1,454 research outputs found

    BioBridge: Bringing Data Exploration to Biologists

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    Since the completion of the Human Genome Project in 2003, biologists have become exceptionally good at producing data. Indeed, biological data has experienced a sustained exponential growth rate, putting effective and thorough analysis beyond the reach of many biologists. This thesis presents BioBridge, an interactive visualization tool developed to bring intuitive data exploration to biologists. BioBridge is designed to work on omics style tabular data in general and thus has broad applicability. This work describes the design and evaluation of BioBridge\u27s Entity View primary visualization as well the accompanying user interface. The Entity View visualization arranges glyphs representing biological entities (e.g. genes, proteins, metabolites) along with related text mining results to provide biological context. Throughout development the goal has been to maximize accessibility and usability for biologists who are not computationally inclined. Evaluations were done with three informal case studies, one of a metabolome dataset and two of microarray datasets. BioBridge is a proof of concept that there is an underexploited niche in the data analysis ecosystem for tools that prioritize accessibility and usability. The use case studies, while anecdotal, are very encouraging. These studies indicate that BioBridge is well suited for the task of data exploration. With further development, BioBridge could become more flexible and usable as additional use case datasets are explored and more feedback is gathered

    SUPPORT EFFECTIVE DISCOVERY MANAGEMENT IN VISUAL ANALYTICS

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    Visual analytics promises to supply analysts with the means necessary to ana- lyze complex datasets and make effective decisions in a timely manner. Although significant progress has been made towards effective data exploration in existing vi- sual analytics systems, few of them provide systematic solutions for managing the vast amounts of discoveries generated in data exploration processes. Analysts have to use off line tools to manually annotate, browse, retrieve, organize, and connect their discoveries. In addition, they have no convenient access to the important discoveries captured by collaborators. As a consequence, the lack of effective discovery manage- ment approaches severely hinders the analysts from utilizing the discoveries to make effective decisions. In response to this challenge, this dissertation aims to support effective discov- ery management in visual analytics. It contributes a general discovery manage- ment framework which achieves its effectiveness surrounding the concept of patterns, namely the results of users’ low-level analytic tasks. Patterns permit construction of discoveries together with users’ mental models and evaluation. Different from the mental models, the categories of patterns that can be discovered from data are pre- dictable and application-independent. In addition, the same set of information is often used to annotate patterns in the same category. Therefore, visual analytics sys- tems can semi-automatically annotate patterns in a formalized format by predicting what should be recorded for patterns in popular categories. Using the formalized an- notations, the framework also enhances the automation and efficiency of a variety of discovery management activities such as discovery browsing, retrieval, organization, association, and sharing. The framework seamlessly integrates them with the visual interactive explorations to support effective decision making. Guided by the discovery management framework, our second contribution lies in proposing a variety of novel discovery management techniques for facilitating the discovery management activities. The proposed techniques and framework are im- plemented in a prototype system, ManyInsights, to facilitate discovery management in multidimensional data exploration. To evaluate the prototype system, two long- term case studies are presented. They investigated how the discovery management techniques worked together to benefit exploratory data analysis and collaborative analysis. The studies allowed us to understand the advantages, the limitations, and design implications of ManyInsights and its underlying framework

    Thinking interactively with visualization

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    Interaction is becoming an integral part of using visualization for analysis. When interaction is tightly and appropriately coupled with visualization, it can transform the visualization from display- ing static imagery to assisting comprehensive analysis of data at all scales. In this relationship, a deeper understanding of the role of interaction, its effects, and how visualization relates to interaction is necessary for designing systems in which the two components complement each other. This thesis approaches interaction in visualization from three different perspectives. First, it considers the cost of maintaining interaction in manipulating visualization of large datasets. Namely, large datasets often require a simplification process for the visualization to maintain interactivity, and this thesis examines how simplification affects the resulting visualization. Secondly, example interactive visual analytical systems are presented to demonstrate how interactivity could be applied in visualization. Specifically, four fully developed systems for four distinct problem domains are discussed to determine the common role of interactivity in these visualizations that make the systems successful. Lastly, this thesis presents evidence that interactions are important for analytical tasks using visualizations. Interaction logs of financial analysts using a visualization were collected, coded, and examined to determine the amount of analysis strategies contained within the interaction logs. The finding supports the benefits of high interactivity in analytical tasks when using a visualization. The example visualizations used to support these three perspectives are diverse in their goals and features. However, they all share similar design guidelines and visualization principles. Based on their characteristics, this thesis groups these visualizations into urban visualization, visual analytical systems, and interaction capturing and discusses them separately in terms of lessons learned and future directions

