality control and for data analysis. We introduce a new approach for choosing and visualizing representative exemplar cells that retain a close connection to the low-level data. By tightly integrating the derived data visualization capabilities with the novel exemplar visualization and providing selection and filtering capabilities, Loon is well suited for making decisions about which drugs are suitable for a specific patient.

This February 2022 issue of theIEEE Transactions on Visualization and Computer Graphics (TVCG)contains the proceedings of IEEE VIS 2021, held online on October 24-29, 2021, with General Chairs from Tulane University and Universidade de Sao Paulo. With IEEE VIS 2021, the conference series is in its 32nd year.

Quantifying user performance with metrics such as time and accuracy does not show the whole picture when researchers evaluate complex, interactive visualization tools. In such systems, performance is often influenced by different analysis strategies that statistical analysis methods cannot account for. To remedy this lack of nuance, we propose a novel analysis methodology for evaluating complex interactive visualizations at scale. We implement our analysis methods in reVISit, which enables analysts to explore participant interaction performance metrics and responses in the context of users’ analysis strategies. Replays of participant sessions can aid in identifying usability problems during pilot studies and make individual analysis processes salient. To demonstrate the applicability of reVISit to visualization studies, we analyze participant data from two published crowdsourced studies. Our findings show that reVISit can be used to reveal and describe novel interaction patterns, to analyze performance differences between different analysis strategies, and to validate or challenge design decisions.

Data science is the practice of deriving insight from data, enabled by modeling, computational methods, interactive visual analysis, and domain-driven problem solving. Data science draws from methodology developed in such fields as applied mathematics, statistics, machine learning, data mining, data management, visualization, and HCI. It drives discoveries in business, economy, biology, medicine, environmental science, the physical sciences, the humanities and social sciences, and beyond. Machine learning and data mining and visualization are integral parts of data science, and essential to enable sophisticated analysis of data. Nevertheless, both research areas are currently still rather separated and investigated by different communities rather independently. The goal of this workshop is to bring researchers from both communities together in order to discuss common interests, to talk about practical issues in application-related projects, and to identify open research problems. This summary gives a brief overview of the ACM KDD Workshop on Visualization in Data Science (VDS at ACM KDD and IEEE VIS), which will take place virtually on Aug 14-18, 2021 (Held in conjunction with KDD'21). The workshop website is available at: http://www.visualdatascience.org/2021/

The size of large, geo-located datasets has reached scales where visualization of all data points is inefficient. Random sampling is a method to reduce the size of a dataset, yet it can introduce unwanted errors. We describe a method for subsampling of spatial data suitable for creating kernel density estimates from very large data and demonstrate that it results in less error than random sampling. We also introduce a method to ensure that thresholding of low values based on sampled data does not omit any regions above the desired threshold when working with sampled data. We demonstrate the effectiveness of our approach using both, artificial and real-world large geospatial datasets.

Design study is an established approach of conducting problem-driven visualization research. The academic visualization community has produced a large body of work for reporting on design studies, informed by a handful of theoretical frameworks, and applied to a broad range of application areas. The result is an abundance of reported insights into visualization design, with an emphasis on novel visualization techniques and systems as the primary contribution of these studies. In recent work we proposed a new, interpretivist perspective on design study and six companion criteria for rigor that highlight the opportunities for researchers to contribute knowledge that extends beyond visualization idioms and software. In this work we conducted a year-long collaboration with evolutionary biologists to develop an interactive tool for visual exploration of multivariate datasets and phylogenetic trees. During this design study we experimented with methods to support three of the rigor criteria: ABUNDANT, REFLEXIVE, and TRANSPARENT. As a result we contribute two novel visualization techniques for the analysis of multivariate phylogenetic datasets, three methodological recommendations for conducting design studies drawn from reflections over our process of experimentation, and two writing devices for reporting interpretivist design study. We offer this work as an example for implementing the rigor criteria to produce a diverse range of knowledge contributions.

Visualizing multivariate networks is challenging because of the trade-offs necessary for effectively encoding network topology and encoding the attributes associated with nodes and edges. A large number of multivariate network visualization techniques exist, yet there is little empirical guidance on their respective strengths and weaknesses. In this paper, we describe a crowdsourced experiment, comparing node-link diagrams with on-node encoding and adjacency matrices with juxtaposed tables. We find that node-link diagrams are best suited for tasks that require close integration between the network topology and a few attributes. Adjacency matrices perform well for tasks related to clusters and when many attributes need to be considered. We also reflect on our method of using validated designs for empirically evaluating complex, interactive visualizations in a crowdsourced setting. We highlight the importance of training, compensation, and provenance tracking.

