Tamara Munzner

A Nested Model for Visualization Design and Validation

We present a nested model for the visualization design and validation with four layers: characterize the task and data in the vocabulary of the problem domain, abstract into operations and data types, design visual encoding and interaction techniques, and create algorithms to execute techniques efficiently. The output from a level above is input to the level below, bringing attention to the design challenge that an upstream error inevitably cascades to all downstream levels. This model provides prescriptive guidance for determining appropriate evaluation approaches by identifying threats to validity unique to each level. We also provide three recommendations motivated by this model: authors should distinguish between these levels when claiming contributions at more than one of them, authors should explicitly state upstream assumptions at levels above the focus of a paper, and visualization venues should accept more papers on domain characterization.

InnateDB: facilitating systems‐level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems‐level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity‐relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user‐supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems‐oriented manner.

H3: laying out large directed graphs in 3D hyperbolic space

We present the H3 layout technique for drawing large directed graphs as node-link diagrams in 3D hyperbolic space. We can lay out much larger structures than can be handled using traditional techniques for drawing general graphs because we assume a hierarchical nature of the data. We impose a hierarchy on the graph by using domain-specific knowledge to find an appropriate spanning tree. Links which are not part of the spanning tree do not influence the layout but can be selectively drawn by user request. The volume of hyperbolic 3-space increases exponentially, as opposed to the familiar geometric increase of euclidean 3-space. We exploit this exponential amount of room by computing the layout according to the hyperbolic metric. We optimize the cone tree layout algorithm for 3D hyperbolic space by placing children on a hemisphere around the cone mouth instead of on its perimeter. Hyperbolic navigation affords a Focus+Context view of the structure with minimal visual clutter. We have successfully laid out hierarchies of over 20,000 nodes. Our implementation accommodates navigation through graphs too large to be rendered interactively by allowing the user to explicitly prune or expand subtrees.

Design Study Methodology: Reflections from the Trenches and the Stacks

Design studies are an increasingly popular form of problem-driven visualization research, yet there is little guidance available about how to do them effectively. In this paper we reflect on our combined experience of conducting twenty-one design studies, as well as reading and reviewing many more, and on an extensive literature review of other field work methods and methodologies. Based on this foundation we provide definitions, propose a methodological framework, and provide practical guidance for conducting design studies. We define a design study as a project in which visualization researchers analyze a specific real-world problem faced by domain experts, design a visualization system that supports solving this problem, validate the design, and reflect about lessons learned in order to refine visualization design guidelines. We characterize two axes - a task clarity axis from fuzzy to crisp and an information location axis from the domain experts head to the computer - and use these axes to reason about design study contributions, their suitability, and uniqueness from other approaches. The proposed methodological framework consists of 9 stages: learn, winnow, cast, discover, design, implement, deploy, reflect, and write. For each stage we provide practical guidance and outline potential pitfalls. We also conducted an extensive literature survey of related methodological approaches that involve a significant amount of qualitative field work, and compare design study methodology to that of ethnography, grounded theory, and action research.

A Multi-Level Typology of Abstract Visualization Tasks

The considerable previous work characterizing visualization usage has focused on low-level tasks or interactions and high-level tasks, leaving a gap between them that is not addressed. This gap leads to a lack of distinction between the ends and means of a task, limiting the potential for rigorous analysis. We contribute a multi-level typology of visualization tasks to address this gap, distinguishing why and how a visualization task is performed, as well as what the task inputs and outputs are. Our typology allows complex tasks to be expressed as sequences of interdependent simpler tasks, resulting in concise and flexible descriptions for tasks of varying complexity and scope. It provides abstract rather than domain-specific descriptions of tasks, so that useful comparisons can be made between visualization systems targeted at different application domains. This descriptive power supports a level of analysis required for the generation of new designs, by guiding the translation of domain-specific problems into abstract tasks, and for the qualitative evaluation of visualization usage. We demonstrate the benefits of our approach in a detailed case study, comparing task descriptions from our typology to those derived from related work. We also discuss the similarities and differences between our typology and over two dozen extant classification systems and theoretical frameworks from the literatures of visualization, human-computer interaction, information retrieval, communications, and cartography.

Visualizing the structure of the World Wide Web in 3D hyperbolic space

We visualize the structure of sections of the World Wide Web by constructing graphical representations in 3D hyperbolic space. The felicitous property that hyperbolic space has “more room” than Euclidean space allows more information to be seen amid less clutter, and motion by hyperbolic isometries provides for mathematically elegant navigation. The 3D graphical representations, available in the WebOOGL or VRML file formats, contain link anchors which point to the original pages on the Web itself. We use the Geomview/WebOOGL 3D Web browser as an interface between the 3D representation and the actual documents on the Web. The Web is just one example of a hierarchical tree structure with links “back up the tree” i.e. a directed graph which contains cycles. Our information visualization techniques are appropriate for other types of directed graphs with cycles, such as filesystems with symbolic links.

Exploring large graphs in 3D hyperbolic space

Drawing graphs as nodes connected by links is visually compelling but computationally difficult. Hyperbolic space and spanning trees can reduce visual clutter, speed up layout, and provide fluid interaction. This article briefly describes a software system that explicitly attempts to handle much larger graphs than previous systems and support dynamic exploration rather than final presentation. It then discusses the applicability of this system to goals beyond simple exploration. A software system that supports graph exploration should include both a layout and an interactive drawing component. I have developed new algorithms for both layout and drawing (H3 and H3Viewer). The H3Viewer drawing algorithm remains under development, so this article presents preliminary results. I have implemented a software library that uses these algorithms. It can handle graphs of more than 100,000 edges by using a spanning tree as the backbone for the layout and drawing algorithms.

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation

UNLABELLED Cerebral (Cell Region-Based Rendering And Layout) is an open-source Java plugin for the Cytoscape biomolecular interaction viewer. Given an interaction network and subcellular localization annotation, Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system. The molecules are separated into layers according to their subcellular localization. Potential products or outcomes of the pathway can be shown at the bottom of the view, clustered according to any molecular attribute data-protein function-for example. Cerebral scales well to networks containing thousands of nodes. AVAILABILITY http://www.pathogenomics.ca/cerebral

LiveRAC: interactive visual exploration of system management time-series data

We present LiveRAC, a visualization system that supports the analysis of large collections of system management time-series data consisting of hundreds of parameters across thousands of network devices. LiveRAC provides high information density using a reorderable matrix of charts, with semantic zooming adapting each charts visual representation to the available space. LiveRAC allows side-by-side visual comparison of arbitrary groupings of devices and parameters at multiple levels of detail. A staged design and development process culminated in the deployment of LiveRAC in a production environment. We conducted an informal longitudinal evaluation of LiveRAC to better understand which proposed visualization techniques were most useful in the target environment.

Glimmer: Multilevel MDS on the GPU

We present Glimmer, a new multilevel algorithm for multidimensional scaling designed to exploit modern graphics processing unit (GPU) hardware. We also present GPU-SF, a parallel, force-based subsystem used by Glimmer. Glimmer organizes input into a hierarchy of levels and recursively applies GPU-SF to combine and refine the levels. The multilevel nature of the algorithm makes local minima less likely while the GPU parallelism improves speed of computation. We propose a robust termination condition for GPU-SF based on a filtered approximation of the normalized stress function. We demonstrate the benefits of Glimmer in terms of speed, normalized stress, and visual quality against several previous algorithms for a range of synthetic and real benchmark datasets. We also show that the performance of Glimmer on GPUs is substantially faster than a CPU implementation of the same algorithm.