Relevant Degree Programs
Affiliations to Research Centres, Institutes & Clusters
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G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.
Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - Nov 2020)
Technological innovations have allowed for a greater variety of data, most notably microbial genomic data, to be collected, integrated, analyzed, and visualized for epidemiological investigations. While analytic methods have evolved in light of this technological change, data visualizations systems have lagged behind.I take a novel approach that integrates methods from information visualization, human computer interaction, machine learning, and statistics to address unmet data visualization needs in microbial genomic epidemiology (genEpi). This approach also enables me to generate study artifacts that can be used to address regulatory and organizational constraints arising in domains where the use of data is highly restricted. I first present a mixed methods approach to understand the needs, data, tasks, and constraints of public health stakeholders that are charged with interpreting the findings of these data. I demonstrate how this approach can be used to communicate new and heterogeneous types of data in a clinical report that is read by stakeholders in different roles. I next present a novel method for systematically reviewing data visualizations that I use to develop a Genomic Epidemiology Visualization Typology (GEViT), which enables others to explore and characterize the way the data could be visualized. Finally, I use these collective findings to inform the design and implementation of data visualization tools: Adjutant, the GEViT Gallery, minCombinR, and GEViTRec. Adjutant enables rapid and unsupervised topic clustering of PubMed article corpuses to aid systematic and literature reviews. The GEViT gallery is a browsable interface for exploring data visualizations specific to the microbial genEpi domain. minCombinR lowers the burden to stakeholders for generating combinations of data visualizations for heterogeneous data. Finally, GEViTRec takes a novel approach to the automatic generation of data visualizations that can help stakeholders familiarize themselves with new data. All of these tools integrate with analytic methods.This research makes novel contributions to the design and implementation of data visualization systems that impact microbial genomic epidemiological data collected for public health investigations. The challenges addressed here are not unique to this domain and my contributions are extensible to other domains grappling with heterogeneous, multidimensional, and restricted data.
Why do people visualize data? People visualize data either to consume or produce information relevant to a domain-specific problem or interest. Visualization design and evaluation involves a mapping between domain problems or interests and appropriate visual encoding and interaction design choices. This mapping translates a domain-specific situation into abstract visualization tasks, which allows for succinct descriptions of tasks and task sequences in terms of why data is visualized, what dependencies a task might have in terms of input and output, and how the task is supported in terms of visual encoding and interaction design choices. Describing tasks in this way facilitates the comparison and cross-pollination of visualization design choices across application domains; the mapping also applies in reverse, whenever visualization researchers aim to contextualize novel visualization techniques. In this dissertation, we present multiple instances of visualization task abstraction, each integrating our proposed typology of abstract visualization tasks. We apply this typology as an analysis tool in an interview study of individuals who visualize dimensionally reduced data in different application domains, in a post-deployment field study evaluation of a visual analysis tool in the domain of investigative journalism, and in a visualization design study in the domain of energy management. In the interview study, we draw upon and demonstrate the descriptive power of our typology to classify five task sequences relating to visualizing dimensionally reduced data. This classification is intended to inform the design of new tools and techniques for visualizing this form of data. In the field study, we draw upon and demonstrate the descriptive and evaluative power of our typology to evaluate Overview, a visualization tool for investigating large text document collections. After analyzing its adoption by investigative journalists, we characterize two abstract tasks relating to document mining and present seven lessons relating to the design of visualization tools for document data. In the design study, we demonstrate the descriptive, evaluative, and generative power of our typology and identify matches and mismatches between visualization design choices and three abstract tasks relating to time series data. Finally, we reflect upon the impact of our task typology.
In this thesis, we explore ways to make practical extensions to Dimensionality Reduction, or DR algorithms with the goal of addressing challenging, real-world cases. The first case we consider is that of how to provide guidance to those users employing DR methods in their data analysis. We specifically target users who are not experts in the mathematical concepts behind DR algorithms. We first identify two levels of guidance: global and local. Global user guidance helps non-experts select and arrange a sequence of analysis algorithms. Local user guidance helps users select appropriate algorithm parameter choices and interpret algorithm output. We then present a software system, DimStiller, that incorporates both types of guidance, validating it on several use-cases. The second case we consider is that of using DR to analyze datasets consisting of documents. In order to modify DR algorithms to handle document datasets effectively, we first analyze the geometric structure of document datasets. Our analysis describes the ways document datasets differ from other kinds of datasets. We then leverage these geometric properties for speed and quality by incorporating ideas from text querying into DR and other algorithms for data analysis. We then present the Overview prototype, a proof-of-concept document analysis system. Overview synthesizes both the goals of designing systems for data analysts who are DR novices, and performing DR on document data. The third case we consider is that of costly distance functions, or when the method used to derive the true proximity between two data points is computationally expensive. Using standard approaches to DR in this important use-case can result in either unnecessarily protracted runtimes or long periods of user monitoring. To address the case of costly distances, we develop an algorithm framework, Glint, which efficiently manages the number of distance function calculations for the Multidimensional Scaling class of DR algorithms. We then show that Glint implementations of Multidimensional Scaling algorithms achieve substantial speed improvements or remove the need for human monitoring.
