Cells are the basic units of life. Studying complex tissues and whole organs requires an understanding of cell heterogeneity and responses to stimuli at the single-cell level. Even the cells, which belong to the same cell type, behave differently at a specific moment and contain different amount of mRNA. Quantitative polymerase chain reaction (qPCR) is one the most sensitive methods for the detection of mRNA, however, gene expression profiling in single cells leads to a large amount of missing data due to the fact that the transcript is missing, or is below the level of detection. Therefore, it is necessary to establish a new statistical approach for analysis of single cells. In this thesis the potential of single-cell gene expression profiling using the high throughput instrument Biomark, focusing on data analysis and biological interpretation, is discussed. Data normalization and handling of missing data are two important steps in data analysis that are performed differently at the single-cell level. Single cells are not normalized by reference genes but the number of cells as a normalizer is applied. Missing data are replaced by value, which is equaled one quarter of transcript amount in the cell. Furthermore it is shown how single-cell gene expression data can be viewed and how subpopulations...

Móveis: da visualidade à visualização é uma pesquisa teóricoprática que pretende discutir como o senso de espaço se transforma na percepção do mundo digitalizado e como isso é manifestado na arte contemporânea. Para isso, visamos aliar a prática artística, através da conclusão de um experimento artístico denominado Móveis, à reflexão. O experimento se realiza por processos híbridos possibilitados pelo digital e consolida-se como uma metacriação a partir do processamento da grande variedade de imagens e informações dispostas e trocadas diariamente pela cultura. No processo de desenvolvimento do experimento artístico Móveis, diferentes práticas e softwares são integrados para a visualização de informações e \"mineração\" visual de dados, composição de arquivos de pesquisa, remixagem e apresentação da obra. Nesses desdobramentos, consideramos práticas como remix e a visualização de dados não apenas como agentes de uma forma final específica ou de análise e demonstração de dados, mas como geradoras de um projeto para a criação. Na construção do projeto, instrumentos são utilizados como meio e não como fim, portanto pretendeu-se enfatizá-los enquanto geradores de métodos, estratégias e etapas para o projeto artístico -- não ficando aparente em sua forma final e sendo possível de ser verificados enquanto processo. No decorrer desse desenvolvimento, a elaboração conceitual funde-se à prática, determinando o caminho de compreensão das atividades envolvidas. / Movable: from Visuality to Visualization is a practise-based research that intends to discuss on how the sense of space changes through the perception of the digitized world and how this is manifested in contemporary art. For this purpose, we aim to combine artistic practice to the reflection, through the conclusion of an artistic experiment called Movable. The experiment was carried out by hybrid processes made possible by digital media and was consolidated as a meta-creation from the processing of a huge variety of imagery and information arranged and exchanged daily by the culture. In the process of developing the artistic experiment \"Movable\", different practices and softwares were integrated for information visualization and visual data mining, for the composition of research files, remixing and for presentation of the work. In these developments, we have considered practices such as remixing and visualization of data not only as agents of a specific final form or of analysis and data demonstration but as generators of a project for creation. In the construction of the project, instruments were used as a medium and not as an end, so it was intended to emphasize them as generators of methods, strategies and stages for the artistic project - not becoming apparent in its final form and being possible to be verified as a process. In the course of this development, conceptual elaboration was based on practice, determining the path of understanding of the activities involved.