Abstract Multivariate networks are made up of nodes and their relationships (links), but also data about those nodes and links as attributes. Most real‐world networks are associated with several attributes, and many analysis tasks depend on analyzing both, relationships and attributes. Visualization of multivariate networks, however, is challenging, especially when both the topology of the network and the attributes need to be considered concurrently. In this state‐of‐the‐art report, we analyze current practices and classify techniques along four axes: layouts, view operations, layout operations, and data operations. We also provide an analysis of tasks specific to multivariate networks and give recommendations for which technique to use in which scenario. Finally, we survey application areas and evaluation methodologies.

Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule.

The majority of diseases that are a significant challenge for public and individual heath are caused by a combination of hereditary and environmental factors. In this paper we introduce Lineage, a novel visual analysis tool designed to support domain experts who study such multifactorial diseases in the context of genealogies. Incorporating familial relationships between cases with other data can provide insights into shared genomic variants and shared environmental exposures that may be implicated in such diseases. We introduce a data and task abstraction, and argue that the problem of analyzing such diseases based on genealogical, clinical, and genetic data can be mapped to a multivariate graph visualization problem. The main contribution of our design study is a novel visual representation for tree-like, multivariate graphs, which we apply to genealogies and clinical data about the individuals in these families. We introduce data-driven aggregation methods to scale to multiple families. By designing the genealogy graph layout to align with a tabular view, we are able to incorporate extensive, multivariate attributes in the analysis of the genealogy without cluttering the graph. We validate our designs by conducting case studies with our domain collaborators.

Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out linearly, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link/adjacency matrix technique. We implement this concept in Juniper and complement it with a set of interaction techniques that enable analysts to dynamically grow, restructure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics and a multitype network of story characters, places, books, etc.

MOTIVATION: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. RESULTS: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. AVAILABILITY AND IMPLEMENTATION: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/ . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. RESULTS: In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. CONCLUSIONS: Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

Multivariate graphs are prolific across many fields, including transportation and neuroscience. A key task in graph analysis is the exploration of connectivity, to, for example, analyze how signals flow through neurons, or to explore how well different cities are connected by flights. While standard node-link diagrams are helpful in judging connectivity, they do not scale to large networks. Adjacency matrices also do not scale to large networks and are only suitable to judge connectivity of adjacent nodes. A key approach to realize scalable graph visualization are queries: instead of displaying the whole network, only a relevant subset is shown. Query-based techniques for analyzing connectivity in graphs, however, can also easily suffer from cluttering if the query result is big enough. To remedy this, we introduce techniques that provide an overview of the connectivity and reveal details on demand. We have two main contributions: (1) two novel visualization techniques that work in concert for summarizing graph connectivity; and (2) Graffinity, an open-source implementation of these visualizations supplemented by detail views to enable a complete analysis workflow. Graffinity was designed in a close collaboration with neuroscientists and is optimized for connectomics data analysis, yet the technique is applicable across domains. We validate the connectivity overview and our open-source tool with illustrative examples using flight and connectomics data.

The primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the non-linear nature of the exploratory process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses. In this paper we present CLUE (Capture, Label, Understand, Explain), a model that tightly integrates data exploration and presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author "Vistories", visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. We discuss how the CLUE approach can be integrated into visualization tools and provide a prototype implementation. Finally, we demonstrate the general applicability of the model in two usage scenarios: a Gapminder-inspired visualization to explore public health data and an example from molecular biology that illustrates how Vistories could be used in scientific journals. (see Figure 1 for visual abstract).

The analysis of paths in graphs is highly relevant in many domains. Typically, path-related tasks are performed in node-link layouts. Unfortunately, graph layouts often do not scale to the size of many real world networks. Also, many networks are multivariate, i.e., contain rich attribute sets associated with the nodes and edges. These attributes are often critical in judging paths, but directly visualizing attributes in a graph layout exacerbates the scalability problem. In this paper, we present visual analysis solutions dedicated to path-related tasks in large and highly multivariate graphs. We show that by focusing on paths, we can address the scalability problem of multivariate graph visualization, equipping analysts with a powerful tool to explore large graphs. We introduce Pathfinder (Figure 1), a technique that provides visual methods to query paths, while considering various constraints. The resulting set of paths is visualized in both a ranked list and as a node-link diagram. For the paths in the list, we display rich attribute data associated with nodes and edges, and the node-link diagram provides topological context. The paths can be ranked based on topological properties, such as path length or average node degree, and scores derived from attribute data. Pathfinder is designed to scale to graphs with tens of thousands of nodes and edges by employing strategies such as incremental query results. We demonstrate Pathfinder's fitness for use in scenarios with data from a coauthor network and biological pathways.

Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.

Content on computer screens is often inaccessible to users because it is hidden, e.g., occluded by other windows, outside the viewport, or overlooked. In search tasks, the efficient retrieval of sought content is important. Current software, however, only provides limited support to visualize hidden occurrences and rarely supports search synchronization crossing application boundaries. To remedy this situation, we introduce two novel visualization methods to guide users to hidden content. Our first method generates awareness for occluded or out-of-viewport content using see-through visualization. For content that is either outside the screen's viewport or for data sources not opened at all, our second method shows off-screen indicators and an on-demand smart preview. To reduce the chances of overlooking content, we use visual links, i.e., visible edges, to connect the visible content or the visible representations of the hidden content. We show the validity of our methods in a user study, which demonstrates that our technique enables a faster localization of hidden content compared to traditional search functionality and thereby assists users in information retrieval tasks.

Answering questions about complex issues often requires analysts to take into account information contained in multiple interconnected datasets. A common strategy in analyzing and visualizing large and heterogeneous data is dividing it into meaningful subsets. Interesting subsets can then be selected and the associated data and the relationships between the subsets visualized. However, neither the extraction and manipulation nor the comparison of subsets is well supported by state-of-the-art techniques. In this paper we present Domino, a novel multiform visualization technique for effectively representing subsets and the relationships between them. By providing comprehensive tools to arrange, combine, and extract subsets, Domino allows users to create both common visualization techniques and advanced visualizations tailored to specific use cases. In addition to the novel technique, we present an implementation that enables analysts to manage the wide range of options that our approach offers. Innovative interactive features such as placeholders and live previews support rapid creation of complex analysis setups. We introduce the technique and the implementation using a simple example and demonstrate scalability and effectiveness in a use case from the field of cancer genomics.

Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.

Jointly analyzing biological pathway maps and experimental data is critical for understanding how biological processes work in different conditions and why different samples exhibit certain characteristics. This joint analysis, however, poses a significant challenge for visualization. Current techniques are either well suited to visualize large amounts of pathway node attributes, or to represent the topology of the pathway well, but do not accomplish both at the same time. To address this we introduce enRoute, a technique that enables analysts to specify a path of interest in a pathway, extract this path into a separate, linked view, and show detailed experimental data associated with the nodes of this extracted path right next to it. This juxtaposition of the extracted path and the experimental data allows analysts to simultaneously investigate large amounts of potentially heterogeneous data, thereby solving the problem of joint analysis of topology and node attributes. As this approach does not modify the layout of pathway maps, it is compatible with arbitrary graph layouts, including those of hand-crafted, image-based pathway maps. We demonstrate the technique in context of pathways from the KEGG and the Wikipathways databases. We apply experimental data from two public databases, the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA) that both contain a wide variety of genomic datasets for a large number of samples. In addition, we make use of a smaller dataset of hepatocellular carcinoma and common xenograft models. To verify the utility of enRoute, domain experts conducted two case studies where they explore data from the CCLE and the hepatocellular carcinoma datasets in the context of relevant pathways.

Rankings are a popular and universal approach to structuring otherwise unorganized collections of items by computing a rank for each item based on the value of one or more of its attributes. This allows us, for example, to prioritize tasks or to evaluate the performance of products relative to each other. While the visualization of a ranking itself is straightforward, its interpretation is not, because the rank of an item represents only a summary of a potentially complicated relationship between its attributes and those of the other items. It is also common that alternative rankings exist which need to be compared and analyzed to gain insight into how multiple heterogeneous attributes affect the rankings. Advanced visual exploration tools are needed to make this process efficient. In this paper we present a comprehensive analysis of requirements for the visualization of multi-attribute rankings. Based on these considerations, we propose LineUp--a novel and scalable visualization technique that uses bar charts. This interactive technique supports the ranking of items based on multiple heterogeneous attributes with different scales and semantics. It enables users to interactively combine attributes and flexibly refine parameters to explore the effect of changes in the attribute combination. This process can be employed to derive actionable insights as to which attributes of an item need to be modified in order for its rank to change. Additionally, through integration of slope graphs, LineUp can also be used to compare multiple alternative rankings on the same set of items, for example, over time or across different attribute combinations. We evaluate the effectiveness of the proposed multi-attribute visualization technique in a qualitative study. The study shows that users are able to successfully solve complex ranking tasks in a short period of time.