A graph consists of a set and a binary relation on that set. Each elementof the set is a node of the graph, while each element of the binary relationis an edge of the graph that encodes a relationship between two nodes.Graph are pervasive in many areas of science, engineering, and the socialsciences: servers on the Internet are connected, proteins interact in largebiological systems, social networks encode the relationships between people,and functions call each other in a program. In these domains, the graphscan become very large, consisting of hundreds of thousands of nodes andmillions of edges.Graph drawing approaches endeavour to place these nodes in two orthree-dimensional space with the intention of fostering an understandingof the binary relation by a human being examining the image. However,many of these approaches to drawing do not exploit higher-level structuresin the graph beyond the nodes and edges. Frequently, these structures canbe exploited for drawing. As an example, consider a large computer networkwhere nodes are servers and edges are connections between those servers.If a user would like understand how servers at UBC connect to the rest ofthe network, a drawing that accentuates the set of nodes representing thoseservers may be more helpful than an approach where all nodes are drawn inthe same way. In a feature-based approach, features are subgraphs exploitedfor the purposes of drawing. We endeavour to depict not only the binaryrelation, but the high-level relationships between features.This thesis extensively explores a feature-based approach to graph visualization and demonstrates the viability of tools that aid in the visualization of large graphs. Our contributions lie in presenting and evaluatingnovel techniques and algorithms for graph visualization. We implement fivesystems in order to empirically evaluate these techniques and algorithms,comparing them to previous approaches.
Large data sets are difficult to analyze. Visualization has been proposed to assist exploratory data analysis (EDA) as our visual systems can process signals inparallel to quickly detect patterns. Nonetheless, designing an effective visualanalytic tool remains a challenge.This challenge is partly due to our incomplete understanding of how commonvisualization techniques are used by human operators during analyses, either inlaboratory settings or in the workplace.This thesis aims to further understand how visualizations can be used to support EDA. More specifically, we studied techniques that display multiple levels of visual information resolutions (VIRs) for analyses using a range of methods.The first study is a summary synthesis conducted to obtain a snapshot ofknowledge in multiple-VIR use and to identify research questions for the thesis:(1) low-VIR use and creation; (2) spatial arrangements of VIRs. The next twostudies are laboratory studies to investigate the visual memory cost of imagetransformations frequently used to create low-VIR displays and overview usewith single-level data displayed in multiple-VIR interfaces.For a more well-rounded evaluation, we needed to study these techniques inecologically-valid settings. We therefore selected the application domain of websession log analysis and applied our knowledge from our first three evaluationsto build a tool called Session Viewer. Taking the multiple coordinated viewand overview + detail approaches, Session Viewer displays multiple levels ofweb session log data and multiple views of session populations to facilitate dataanalysis from the high-level statistical to the low-level detailed session analysisapproaches.Our fourth and last study for this thesis is a field evaluation conducted atGoogle Inc. with seven session analysts using Session Viewer to analyze theirown data with their own tasks. Study observations suggested that displayingweb session logs at multiple levels using the overview + detail technique helped bridge between high-level statistical and low-level detailed session analyses, andthe simultaneous display of multiple session populations at all data levels usingmultiple views allowed quick comparisons between session populations. We alsoidentified design and deployment considerations to meet the needs of diversedata sources and analysis styles.
Master's Student Supervision (2010 - 2018)
Clickstream data has the potential to provide actionable insights into e-commerce consumer behavior, but previous techniques fall short of handling the scale and complexity of real-world datasets. We present Segmentifier, a novel visual analytics interface that supports an iterative process of refining collections of action sequences into meaningful segments that are suitable for downstream analysis with techniques that require relatively small and clean input. We also present task and data abstractions for the application domain of clickstream data analysis, leading to a framework that abstracts the segment analysis process in terms of six functions: view, refine, record, export, abandon, and conclude. The Segmentifier interface is simple to use for analysts operating under tight time constraints. It supports filtering and partitioning through visual queries for both quantitative attributes and custom sequences of events, which are aggregated according to a three-level hierarchy. It features a rich set of views that show the underlying raw sequence details and the derived data of segment attributes, and a detailed glyph-based visual history of the automatically recorded analysis process showing the provenance of eachsegment in terms of an analysis path of attribute constraints. We demonstrate the effectiveness of our approach through a usage scenario with real-world data and a case study documenting the insights gained by an e-commerce analyst.