Submitted by PPG Ci?ncia da Computa??o (ppgcc@pucrs.br) on 2018-05-30T17:58:54Z No. of bitstreams: 1 JULIA_MARA _COLLEONI_COUTO_DIS.pdf: 14083152 bytes, checksum: 6cf58ce4aafa66a5dee5876f3807b23f (MD5) / Approved for entry into archive by Sheila Dias (sheila.dias@pucrs.br) on 2018-06-11T11:15:59Z (GMT) No. of bitstreams: 1 JULIA_MARA _COLLEONI_COUTO_DIS.pdf: 14083152 bytes, checksum: 6cf58ce4aafa66a5dee5876f3807b23f (MD5) / Made available in DSpace on 2018-06-11T11:24:23Z (GMT). No. of bitstreams: 1 JULIA_MARA _COLLEONI_COUTO_DIS.pdf: 14083152 bytes, checksum: 6cf58ce4aafa66a5dee5876f3807b23f (MD5) Previous issue date: 2018-03-27 / Although human brain stores image more easily than text, most of the tools we use when it comes to project management are based on textual reports, such as Microsoft Office files. The number of projects that fail is still large due to several reasons, among which is the lack of understanding of the project by the stakeholders. When it comes to software development, the uncertainties, ambiguities, and complexities inherent in these projects can amplify the chances of failures. Data visualization tools and techniques can help clarify understanding of the context and project details for stakeholders, reducing the risk of project failure and facilitating communication processes. The objective of this work is to identify what is used of visual management applied to project management, in general, and by projects of various types, and verify, among the results, what can be applied in software development project management, and how it can be done. The method designed for the study is composed of 4 phases: foundation, evaluation, compilation, and proposal. Throughout the research, a systematic literature mapping was developed, followed by a survey and a focus group, resulting in the main contribution of this work: the PMBoK (PMI project management practice guide) extension proposal, containing a process, data visualization tools and techniques that can be used as support by the manager and stakeholders in a software development project. / Apesar de o c?rebro humano armazenar imagens com maior facilidade do que texto, grande parte das ferramentas utilizadas quando se trata de gest?o de projetos ? baseada em relat?rios textuais, como arquivos do pacote Microsoft Office. Atualmente, ainda ? grande a quantidade de projetos que falham, devido a motivos diversos, dentre os quais est? o n?o entendimento do projeto por parte das partes envolvidas. Quando se trata de desenvolvimento de software, as incertezas, ambiguidades e complexidades inerentes a estes projetos podem amplificar as chances de falhas. As ferramentas e t?cnicas de visualiza??o de dados podem ajudar a esclarecer o entendimento do contexto e de detalhes do projeto para todas as partes envolvidas, reduzindo o risco de insucesso no projeto e facilitando os processos de comunica??o. O objetivo deste trabalho ? identificar o que ? utilizado de gest?o visual aplicada ao gerenciamento de projetos, de maneira geral e por projetos de diversos tipos, e verificar, dentre os resultados, o que pode ser aplicado no gerenciamento de projetos de desenvolvimento de software, e de que maneira isso pode ser feito. A metodologia desenhada para o estudo ? composta por 4 fases: fundamenta??o, compila??o, avalia??o e proposta. Ao longo da pesquisa foram desenvolvidos um mapeamento sistem?tico da literatura, seguido por uma survey e um focus group, resultando na principal contribui??o deste trabalho: a proposta de extens?o do PMBoK (o guia de pr?ticas de gerenciamento de projetos do PMI), contendo um processo, t?cnicas e ferramentas de visualiza??o de dados que podem ser utilizadas como apoio pelo gerente e demais partes envolvidas em um projeto de desenvolvimento de software.