    A Qualitative Analysis of Common Practices in Annotations: A Taxonomy and Design Space

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    Annotations are a vital component of data externalization and collaborative analysis, directing readers' attention to important visual elements. Therefore, it is crucial to understand their design space for effectively annotating visualizations. However, despite their widespread use in visualization, we have identified a lack of a design space for common practices for annotations. In this paper, we present two studies that explore how people annotate visualizations to support effective communication. In the first study, we evaluate how visualization students annotate bar charts when answering high-level questions about the data. Qualitative coding of the resulting annotations generates a taxonomy comprising enclosure, connector, text, mark, and color, revealing how people leverage different visual elements to communicate critical information. We then extend our taxonomy by performing thematic coding on a diverse range of real-world annotated charts, adding trend and geometric annotations to the taxonomy. We then combine the results of these studies into a design space of annotations that focuses on the key elements driving the design choices available when annotating a chart, providing a reference guide for using annotations to communicate insights from visualizations

    plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

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    Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: Biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery.</p

    Integrating Statistics and Visualization to Improve Exploratory Social Network Analysis

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    Social network analysis is emerging as a key technique to understanding social, cultural and economic phenomena. However, social network analysis is inherently complex since analysts must understand every individual's attributes as well as relationships between individuals. There are many statistical algorithms which reveal nodes that occupy key social positions and form cohesive social groups. However, it is difficult to find outliers and patterns in strictly quantitative output. In these situations, information visualizations can enable users to make sense of their data, but typical network visualizations are often hard to interpret because of overlapping nodes and tangled edges. My first contribution improves the process of exploratory social network analysis. I have designed and implemented a novel social network analysis tool, SocialAction (http://www.cs.umd.edu/hcil/socialaction) , that integrates both statistics and visualizations to enable users to quickly derive the benefits of both. Statistics are used to detect important individuals, relationships, and clusters. Instead of tabular display of numbers, the results are integrated with a network visualization in which users can easily and dynamically filter nodes and edges. The visualizations simplify the statistical results, facilitating sensemaking and discovery of features such as distributions, patterns, trends, gaps and outliers. The statistics simplify the comprehension of a sometimes chaotic visualization, allowing users to focus on statistically significant nodes and edges. SocialAction was also designed to help analysts explore non-social networks, such as citation, communication, financial and biological networks. My second contribution extends lessons learned from SocialAction and provides designs guidelines for interactive techniques to improve exploratory data analysis. A taxonomy of seven interactive techniques are augmented with computed attributes from statistics and data mining to improve information visualization exploration. Furthermore, systematic yet flexible design goals are provided to help guide domain experts through complex analysis over days, weeks and months. My third contribution demonstrates the effectiveness of long term case studies with domain experts to measure creative activities of information visualization users. Evaluating information visualization tools is problematic because controlled studies may not effectively represent the workflow of analysts. Discoveries occur over weeks and months, and exploratory tasks may be poorly defined. To capture authentic insights, I designed an evaluation methodology that used structured and replicated long-term case studies. The methodology was implemented on unique domain experts that demonstrated the effectiveness of integrating statistics and visualization

    VizRank: Data Visualization Guided by Machine Learning

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    Data visualization plays a crucial role in identifying interesting patterns in exploratory data analysis. Its use is, however, made difficult by the large number of possible data projections showing different attribute subsets that must be evaluated by the data analyst. In this paper, we introduce a method called VizRank, which is applied on classified data to automatically select the most useful data projections. VizRank can be used with any visualization method that maps attribute values to points in a two-dimensional visualization space. It assesses possible data projections and ranks them by their ability to visually discriminate between classes. The quality of class separation is estimated by computing the predictive accuracy of k-nearest neighbor classifier on the data set consisting of x and y positions of the projected data points and their class information. The paper introduces the method and presents experimental results which show that VizRank's ranking of projections highly agrees with subjective rankings by data analysts. The practical use of VizRank is also demonstrated by an application in the field of functional genomics
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