Path tracing is a common task in many real world uses of graphs that display networks of relationships. Despite previous work in the evaluation of how factors, such as edge-edge crossings, impact the readability of graph layouts, what makes one path-tracing task more difficult than another is not well understood.To address this question we conducted an observational user study with 12 participants completing a path-tracing task. Our extensive qualitative analysis of the study data led to a detailed characterization of common path-tracing behaviours. We then created a predictive model of the paths that users are most likely to search, which we name the search set, based on the behaviours we observed. To validate our predictive behavioural model, and to demonstrate how the search set could be used, we conducted a careful comparison of graph readability factors through a hierarchical multiple regression analysis.
Scientists use DNA sequence differences between an individual's genome and a standard reference genome to study the genetic basis of disease. Such differences are called sequence variants, and determining their impact in the cell is difficult because it requires reasoning about both the type and location of the variant across several levels of biological context. In this design study, we worked with four analysts to design a visualization tool supporting variant impact assessment for three different tasks. We contribute data and task abstractions for the problem of variant impact assessment, and the carefully justified design and implementation of the Variant View tool. Variant View features an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers. We provide initial evidence that the tool simplified and accelerated workflows for these three tasks through three case studies. Finally, we reflect on the lessons learned in creating and refining data and task abstractions that allow for concise overviews of sprawling information spaces that can reduce or remove the need for the memory-intensive use of navigation.
- Aggregated Dendrograms for Visual Comparison between Many Phylogenetic Trees (2020)
IEEE Transactions on Visualization and Computer Graphics, 26 (9), 2732--2747
- Aggregated Dendrograms for Visual Comparison Between Many Phylogenetic Trees (2019)
IEEE Transactions on Visualization and Computer Graphics,
- A Novel Methodology for Characterizing Cell Subpopulations in Automated Time-lapse Microscopy (2018)
Frontiers in bioengineering and biotechnology, 6, 17
- A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT (2018)
- Adjutant: an R-based tool to support topic discovery for systematic and literature reviews (2018)
- Bridging from goals to tasks with design study analysis reports (2018)
IEEE Transactions on Visualization and Computer Graphics, 24 (1), 435--445
- Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory (2018)
PeerJ, 6, e4218
- GaRSIVis: improving the predicting of self-interruption during reading using gaze data. (2018)
- Timelines revisited: A design space and considerations for expressive storytelling (2017)
IEEE transactions on visualization and computer graphics, 23 (9), 2151--2164
- Matches, mismatches, and methods: multiple-view workflows for energy portfolio analysis (2016)
IEEE transactions on visualization and computer graphics, 22 (1), 449--458
- On regulatory and organizational constraints in visualization design and evaluation (2016)
Proceedings of the Sixth Workshop on Beyond Time and Errors on Novel Evaluation Methods for Visualization, , 1--9
- PaperQuest: A visualization tool to support literature review (2016)
Proceedings of the 2016 CHI Conference Extended Abstracts on Human Factors in Computing Systems, , 2264--2271
- Pathways for Theoretical Advances in Visualization (Panel) (2016)
IEEE Visualization 2016,
- TimeLineCurator: Interactive authoring of visual timelines from unstructured text (2016)
IEEE transactions on visualization and computer graphics, 22 (1), 300--309
- A search-set model of path tracing in graphs (2015)
Information Visualization, 14 (4), 308--338
- Bridging information visualization with machine learning (Dagstuhl Seminar 15101) (2015)
Dagstuhl Reports, 5 (3)
- Detangler: Visual analytics for multiplex networks (2015)
Computer Graphics Forum, 34 (3), 321--330
- Dimensionality reduction for documents with nearest neighbor queries (2015)
Neurocomputing, 150, 557--569
- The nested blocks and guidelines model (2015)
Information Visualization, 14 (3), 234--249
- Overview: The design, adoption, and analysis of a visual document mining tool for investigative journalists (2014)