A sociedade está cada vez mais digitalizada, dados em diferentes extensões são passíveis de serem armazenados e correlacionados, temos um volume, variedade e velocidade de dados humanamente imensuráveis sem o auxílio de computadores. Neste cenário, falamos de um jornalismo de dados que visa o entendimento de temas complexos de relevância social e que sintoniza a profissão com as novas necessidades de compreensão informativa contemporânea. O intuito desta dissertação é problematizar a visualização de dados no jornalismo brasileiro partindo exatamente do que é esta visualização de dados jornalísticos e diante dos apontamentos sobre seu conceito e prática questionar como proporciona diferenciais relevantes. Por relevantes entendemos pautas de interesse público, que envolvem maior criticidade, maior aprofundamento e contextualização dos conteúdos no Big Data. As iniciativas que reúnem imagens relacionadas a dados e metadados ocorrem nas práticas de mercado, laboratórios acadêmicos, assim como em mídias independentes. Neste sistema narrativo atuam diferentes atores humanos e não-humanos, em construções iniciadas em codificações maquínicas, com bases de dados que dialogam com outras camadas até chegar a uma interface com o usuário. Há a necessidade de novas expertises por parte dos profissionais, trabalhos em equipe e conhecimento básico, muitas vezes, em linguagem de programação, estatística e a operacionalização de ferramentas na construção de narrativas dinâmicas e que cada vez mais envolvam o leitor. Sendo importante o pensar sobre um conteúdo que seja disponível para diferentes formatos. Para o desenvolvimento da pesquisa foi adotada uma estratégia multimetodológica, tendo os pressupostos da centralidade da comunicação, que perpassa todas as atividades comunicativas e informativas de forma transversal, sejam elas analógicas ou não. Um olhar que requer resiliências diante das abordagens teórico-metodológicas para que as mesmas consigam abarcar e sustentar as reflexões referentes ao dinâmico campo de estudos. Para se fazer as proposições e interpretações adotou-se como base o paradigma Jornalismo Digital em Base de Dados, tendo as contribuições dos conceitos de formato (RAMOS, 2012 e MACHADO, 2003), de jornalismo pós-industrial (COSTA, 2014), sistema narrativo e antenarrativa (BERTOCCHI, 2013) como meios de amadurecimento da compreensão do objeto proposto. / Society is increasingly digitalized. Different scopes of data are likely to be stored and correlated, having volumes, variety and accumulating speeds humanly impossible to track and analyze without the aid of computers. In this scenario we explore the realm of data-driven journalism with its aim of helping us understand complex issues of social relevance and which integrates journalism with the new needs of contemporary informative understanding. The purpose of this paper is to discuss data visualization in Brazilian journalism, starting with what data visualization is and then, upon its concept and practical uses, determine how this view provides relevant advantages. By relevant advantages we mean matters of public interest with more critical, greater depth and context of content on Big Data. Initiatives that bring together images related to data and metadata occur on market practices, academic laboratories, as well as independent media. This narrative system is acted upon different human and nonhuman agents, whose structures are being built with machinic codifications, using databases that communicate with other layers until reaching a user interface. There is a need for new expertise from professionals, teamwork and basic knowledge, often in programming languages, statistics and operational tools to build dynamic narratives and increasingly involve the reader. It is important to think about content that is available to different formats. For this research we adopted a multi-methodological strategy and the assumptions of the centrality of communication that permeates all communication and informational activities across the board, whether analog or not. A view that requires resilience in the face of theoretical and methodological approaches, so that they are able to embrace and support the reflections for this dynamic field of study. To make propositions and interpretations, adopted based on the Database Digital Journalism paradigm, and the contributions of format concepts (RAMOS, 2012 and MACHADO, 2003), post-industrial journalism (COSTA, 2014), system narrative and antenarrative (BERTOCCHI, 2013) maturing as means of understanding the proposed object.

Le phénomène de massification des données de santé constitue une opportunité de répondre aux questions des vigilances et de qualité des soins. Dans les travaux effectués au cours de cette thèse, nous présenterons des approches permettant d’exploiter la richesse et le volume des données intra hospitalières pour des cas d’usage de pharmacovigilance et de surveillance de bon usage du médicament. Cette approche reposera sur la modélisation de trajectoires de soins intra hospitalières adaptées aux besoins spécifiques de la pharmacovigilance. Il s’agira, à partir des données d’un entrepôt hospitalier de caractériser les événements d’intérêt et d’identifier un lien entre l’administration de ces produits de santé et l’apparition des effets indésirables, ou encore de rechercher les cas de mésusage du médicament. L’hypothèse posée dans