Arsenic is a universal environmental toxicant associated mostly with skin related diseases in people exposed to low doses over a long term. Low dose arsenic trioxide (ATO) with long exposure will lead to chronic exposure. Experiments were performed to provide new knowledge on the incompletely understood mechanisms of action of chronic low dose inorganic arsenic in keratinocytes. Cytotoxicity patterns of ATO on long-term cultures of HaCaT cells on collagen IV was studied over a time course of 14 days. DNA damage was also assessed. The percentages of viable cells after exposure were measured on Day 2, Day 5, Day 8, and Day 14. Statistical and visual analytics approaches were used for data analysis. In the result, a biphasic toxicity response was observed at a 5 μg/ml dose with cell viability peaking on Day 8 in both chronic and acute exposures. Furthermore, a low dose of 1 μg/ml ATO enhanced HaCaT keratinocyte proliferation but also caused DNA damage. Global gene expression study using microarray technique demonstrated differential expressions of genes in HaCaT cell exposed to 0.5 μg/ml dose of ATO up to 22 passages. Four of the up-regulated and 1 down-regulated genes were selected and confirmed with qRT-PCR technique. These include; Aldo-Keto Reductase family 1, member C3 (AKR1C3), Insulin Growth Factor-Like family member 1 (IGFL1), Interleukin 1 Receptor, type 2 (IL1R2) and Tumour Necrosis Factor [ligand] Super-Family, member 18 (TNFSF18), and down-regulated Regulator of G-protein Signalling 2 (RGS2). The decline in growth inhibiting gene (RGS2) and increase in AKR1C3 may be the contributory path to chronic inflammation leading to metaplasia. This pathway is proposed to be a mechanism leading to carcinogenesis in skin keratinocytes. The observed over expression of IGFL1 may be a means of triggering carcinogenesis in HaCaT keratinocytes. In conclusion, it was established that at very low doses, arsenic is genotoxic and induces aberrations in gene expression though it may appear to enhance cell proliferation. The expression of two genes encoding membrane proteins IL1R2 and TNFSF18 may serve as possible biomarkers of skin keratinocytes intoxication due to arsenic exposure. This research provides insights into previously unknown gene markers that may explain the mechanisms of arsenic-induced dermal disorders including skin cancer / Environmental Sciences / D. Phil. (Environmental science)

Visual Analytics is a multi-disciplinary field that uses interactive visualisations to promote and assist the analytic reasoning and generate insights. Understanding the perceptual and cognitive factors is key to the progress in this field. This research focuses on understanding the benefits of interaction in terms of insight generation Moreover, this investigation explores the compounding effects individual differences have with interaction when analysing data to generate insights. This study investigated the individual differences in two sets; psychometric set measures, and a sensorial preferences multimodal learning style. Interaction was analysed from an information visualisation perspective, exploring the Visual Mapping and View Transformation interaction, by isolating interaction as an independent variable. Moreover, the View Transformation experiment used two different visual representations 2D and 3D. Additionally, the individual differences were analysed using the aptitude-by-treatment interaction (ATI) methodology. The ATI approach enabled the assessment of the performance gains in terms of insight generation according to pre-defined set levels of individual differences measures. This thesis confirms the benefits of interaction in generating more insights and increasing their accuracy, whilst facilitating the generation of insights requiring lower mental effort. Further, the results show significant conjoint effects between interaction and individual differences. Furthermore this research revealed a performance difference between 2D and 3D visual representation in the serious game problem solving context. Overall, this thesis provides tangible proof that both visual mapping and view transformation interaction are beneficial to visual analytics in generating insights. Strengthening the view that interaction with the problem-set improves understanding, and the number of insights gleaned into the problem and that more research into the use of individual differences, as a performance predictor in Visual Analytics is beneficial.