IEEE transactions on visualization and computer graphics, 20 (12), 2271--2280
- Visualization analysis and design (2014)
- Visualizing dimensionally-reduced data: Interviews with analysts and a characterization of task sequences (2014)
Proceedings of the Fifth Workshop on Beyond Time and Errors: Novel Evaluation Methods for Visualization, , 1--8
- A multi-level typology of abstract visualization tasks (2013)
IEEE Transactions on Visualization and Computer Graphics, 19 (12), 2376--2385
- Empirical guidance on scatterplot and dimension reduction technique choices (2013)
IEEE Transactions on Visualization and Computer Graphics, 19 (12), 2634--2643
- Variant view: Visualizing sequence variants in their gene context (2013)
IEEE Transactions on Visualization and Computer Graphics, 19 (12), 2546--2555
- A taxonomy of visual cluster separation factors (2012)
Computer Graphics Forum, 31 (3pt4), 1335--1344
- Design study methodology: Reflections from the trenches and the stacks (2012)
IEEE Transactions on Visualization and Computer Graphics, 18 (12), 2431--2440
- Dimensionality reduction in the wild: Gaps and guidance (2012)
Dept. Comput. Sci., Univ. British Columbia, Vancouver, BC, Canada, Tech. Rep. TR-2012-03,
- Glint: An MDS framework for costly distance functions (2012)
Proceedings of SIGRAD 2012; Interactive Visual Analysis of Data; November 29-30; 2012; Växjö; Sweden, (081), 29--38
- Hierarchical clustering and tagging of mostly disconnected data (2012)
Technical report, Dept. Computer Science, University of British Columbia,,
- RelEx: Visualization for actively changing overlay network specifications (2012)
IEEE Transactions on Visualization and Computer Graphics, 18 (12), 2729--2738
- The design space of opinion measurement interfaces: exploring recall support for rating and ranking (2012)
Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, , 2035--2044
- The four-level nested model revisited: blocks and guidelines (2012)
Proceedings of the 2012 BELIV Workshop: Beyond Time and Errors-Novel Evaluation Methods for Visualization, , 11
- Vismon: Facilitating analysis of trade-offs, uncertainty, and sensitivity in fisheries management decision making (2012)
Computer Graphics Forum, 31 (3pt3), 1235--1244
- Applying information visualization principles to biological network displays (2011)
Human Vision and Electronic Imaging XVI, 7865, 78650D
- Reflections on QuestVis: A visualization system for an environmental sustainability model (2011)
Dagstuhl Follow-Ups, 2
- Tugging graphs faster: Efficiently modifying path-preserving hierarchies for browsing paths (2011)
IEEE Transactions on Visualization and Computer Graphics, 17 (3), 276--289
- A guide to visual multi-level interface design from synthesis of empirical study evidence (2010)
Synthesis Lectures on Visualization, 1 (1), 1--117
- Dimstiller: Workflows for dimensional analysis and reduction (2010)
2010 IEEE Symposium on Visual Analytics Science and Technology, , 3--10
- MulteeSum: A tool for comparative spatial and temporal gene expression data (2010)
IEEE Transactions on Visualization and Computer Graphics, 16 (6), 908--917
- Pathline: A tool for comparative functional genomics (2010)
Computer Graphics Forum, 29 (3), 1043--1052
- A nested model for visualization design and validation (2009)
IEEE Transactions on Visualization and Computer Graphics, 15 (6), 921--928
- Glimmer: Multilevel MDS on the GPU (2009)
IEEE Transactions on Visualization and Computer Graphics, 15 (2), 249--261
- MizBee: a multiscale synteny browser (2009)
IEEE Transactions on Visualization and Computer Graphics, 15 (6), 897--904
- TugGraph: Path-preserving hierarchies for browsing proximity and paths in graphs (2009)
IEEE Pacific Visualization Symposium (PacificVis) 2009, , 113--120
- Visualization (2009)
Fundamentals of Graphics, , 675--707
- Cerebral: Visualizing multiple experimental conditions on a graph with biological context (2008)
IEEE transactions on visualization and computer graphics, 14 (6), 1253--1260
- GrouseFlocks: Steerable exploration of graph hierarchy space (2008)
IEEE Transactions on Visualization and Computer Graphics, 14 (4), 900--913
- Increasing the utility of quantitative empirical studies for meta-analysis (2008)
Proceedings of the 2008 Workshop on BEyond time and errors: novel evaLuation methods for Information Visualization, , 2
- InnateDB: facilitating systems-level analyses of the mammalian innate immune response (2008)
Molecular systems biology, 4 (1), 218
- LiveRAC: Interactive visual exploration of system management time-series data (2008)
Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems, , 1483--1492