cette thèse est qu’une approche visuelle interactive serait adaptée pour l’exploitation de ces données biomédicales hétérogènes et multi-domaines dans le champ de la pharmacovigilance. Nous avons développé deux prototypes permettant la visualisation et l’analyse des trajectoires de soins. Le premier prototype est un outil de visualisation du dossier patient sous forme de frise chronologique. La deuxième application est un outil de visualisation et fouille d’une cohorte de séquences d’événements. Ce dernier outil repose sur la mise en œuvre d’algorithme d’analyse de séquences (Smith-Waterman, Apriori, GSP) pour la recherche de similarité ou de motifs d’événements récurrents. Ces interfaces homme-machine ont fait l’objet d’études d’utilisabilité sur des cas d’usage tirées de la pratique réelle qui ont prouvé leur potentiel pour un usage en routine. / The massification of health data is an opportunity to answer questions about vigilance and quality of care. The emergence of big data in health is an opportunity to answer questions about vigilance and quality of care. In this thesis work, we will present approaches to exploit the diversity and volume of intra-hospital data for pharmacovigilance use and monitoring the proper use of drugs. This approach will be based on the modelling of intra-hospital care trajectories adapted to the specific needs of pharmacovigilance. Using data from a hospital warehouse, it will be necessary to characterize events of interest and identify a link between the administration of these health products and the occurrence of adverse reactions, or to look for cases of misuse of the drug. The hypothesis put forward in this thesis is that an interactive visual approach would be suitable for the exploitation of these heterogeneous and multi-domain biomedical data in the field of pharmacovigilance. We have developed two prototypes allowing the visualization and analysis of care trajectories. The first prototype is a tool for visualizing the patient file in the form of a timeline. The second application is a tool for visualizing and searching a cohort of event sequences The latter tool is based on the implementation of sequence analysis algorithms (Smith-Waterman, Apriori, GSP) for the search for similarity or patterns of recurring events. These human-machine interfaces have been the subject of usability studies on use cases from actual practice that have proven their potential for routine use.

Móveis: da visualidade à visualização é uma pesquisa teóricoprática que pretende discutir como o senso de espaço se transforma na percepção do mundo digitalizado e como isso é manifestado na arte contemporânea. Para isso, visamos aliar a prática artística, através da conclusão de um experimento artístico denominado Móveis, à reflexão. O experimento se realiza por processos híbridos possibilitados pelo digital e consolida-se como uma metacriação a partir do processamento da grande variedade de imagens e informações dispostas e trocadas diariamente pela cultura. No processo de desenvolvimento do experimento artístico Móveis, diferentes práticas e softwares são integrados para a visualização de informações e \"mineração\" visual de dados, composição de arquivos de pesquisa, remixagem e apresentação da obra. Nesses desdobramentos, consideramos práticas como remix e a visualização de dados não apenas como agentes de uma forma final específica ou de análise e demonstração de dados, mas como geradoras de um projeto para a criação. Na construção do projeto, instrumentos são utilizados como meio e não como fim, portanto pretendeu-se enfatizá-los enquanto geradores de métodos, estratégias e etapas para o projeto artístico -- não ficando aparente em sua forma final e sendo possível de ser verificados enquanto processo. No decorrer desse desenvolvimento, a elaboração conceitual funde-se à prática, determinando o caminho de compreensão das atividades envolvidas. / Movable: from Visuality to Visualization is a practise-based research that intends to discuss on how the sense of space changes through the perception of the digitized world and how this is manifested in contemporary art. For this purpose, we aim to combine artistic practice to the reflection, through the conclusion of an artistic experiment called Movable. The experiment was carried out by hybrid processes made possible by digital media and was consolidated as a meta-creation from the processing of a huge variety of imagery and information arranged and exchanged daily by the culture. In the process of developing the artistic experiment \"Movable\", different practices and softwares were integrated for information visualization and visual data mining, for the composition of research files, remixing and for presentation of the work. In these developments, we have considered practices such as remixing and visualization of data not only as agents of a specific final form or of analysis and data demonstration but as generators of a project for creation. In the construction of the project, instruments were used as a medium and not as an end, so it was intended to emphasize them as generators of methods, strategies and stages for the artistic project - not becoming apparent in its final form and being possible to be verified as a process. In the course of this development, conceptual elaboration was based on practice, determining the path of understanding of the activities involved.