Biological pathway maps are highly relevant tools for many tasks in molecular biology. They reduce the complexity of the overall biological network by partitioning it into smaller manageable parts. While this reduction of complexity is their biggest strength, it is, at the same time, their biggest weakness. By removing what is deemed not important for the primary function of the pathway, biologists lose the ability to follow and understand cross-talks between pathways. Considering these cross-talks is, however, critical in many analysis scenarios, such as judging effects of drugs. In this paper we introduce Entourage, a novel visualization technique that provides contextual information lost due to the artificial partitioning of the biological network, but at the same time limits the presented information to what is relevant to the analyst's task. We use one pathway map as the focus of an analysis and allow a larger set of contextual pathways. For these context pathways we only show the contextual subsets, i.e., the parts of the graph that are relevant to a selection. Entourage suggests related pathways based on similarities and highlights parts of a pathway that are interesting in terms of mapped experimental data. We visualize interdependencies between pathways using stubs of visual links, which we found effective yet not obtrusive. By combining this approach with visualization of experimental data, we can provide domain experts with a highly valuable tool. We demonstrate the utility of Entourage with case studies conducted with a biochemist who researches the effects of drugs on pathways. We show that the technique is well suited to investigate interdependencies between pathways and to analyze, understand, and predict the effect that drugs have on different cell types.

Identification and characterization of cancer subtypes are important areas of research that are based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools supporting this process, much of this work is done using ad-hoc scripts and static plots, which is inefficient and limits visual exploration of the data. To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data. StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill-down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi-dataset, multi-view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data-view relationships. StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.

As heterogeneous data from different sources are being increasingly linked, it becomes difficult for users to understand how the data are connected, to identify what means are suitable to analyze a given data set, or to find out how to proceed for a given analysis task. We target this challenge with a new model-driven design process that effectively codesigns aspects of data, view, analytics, and tasks. We achieve this by using the workflow of the analysis task as a trajectory through data, interactive views, and analytical processes. The benefits for the analysis session go well beyond the pure selection of appropriate data sets and range from providing orientation or even guidance along a preferred analysis path to a potential overall speedup, allowing data to be fetched ahead of time. We illustrate the design process for a biomedical use case that aims at determining a treatment plan for cancer patients from the visual analysis of a large, heterogeneous clinical data pool. As an example for how to apply the comprehensive design approach, we present Stack'n'flip, a sample implementation which tightly integrates visualizations of the actual data with a map of available data sets, views, and tasks, thus capturing and communicating the analytical workflow through the required data sets.

Filtering data is an essential process in a drill-down analysis of large data sets. Filtering can be necessary for several reasons. The main objective for filters is to uncover the relevant subsets of a dataset. Another, equally relevant goal is to reduce a dataset to dimensions to which either visualization or algorithmic analysis techniques scale. However, with multiple filters applied and possibly even logically combined, it becomes difficult for users to judge the effects of a filter chain. In this paper we present a simple, yet effective way to interactively visualize a sequence of filters and logical combinations of these. Such a visualized filter-pipeline allows analysts to easily judge the effect of every single filter and also their combination on the data set under investigation and therefore, leads to a faster and more efficient workflow. We also present an implementation of the proposed technique in an information visualization framework for the life sciences. The technique, however, could be employed in many other information visualization contexts as well.

Large volumes of real-world data often exhibit inhomogeneities: vertically in the form of correlated or independent dimensions and horizontally in the form of clustered or scattered data items. In essence, these inhomogeneities form the patterns in the data that researchers are trying to find and understand. Sophisticated statistical methods are available to reveal these patterns, however, the visualization of their outcomes is mostly still performed in a one-view-fits-all manner. In contrast, our novel visualization approach, VisBricks, acknowledges the inhomogeneity of the data and the need for different visualizations that suit the individual characteristics of the different data subsets. The overall visualization of the entire data set is patched together from smaller visualizations, there is one VisBrick for each cluster in each group of interdependent dimensions. Whereas the total impression of all VisBricks together gives a comprehensive high-level overview of the different groups of data, each VisBrick independently shows the details of the group of data it represents. State-of-the-art brushing and visual linking between all VisBricks furthermore allows the comparison of the groupings and the distribution of data items among them. In this paper, we introduce the VisBricks visualization concept, discuss its design rationale and implementation, and demonstrate its usefulness by applying it to a use case from the field of biomedicine.