- Process and pitfalls in writing information visualization research papers (2008)
Information visualization, , 134--153
- Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation (2007)
Bioinformatics, 23 (8), 1040--1042
- Grouse: Feature-Based, Steerable Graph Hierarchy Exploration. (2007)
EuroVis, 2007, 67--74
- Overview use in multiple visual information resolution interfaces (2007)
IEEE Transactions on Visualization and Computer Graphics, 13 (6), 1278--1285
- Session Viewer: Visual exploratory analysis of web session logs (2007)
2007 IEEE Symposium on Visual Analytics Science and Technology, , 147--154
- Spatialization design: Comparing points and landscapes (2007)
IEEE Transactions on Visualization and Computer Graphics, 13 (6), 1262--1269
- TopoLayout: Multilevel graph layout by topological features (2007)
IEEE Transactions on Visualization and Computer Graphics, 13 (2), 305--317
- An evaluation of pan & zoom and rubber sheet navigation with and without an overview (2006)
Proceedings of the SIGCHI conference on Human Factors in computing systems, , 11--20
- Composite rectilinear deformation for stretch and squish navigation (2006)
IEEE transactions on visualization and computer graphics, 12 (5), 901--908
- Effects of 2D geometric transformations on visual memory (2006)
Proceedings of the 3rd symposium on Applied perception in graphics and visualization, , 119--126
- NIH-NSF visualization research challenges report summary (2006)
IEEE Computer Graphics and Applications, 26 (2), 20--24
- PRISAD: A partitioned rendering infrastructure for scalable accordion drawing (extended version) (2006)
Information Visualization, 5 (2), 137--151
- Smashing peacocks further: Drawing quasi-trees from biconnected components (2006)
IEEE Transactions on Visualization and Computer Graphics, 12 (5), 813--820
- Visualization research challenges: a report summary (2006)
Computing in Science & Engineering, 8 (4), 66--73
- NIH-NSF visualization research challenges report (2005)
- PRISAD: A partitioned rendering infrastructure for scalable accordion drawing (2005)
IEEE Symposium on Information Visualization, 2005. INFOVIS 2005., , 41--48
- Scalable, Robust Visualization of Very Large Trees. (2005)
Proceedings EuroVis 2005, , 37--44
- Visual mining of power sets with large alphabets (2005)
Technical Report, Department of Computer Science, The University of British Columbia, 2
- Perceptual invariance of nonlinear focus+ context transformations (2004)
Proceedings of the 1st Symposium on Applied perception in graphics and visualization, , 65--72
- Seeing, hearing, and touching: putting it all together (2004)
ACM SIGGRAPH 2004 Course Notes, , 8
- SequenceJuxtaposer: Fluid navigation for large-scale sequence comparison in context. (2004)
German conference on bioinformatics, 53
- Steerable, progressive multidimensional scaling (2004)
IEEE Symposium on information Visualization, , 57--64
- TreeJuxtaposer: scalable tree comparison using Focus+ Context with guaranteed visibility (2003)
ACM Transactions on Graphics (Proc. SIGGRAPH), 22 (3), 453--462
- An initial examination of ease of use for 2D and 3D information visualizations of web content (2000)
International Journal of Human-Computer Studies, 53 (5), 695--714
- Artistic multiprojection rendering (2000)
Eurographics Symposium on Rendering 2000, , 125--136
- Interactive visualization of large graphs and networks (2000)
- Constellation: a visualization tool for linguistic queries from MindNet. (1999)
Proceedings of the IEEE Symposium on Information Visualization (InfoVis), , 132--135
- Drawing large graphs with H3Viewer and Site Manager (1998)
Graph Drawing, , 384--393
- Exploring large graphs in 3D hyperbolic space (1998)
IEEE Computer Graphics and Applications, 18 (4), 18--23
- H3: Laying out large directed graphs in 3D hyperbolic space. (1997)
Proceedings of the IEEE Symposium on Information Visualization (InfoVis), , 2--10
- Visualizing the global topology of the MBone (1996)
Proceedings IEEE Symposium on Information Visualization'96, , 85--92
- Geomview: A system for geometric visualization (1995)
Proceedings of the eleventh annual symposium on Computational geometry, , 412--413
- Visualizing the structure of the world wide web in 3D hyperbolic space (1995)
Proceedings of the first symposium on Virtual reality modeling language, , 33--38
- Interactive methods for visualizable geometry (1994)
Computer, 27 (7), 73--83
- Geomview (1993)
Geometry Center Software, Geometry Center GCG62,
- Geomview: An interactive geometry viewer (1993)
Notices of the American Mathematical Society, 40 (8), 985--988