Made available in DSpace on 2016-04-29T14:23:04Z (GMT). No. of bitstreams: 1 Paulo Sergio Rangel Garcia.pdf: 2904735 bytes, checksum: 788a6453214c9f0a41c9629423741347 (MD5) Previous issue date: 2011-11-22 / This paper aims to discuss a model for constructing a transparent portal that contains historical trends of public social, economical and financial indicators, preferably if collected at e-Gov websites. In order to reach that objective, we researched extensively within Manuel Castells, Tim Berners-Lee, Vinton Cerf, Karin K. Breitman, Martha Gabriel and Fernanda Viegas s work, amongst others, about semantic web, ontologies, search engine optimization and data visualization. Starting from a study of the historical evolution of internet, we try to understand how was possible to forge this context of highly productive disorganized dynamics that provided the conditions of the massive availability of information and data that we see today. By utilizing concepts and technologies such as metadata, ontologies, web services, software agents, data visualization and optimization of research mechanisms, we discuss techniques and methodologies that could make collecting data as fast as possible feasible, as well as putting it together in a way that either humans or other computer systems may easily understand. We also analyze the current e-Gov services provided by the Brazilian government by evaluating its characteristics, tendencies and possibilities for evolution and growth by utilizing data and research provided by NIC.BR and W3C BR. Thus, based on research and the author s own experience, this dissertation will try to propose a model for a portal that allows human interaction and integration with other computer systems for historical trends collected via web and formats and provides this data to society in a structured way. Finally, we indicate future researches that may contribute to the discussion and development of websites and services that apropriate public open data / Este trabalho tem como objetivo discutir um modelo para a construção de portal que dê transparência a séries históricas de indicadores sociais, econômicos e financeiros, públicos e disponíveis na web. Para se chegar a esse objetivo, foram realizados estudos em autores como Manuel Castells, Tim Berners-Lee, Vinton Cerf, Karin K. Breitman, Martha Gabriel e Fernanda Viegas entre outros, sobre web semântica, ontologias, otimização em mecanismos de buscas e visualização de dados. A partir do estudo da evolução histórica da Internet, buscou-se compreender como foi possível formar esse contexto de dinamismo não ordenado, com alta produção, criando condições para a alta disponibilidade de dados e informações que existem hoje. Abordando conceitos e tecnologias relacionadas à web semântica, ontologias, web services, agentes de software, visualização de dados e otimização dos mecanismos de buscas, discutiu-se técnicas e metodologias que viabilizem a sua construção de maneira a permitir que tais dados sejam coletados e que estejam disponíveis em formatos compreensíveis para seres humanos e integráveis a outros sistemas computacionais. Foi também analisado o e-Gov atual, especialmente no Brasil, avaliando suas características, tendências e oportunidades de evolução utilizando dados e estudos disponibilizados pelo NIC.BR e W3C BR. Assim, com base nesses estudos e na experiência do autor, esta dissertação tem o objetivo de propor um modelo de portal que permita a interatividade humana e integração com outros sistemas computacionais, das séries históricas públicas coletadas, formatando e disponibilizando-as de maneira estruturada para a sociedade. ` Por fim, é feita a indicação de pesquisas futuras, as quais venham contribuir para a discussão e o desenvolvimento de sites e serviços que apropriem dados abertos públicos.

