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's 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.

Many individuals with low health literacy (LHL) and limited English proficiency (LEP) have poor experiences consuming health information: they find it unengaging, unappealing, difficult to understand, and un-motivating. These negative experiences may blunt, or even sabotage, the desired effect of communicating health information: to increase engagement and ability to manage health. It is imperative to find solutions to improve poor experiences of health information, because such experiences heighten vulnerability to poor health outcomes. We aimed to address a gap in the health literacy literature by studying the patient experience of health information and how visualization might be able to help. Our four studies involved patients presented with health information in various settings to improve understanding and management of their care. We used semi-structured interviews and observations to understand patient experiences of receiving personal health information in the hospital. We learned that the return of results is desired and has the potential to promote patient engagement with care. We developed a novel method to analyze LHL, LEP caregiver experience and information needs in the community setting. The novel method increased our understanding and ability to detect differences in experiences within the same ethnic group, based on language preference. Next, we interrogated the literature for a solution to easily communicate complicated health information to disinterested, LHL, LEP individuals. We found that visualizations can help increase interest, comprehension, support faster communication, and even help broach difficult topics. Finally, our findings were used to develop a novel prototype to improve experiences of consuming genetic risk information for those having LHL and LEP. Unlike traditional approaches that focus on communicating risk numbers and probabilities, the novelty of our approach was that we focused on communicating risk as a feeling. We achieved this by leveraging vicarious learning via real patient experience materials (e.g., quotes, videos) and empathy with an emotive relational agent. We evaluated and compared the prototype to standard methods of communicating genetic risk information via a mixed methods approach that included surveys, questionnaires, interviews, observations, image analysis, and facial analysis. Main outcome variables were perceived ease of understanding, comprehension, emotional response, and motivation. We employed t-tests, ANOVAs, directed content analysis, correlation, regression, hierarchical clustering, and Chernoff faces to answer the research questions. All variables were significantly different for the prototype compared to the standard method, except for motivation as rated by 32 LHL, LEP community members. Findings revealed that LHL, LEP individuals have difficulty appropriately processing standard methods of communicating risk information, such as risk numbers supported by visual aids. Further, appealing visuals may inappropriately increase confidence in understanding of information. Visualizations affected emotions, which influenced perceived ease of understanding and motivation to take action on the information. Comprehension scores did not correlate with perceived ease of understanding, emotional response, or motivation. Findings suggest that providing access to comprehensible health information may not be enough to motivate patients to engage with their care; providing a good experience (taking into account the aesthetics and emotional response) of health information may be essential to optimize outcomes.

With increasing availability and diversity of visual data generated in research labs and everyday life, it is becoming critical to develop disciplined and practical computation tools for such data. This thesis focuses on the low complexity representations and algorithms for visual data, in light of recent theoretical and algorithmic developments in high-dimensional data analysis. We first consider the problem of modeling a given dataset as superpositions of basic motifs. This model arises from several important applications, including microscopy image analysis, neural spike sorting and image deblurring. This motif-finding problem can be phrased as "short-and-sparse" blind deconvolution, in which the goal is to recover a short convolution kernel from its convolution with a sparse and random spike train. We normalize the convolution kernel to have unit Frobenius norm and then cast the blind deconvolution problem as a nonconvex optimization problem over the kernel sphere. We demonstrate that (i) in a certain region of the sphere, every local optimum is close to some shift truncation of the ground truth, when the activation spike is sufficiently sparse and long, and (ii) there exist efficient algorithms that recover some shift truncation of the ground truth under the same conditions. In addition, the geometric characterization of the local solution as well as the proposed algorithm naturally extend to more complicated sparse blind deconvolution problems, including image deblurring, convolutional dictionary learning. We next consider the problem of modeling physical nuisances across a collection of images, in the context of illumination-invariant object detection and recognition. Illumination variation remains a central challenge in object detection and recognition. Existing analyses of illumination variation typically pertain to convex, Lambertian objects, and guarantee quality of approximation in an average case sense. We show that it is possible to build vertex-description convex cone models with worst-case performance guarantees, for nonconvex Lambertian objects. Namely, a natural detection test based on the angle to the constructed cone guarantees to accept any image which is sufficiently well approximated with an image of the object under some admissible lighting condition, and guarantees to reject any image that does not have a sufficiently approximation. The cone models are generated by sampling point illuminations with sufficient density, which follows from a new perturbation bound for point images in the Lambertian model. As the number of point images required for guaranteed detection may be large, we introduce a new formulation for cone preserving dimensionality reduction, which leverages tools from sparse and low-rank decomposition to reduce the complexity, while controlling the approximation error with respect to the original cone. Preliminary numerical experiments suggest that this approach can significantly reduce the complexity of the resulting model.