Neuroscientists are increasingly overwhelmed by new recordings of the nervous system. These recordings are significantly increasing in size due to new electrophysiological techniques, such as multi-electrode arrays. These techniques can simultaneously record the electrical activity (or spike trains) from thousands of neurons. These new datasets are larger than the traditional datasets recorded from single electrodes where fewer than ten spike trains are usually recorded. Consequently, new tools are now required to effectively analyse these new datasets. This thesis describes how techniques from the field of Visual Analytics can be applied to detect specific patterns in spike train data. These techniques are realised in a software tool called Neurigma. Neurigma is a collection of visual representations of spike train data that are unified to provide a coordinated representation of the data. The visual representations within Neurigma include: an interactive raster plot, an improved correlation grid, a novel representation called the correlation plot (which includes a novel coupling estimation algorithm), and a novel network diagram. These views provide insight into spike train data, and particularly, they identify correlated patterns, called functional connectivity. Within this thesis Neurigma is used to analyse synthetically generated datasets and experimental recordings. Three main findings are presented. First, propagating spiral patterns are identified within recordings from the neonatal mouse retina. Second, functional connectivity is identified within the cat visual cortex. Finally, the functional connectivity of a large synthetic dataset, of 1000 spike trains, is accurately classified into direct, indirect and common input coupling.

Cette thèse présente une nouvelle méthodologie pour analyser des réseaux. Nous développons l'intrication d'un réseau multiplex, qui se matérialise sous forme d'une mesure d'intensité et d'homogénéité, et d'une abstraction, le réseau d'interaction des catalyseurs, auxquels sont associés des indices d'intrication. Nous présentons ensuite la mise en place d'outils spécifiques pour l'analyse visuelle des réseaux complexes qui tirent profit de cette méthodologie. Ces outils présente une vue double de deux réseaux,qui inclue une un algorithme de dessin, une interaction associant brossage d'une sélection et de multiples liens pré-attentifs. Nous terminons ce document par la présentation détaillée d'applications dans de multiples domaines. / When it comes to comprehension of complex phenomena, humans need to understand what interactions lie within them.These interactions are often captured with complex networks. However, the interaction pluralism is often shallowed by traditional network models. We propose a new way to look at these phenomena through the lens of multiplex networks, in which catalysts are drivers of the interaction through substrates. To study the entanglement of a multiplex network is to study how edges intertwine, in other words, how catalysts interact. Our entanglement analysis results in a full set of new objects which completes traditional network approaches: the entanglement homogeneity and intensity of the multiplex network, and the catalyst interaction network, with for each catalyst, an entanglement index. These objects are very suitable for embedment in a visual analytics framework, to enable comprehension of a complex structure. We thus propose of visual setting with coordinated multiple views. We take advantage of mental mapping and visual linking to present simultaneous information of a multiplex network at three different levels of abstraction. We complete brushing and linking with a leapfrog interaction that mimics the back-and-forth process involved in users' comprehension. The method is validated and enriched through multiple applications including assessing group cohesion in document collections, and identification of particular associations in social networks.