La majorité des méthodes de classification de textes utilisent le paradigme du sac de mots pour représenter les textes. Pourtant cette technique pose différents problèmes sémantiques : certains mots sont polysémiques, d'autres peuvent être des synonymes et être malgré tout différenciés, d'autres encore sont liés sémantiquement sans que cela soit pris en compte et enfin, certains mots perdent leur sens s'ils sont extraits de leur groupe nominal. Pour pallier ces problèmes, certaines méthodes ne représentent plus les textes par des mots mais par des concepts extraits d'une ontologie de domaine, intégrant ainsi la notion de sens au modèle. Les modèles intégrant la représentation des textes par des concepts restent peu utilisés à cause des résultats peu satisfaisants. Afin d'améliorer les performances de ces modèles, plusieurs méthodes ont été proposées pour enrichir les caractéristiques des textes à l'aide de nouveaux concepts extraits de bases de connaissances. Mes travaux donnent suite à ces approches en proposant une étape d'enrichissement des modèles à l'aide d'une ontologie de domaine associée. J'ai proposé deux mesures permettant d'estimer l'appartenance aux catégories de ces nouveaux concepts. A l'aide de l'algorithme du classifieur naïf Bayésien, j'ai testé et comparé mes contributions sur le corpus de textes labéllisés Ohsumed et l'ontologie de domaine Disease Ontology. Les résultats satisfaisants m'ont amené à analyser plus précisément le rôle des relations sémantiques dans l'enrichissement des modèles. Ces nouveaux travaux ont été le sujet d'une seconde expérience où il est question d'évaluer les apports des relations hiérarchiques d'hyperonymie et d'hyponymie. / Most of text-classification methods use the ``bag of words” paradigm to represent texts. However Bloahdom and Hortho have identified four limits to this representation: (1) some words are polysemics, (2) others can be synonyms and yet differentiated in the analysis, (3) some words are strongly semantically linked without being taken into account in the representation as such and (4) certain words lose their meaning if they are extracted from their nominal group. To overcome these problems, some methods no longer represent texts with words but with concepts extracted from a domain ontology (Bag of Concept), integrating the notion of meaning into the model. Models integrating the bag of concepts remain less used because of the unsatisfactory results, thus several methods have been proposed to enrich text features using new concepts extracted from knowledge bases. My work follows these approaches by proposing a model-enrichment step using a domain ontology, I proposed two measures to estimate to belong to the categories of these new concepts. Using the naive Bayes classifier algorithm, I tested and compared my contributions on the Ohsumed corpus using the domain ontology ``Disease Ontology”. The satisfactory results led me to analyse more precisely the role of semantic relations in the enrichment step. These new works have been the subject of a second experiment in which we evaluate the contributions of the hierarchical relations of hypernymy and hyponymy.

The sixth volume of the DIGAREC Series holds the contributions to the DIGAREC Keynote-Lectures given at the University of Potsdam in the winter semester 2009/10. With contributions by Mark J.P. Wolf (Concordia University Wisconsin), Espen Aarseth (Center for Computer Games Research, IT University of Copenhagen), Katie Salen (Parsons New School of Design, New York), Laura Ermi and Frans Mäyrä (University of Tampere), and Lev Manovich (University of Southern California, San Diego).

Disertacijos tyrimų sritis yra daugiamačių duomenų analizė, bei tų duomenų suvokimo gerinimo būdai. Duomenų suvokimas yra sudėtingas uždavinys, ypač kai duomenys nurodo sudėtingą objektą, kuris aprašytas daugeliu parametrų. Disertacijoje nagrinėjami dirbtinių neuroninių tinklų algoritmai daugiamačiams duomenims vizualizuoti. Darbo tyrimų objektas yra dirbtiniai neuroniniai tinklai, skirti daugiamačių duomenų vizualizavimui. Su šiuo objektu yra betarpiškai susiję dalykai: daugiamačių duomenų vizualizavimas; dimensijos mažinimo algoritmai; projekcijos paklaidos; naujų taškų atvaizdavimas; vizualizavimui skirto neuroninio tinklo permokymo strategijos ir parametrų optimizavimas; lygiagretieji skaičiavimai. Pagrindinis disertacijos tikslas yra sukurti ir tobulinti metodus, kuriuos taikant būtų efektyviai minimizuojamos daugiamačių duomenų projekcijos paklaidos naudojantis dirbtiniais neuroniniais tinklais bei projekcijos algoritmais. Darbe atliktų tyrimų rezultatai atskleidė naujas medicininių (fiziologinių) duomenų analizės galimybes. / The research area of this work is the analysis of multidimensional data and the ways of improving apprehension of the data. Data apprehension is rather a complicated problem especially if the data refer to a complex object or phenomenon described by many parameters. The research object of the dissertation is artificial neural networks for multidimensional data projection. General topics that are related with this object: multidimensional data visualization; dimensionality reduction algorithms; errors of projecting data; the projection of the new data; strategies for retraining the neural network that visualizes multidimensional data; optimization of control parameters of the neural network for multidimensional data projection; parallel computing. The key aim of the work is to develop and improve methods how to efficiently minimize visualization errors of multidimensional data by using artificial neural networks. The results of the research are applied in solving some problems in practice. Human physiological data that describe the human functional state have been investigated.