Devido ao crescimento acelerado da quantidade de dados disponíveis para análise hoje, é comum lidar com grandes conjuntos de dados, por vezes complexos demais para serem interpretados na sua forma bruta. Por isso, as técnicas de Visualização de Informação têm o objetivo de facilitar para o ser humano a tarefa de análise e interação dos dados por meio da sua abstração em forma gráfica. Justificado pela necessidade de dar autonomia ao usuário final na criação de visualizações, este trabalho pretende delinear a importância da participação do usuário na criação e suporte à abstração da informação em forma gráfica. Para isso, foi desenvolvido o InterVis um sistema para criação interativa de visualizações de informação a partir de dados dinâmicos, que visa a permitir que o usuário final possa gerar e editar visualizações de acordo com a sua necessidade, independentemente da natureza da informação que deve ser analisada. O sistema foi testado utilizando o questionário USE a fim de verificar se a criação interativa de visualizações de informação, sem programação, aliada ao conhecimento do usuário sobre o domínio da aplicação, é mais eficiente da perspectiva da usabilidade sem perda significativa de flexibilidade. Os testes envolveram a execução de tarefas por indivíduos de um grupo de usuários. Todos os usuários conseguiram realizar todas as tarefas de criação e exploração em tempo hábil e avaliaram positivamente o sistema, além de terem sugerido diversas melhorias e novas funcionalidades. É possível concluir que o InterVis atualmente já atende às expectativas iniciais do trabalho, ainda que haja pontos a serem aprimorados em trabalhos futuros / Because of the growing amount of data available for analysis today, it is common to deal with large data sets, often too complex to be interpreted in their brute form. That is why Information Visualization techniques exist, to facilitate the analysis and interaction with data by humans through graphical abstractions. Motivated by the need to allow end users the autonomy to generate and edit visualizations, this work aims to underscore the importance of end user participation in the creation and support of these graphical abstractions of data. For this purpose, it was developed a system for interactive creation of Information Visualizations based on dynamic data, which aims to allow the final user to generate e edit visualizations according to their need and independently of the nature of the information that should be analyzed. This system was tested using the USE questionnaire, to verify whether this interactive creation of Information Visualizations, without programming, allied to the user knowledge of each applications domain, will be more efficient from the perspective of usability without significant loss of flexibility, as expected. The tests were compound of the tasks execution by individuals of a users group. All the users were able to conclude all tasks of creation and exploration in due time and evaluated positively the system, besides they have been suggested diverse improvement and new functionalities. It is possible to conclude that InterVis already fulfills the initial expectations of this work, although there are still points to be refined in future work

Técnicas de visualização de informaçoes têm sido usadas para a representação de ontologias visando permitir a compreensão de conceitos e propriedades em domínios específicos. A visualização de ontologias deve ser baseada em representaccões gráficas efetivas e téquinas de interação que auxiliem tarefas de usuários relacionadas a diferentes entidades e aspectos. Ontologias podem ser complexas devido tanto à grande quantidade de níveis da hierarquia de classes como também aos diferentes atributos. Neste trabalho, propo˜e-se uma abordagem baseada no uso de múltiplas e coordenadas visualizações para explorar ambos os níceis intensional e extensional de uma ontologia. Para tanto, são empregadas estruturas visuais baseadas em árvores que capturam a característica hierárquiva de partes da ontologia enquanto preservam as diferentes categorias de classes. Além desta contribuição, propõe-se um inovador emprego do conceito "Degree of Interest" de modo a reduzir a complexidade da representação da ontologia ao mesmo tempo que procura direcionar a atenção do usuádio para os principais conceitos de uma determinada tarefa. Através da análise automáfica dos diferentes aspectos da ontologia, o principal conceito é colocado em foco, distinguindo-o, assim, da informação desnecessária e facilitando a análise e o entendimento de dados correlatos. De modo a sincronizar as visualizações propostas, que se adaptam facilmente às tarefas de usuários, e implementar esta nova proposta de c´calculo baseado em "Degree of Interest", foi desenvolvida uma ferramenta de visualização de ontologias interativa chamada OntoViewer, cujo desenvolvimento seguiu um ciclo interativo baseado na coleta de requisitos e avaliações junto a usuários em potencial. Por fim, uma última contribuição deste trabalho é a proposta de um conjunto de "guidelines"visando auxiliar no projeto e na avaliação de téncimas de visualização para os níceis intensional e extensional de ontologias. / Visualization techniques have been used for the representation of ontologies to allow the comprehension of concepts and properties in specific domains. Techniques for visualizing ontologies should be based on effective graphical representations and interaction techniques that support users tasks related to different entities and aspects. Ontologies can be very large and complex due to many levels of classes’ hierarchy as well as diverse attributes. In this work we propose a multiple, coordinated views approach for exploring the intensional and extensional levels of an ontology. We use linked tree structures that capture the hierarchical feature of parts of the ontology while preserving the different categories of classes. We also present a novel use of the Degree of Interest notion in order to reduce the complexity of the representation itself while drawing the user attention to the main concepts for a given task. Through an automatic analysis of ontology aspects, we place the main concept in focus, distinguishing it from the unnecessary information and facilitating the analysis and understanding of correlated data. In order to synchronize the proposed views, which can be easily adapted to different user tasks, and implement this new Degree of Interest calculation, we developed an interactive ontology visualization tool called OntoViewer. OntoViewer was developed following an iterative cycle of refining designs and getting user feedback, and the final version was again evaluated by ten experts. As another contribution, we devised a set of guidelines to help the design and evaluation of visualization techniques for both the intensional and extensional levels of ontologies.