Evaluating, comparing, and interpreting related pieces of information are tasks that are commonly performed during visual data analysis and in many kinds of information-intensive work. Synchronized visual highlighting of related elements is a well-known technique used to assist this task. An alternative approach, which is more invasive but also more expressive is visual linking in which line connections are rendered between related elements. In this work, we present context-preserving visual links as a new method for generating visual links. The method specifically aims to fulfill the following two goals: first, visual links should minimize the occlusion of important information; second, links should visually stand out from surrounding information by minimizing visual interference. We employ an image-based analysis of visual saliency to determine the important regions in the original representation. A consequence of the image-based approach is that our technique is application-independent and can be employed in a large number of visual data analysis scenarios in which the underlying content cannot or should not be altered. We conducted a controlled experiment that indicates that users can find linked elements in complex visualizations more quickly and with greater subjective satisfaction than in complex visualizations in which plain highlighting is used. Context-preserving visual links were perceived as visually more attractive than traditional visual links that do not account for the context information.

The goal of our work is to support experts in the process of hypotheses generation concerning the roles of genes in diseases. For a deeper understanding of the complex interdependencies between genes, it is important to bring gene expressions (measurements) into context with pathways. Pathways, which are models of biological processes, are available in online databases. In these databases, large networks are decomposed into small sub-graphs for better manageability. This simplification results in a loss of context, as pathways are interconnected and genes can occur in multiple instances scattered over the network. Our main goal is therefore to present all relevant information, i.e., gene expressions, the relations between expression and pathways and between multiple pathways in a simple, yet effective way. To achieve this we employ two different multiple-view approaches. Traditional multiple views are used for large datasets or highly interactive visualizations, while a 2.5D technique is employed to support a seamless navigation of multiple pathways which simultaneously links to the expression of the contained genes. This approach facilitates the understanding of the interconnection of pathways, and enables a non-distracting relation to gene expression data. We evaluated Caleydo with a group of users from the life science community. Users were asked to perform three tasks: pathway exploration, gene expression analysis and information comparison with and without visual links, which had to be conducted in four different conditions. Evaluation results show that the system can improve the process of understanding the complex network of pathways and the individual effects of gene expression regulation considerably. Especially the quality of the available contextual information and the spatial organization was rated good for the presented 2.5D setup.

When analyzing multidimensional, quantitative data, the comparison of two or more groups of dimensions is a common task. Typical sources of such data are experiments in biology, physics or engineering, which are conducted in different configurations and use replicates to ensure statistically significant results. One common way to analyze this data is to filter it using statistical methods and then run clustering algorithms to group similar values. The clustering results can be visualized using heat maps, which show differences between groups as changes in color. However, in cases where groups of dimensions have an a priori meaning, it is not desirable to cluster all dimensions combined, since a clustering algorithm can fragment continuous blocks of records. Furthermore, identifying relevant elements in heat maps becomes more difficult as the number of dimensions increases. To aid in such situations, we have developed Matchmaker, a visualization technique that allows researchers to arbitrarily arrange and compare multiple groups of dimensions at the same time. We create separate groups of dimensions which can be clustered individually, and place them in an arrangement of heat maps reminiscent of parallel coordinates. To identify relations, we render bundled curves and ribbons between related records in different groups. We then allow interactive drill-downs using enlarged detail views of the data, which enable in-depth comparisons of clusters between groups. To reduce visual clutter, we minimize crossings between the views. This paper concludes with two case studies. The first demonstrates the value of our technique for the comparison of clustering algorithms. In the second, biologists use our system to investigate why certain strains of mice develop liver disease while others remain healthy, informally showing the efficacy of our system when analyzing multidimensional data containing distinct groups of dimensions.

This paper presents a visual data mining approach using the combination of clinical data, pathways and gene-expression data. The visual exploration of medical data using pathways to navigate and filter the data allows a more systematic and efficient investigation of problems in modern life science. A multiplicity of hypothesis can be evaluated in the same period of time, enabling a much better exploitation of the data. We present a system for data preprocessing and automatic classification, a set of visualization views and finally the integration in the Caleydo visualization framework, which enables the ldquocouplingrdquo of genetic and a broad spectrum of clinical data. With the help of the Caleydo framework the medical expert can identify connections between genetic parameters, patient subgroups, and drug responses.

UNLABELLED: Understanding the relationships between pathways and the altered expression of their components in disease conditions can be addressed in a visual data analysis process. Caleydo uses novel visualization techniques to support life science experts in their analysis of gene expression data in the context of pathways and functions of individual genes. Pathways and gene expression visualizations are placed in a 3D scene where selected entities (i.e. genes) are visually connected. This allows Caleydo to seamlessly integrate interactive gene expression visualization with cross-database pathway exploration. AVAILABILITY: The Caleydo visualization framework is freely available on www.caleydo.org for non-commercial use. It runs on Windows and Linux and requires a 3D capable graphics card.