The large amount of available data on a diverse range of human activities provides many opportunities for understanding, improving and revealing unknown patterns in them. Powerful automatic methods for extracting this knowledge from data are already available from machine learning and data mining. They, however, rely on the expertise of analysts to improve their results when those are not satisfactory. In this context, interactive multidimensional projections are a useful tool for the analysis of multidimensional data by revealing their underlying structure while allowing the user to manipulate the results to provide further insight into this structure. This manipulation, however, has received little attention regarding their influence on the mappings, as they can change the final layout in unpredictable ways. This is the main motivation for this research: understanding the effects caused by changes in these mappings. We approach this problem from two perspectives. First, the user perspective, we designed and developed visualizations that help reduce the trial and error in this process by providing the right piece of information for performing manipulations. Furthermore, these visualizations help explain the changes in the map caused by such manipulations. Second, we defined the effectiveness of manipulation in quantitative terms, then developed an experimental framework for assessing manipulations in multidimensional projections under this view. This framework is based on improving mappings using known evaluation measures for these techniques. Using the improvement of measures as different types of manipulations, we perform a series of experiments on five datasets, five measures, and four techniques. Our experimental results show that there are possible types of manipulations that can happen effectively, with some techniques being more susceptible to manipulations than others. / O grande volume de dados disponíveis em uma diversa gama de atividades humanas cria várias oportunidades para entendermos, melhorarmos e revelarmos padrões previamente desconhecidos em tais atividades. Métodos automáticos para extrair esses conhecimentos a partir de dados já existem em áreas como aprendizado de máquina e mineração de dados. Entretanto, eles dependem da perícia do analista para obter melhores resultados quando estes não são satisfatórios. Neste contexto, técnicas de projeção multidimensional interativas são uma ferramenta útil para a análise de dados multidimensionais, revelando sua estrutura subjacente ao mesmo tempo que permite ao analista manipular os resultados interativamente, estendendo o processo de exploração. Essa interação, entretanto, não foi estudada com profundidade com respeito à sua real influência nos mapeamentos, já que podem causar mudanças não esperadas no mapeamento final. Essa é a principal motivação desta pesquisa: entender os efeitos causados pelas mudanças em tais mapeamentos. Abordamos o problema de duas perspectivas. Primeiro, da perspectiva do usuário, desenvolvemos visualizações que ajudam a diminuir tentativas e erros neste processo provendo a informação necessária a cada passo da interação. Além disso, essas visualizações ajudam a explicar as mudanças causadas no mapeamento pela manipulação. A segunda perspectiva é a efetividade da manipulação. Definimos de forma quantitativa a efetividade da manipulação, e então desenvolvemos um arcabouço para avaliar manipulações sob a visão da efetividade. Este arcabouço é baseado em melhorias nos mapeamentos usando medidas de avaliação conhecidas para tais técnicas. Usando tais melhorias como diferentes formas de manipulação, realizamos uma série de experimentos em cinco bases de dados, cinco medidas e quatro técnicas. Nossos resultados experimentais nos dão evidências que existem certos tipos de manipulação que podem acontecer efetivamente, com algumas técnicas sendo mais suscetíveis a manipulações do que outras.

This development project originated in response to the enormous daily increase of information that becomes available on the internet as a result of social media activities. Twitter, a quintessential example of social media, can also be considered a framework for collaborative note-taking. The October 2010 General Conference of the Church of Jesus Christ of Latter-day Saints provided an interesting example of distributed collaborative note-taking as thousands of Twitter users took notes on the conference addresses. The result was a collection of 26,479 tweets. The purpose of this project is to describe a novel information visualization algorithm that generates a centralized visual representation of the conference tweets to facilitate absorption of the ideas presented therein. This algorithm could feasibly be used in many other massively distributed collaborative note-taking activities. It is hoped that this algorithm, as well as the variant approaches that it may inspire, will assist larger groups to deal with the potential information overload that can arise in these collaborative note-taking activities.

<p><p>This paper focus on the development of a tool for Ship and Weather Information Monitoring (SWIM) visualizing weather data combined with data from ship voyages. The project was done in close collaboration with the Swedish Meteorological and Hydrological Institute (SMHI) who also evaluated the result. The goal was to implement a tool which will help shipping companies to monitor their feet and the weather development along planned routes and provide support for decisions regarding route choice and to evade hazard. A qualitative usability study was performed to gather insight about usability issues and to aid future development. Overall the result of the study was positive and the users felt that the tool would aid them in the daily work.</p></p>

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 116-123).

Thesis (M.S.)--University of Missouri-Columbia, 2006. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file viewed on (February 23, 2006) Includes bibliographical references.