Representações visuais têm sido adotadas na exploração de conjuntos de documentos, auxiliando a extração de conhecimento sem que seja necessária a análise individual de milhares de textos. Mapas de documentos, em particular, apresentam documentos individualmente representados espalhados em um espaço visual, refletindo suas relações de similaridade ou conexões. A construção destes mapas de documentos inclui, entre outras tarefas, o posicionamento dos textos e a identificação automática de áreas temáticas. Um desafio é a visualização de conjuntos dinâmicos de documentos. Na visualização de informação, é comum que alterações no conjunto de dados tenham um forte impacto na organização do espaço visual, dificultando a manutenção, por parte do usuário, de um mapa mental que o auxilie na interpretação dos dados apresentados e no acompanhamento das mudanças sofridas pelo conjunto de dados. Esta tese introduz um algoritmo para a construção dinâmica de mapas de documentos, capaz de manter uma disposição coerente à medida que elementos são adicionados ou removidos. O processo, inerentemente incremental e de baixa complexidade, utiliza um espaço bidimensional dividido em células, análogo a um tabuleiro de xadrez. Resultados consistentes foram alcançados em comparação com técnicas não incrementais de projeção de dados multidimensionais, tendo sido a técnica aplicada também em outros domínios, além de conjuntos de documentos. A visualização resultante não está sujeita a problemas de oclusão. A identificação de áreas temáticas é alcançada com técnicas de extração de regras de associação representativas para a identificação automática de tópicos. A combinação da extração de tópicos com a projeção incremental de dados em um processo integrado de mineração visual de textos compõe um espaço visual em que tópicos e áreas de interesse são destacados e atualizados à medida que o conjunto de dados é modificado / Visual representations are often adopted to explore document collections, assisting in knowledge extraction, and avoiding the thorough analysis of thousands of documents. Document maps present individual documents in visual spaces in such a way that their placement reflects similarity relations or connections between them. Building these maps requires, among other tasks, placing each document and identifying interesting areas or subsets. A current challenge is to visualize dynamic data sets. In Information Visualization, adding and removing data elements can strongly impact the underlying visual space. That can prevent a user from preserving a mental map that could assist her/him on understanding the content of a growing collection of documents or tracking changes on the underlying data set. This thesis presents a novel algorithm to create dynamic document maps, capable of maintaining a coherent disposition of elements, even for completely renewed sets. The process is inherently incremental, has low complexity and places elements on a 2D grid, analogous to a chess board. Consistent results were obtained as compared to (non-incremental) multidimensional scaling solutions, even when applied to visualizing domains other than document collections. Moreover, the corresponding visualization is not susceptible to occlusion. To assist users in indentifying interesting subsets, a topic extraction technique based on association rule mining was also developed. Together, they create a visual space where topics and interesting subsets are highlighted and constantly updated as the data set changes

The classical wavelet transform has been widely used in image and signal processing, where a signal is decomposed into a combination of basis signals. By analyzing the individual contribution of the basis signals, one can infer properties of the original signal. This dissertation presents an overview of the extension of the classical signal processing theory to graph domains. Specifically, we review the graph Fourier transform and graph wavelet transforms both of which based on the spectral graph theory, and explore their properties through illustrative examples. The main features of the spectral graph wavelet transforms are presented using synthetic and real-world data. Furthermore, we introduce in this dissertation a novel method for visual analysis of dynamic networks, which relies on the graph wavelet theory. Dynamic networks naturally appear in a multitude of applications from different domains. Analyzing and exploring dynamic networks in order to understand and detect patterns and phenomena is challenging, fostering the development of new methodologies, particularly in the field of visual analytics. Our method enables the automatic analysis of a signal defined on the nodes of a network, making viable the detection of network properties. Specifically, we use a fast approximation of the graph wavelet transform to derive a set of wavelet coefficients, which are then used to identify activity patterns on large networks, including their temporal recurrence. The wavelet coefficients naturally encode spatial and temporal variations of the signal, leading to an efficient and meaningful representation. This method allows for the exploration of the structural evolution of the network and their patterns over time. The effectiveness of our approach is demonstrated using different scenarios and comparisons involving real dynamic networks. / A transformada wavelet clássica tem sido amplamente usada no processamento de imagens e sinais, onde um sinal é decomposto em uma combinação de sinais de base. Analisando a contribuição individual dos sinais de base, pode-se inferir propriedades do sinal original. Esta tese apresenta uma visão geral da extensão da teoria clássica de processamento de sinais para grafos. Especificamente, revisamos a transformada de Fourier em grafo e as transformadas wavelet em grafo ambas fundamentadas na teoria espectral de grafos, e exploramos suas propriedades através de exemplos ilustrativos. As principais características das transformadas wavelet espectrais em grafo são apresentadas usando dados sintéticos e reais. Além disso, introduzimos nesta tese um método inovador para análise visual de redes dinâmicas, que utiliza a teoria de wavelets em grafo. Redes dinâmicas aparecem naturalmente em uma infinidade de aplicações de diferentes domínios. Analisar e explorar redes dinâmicas a fim de entender e detectar padrões e fenômenos é desafiador, fomentando o desenvolvimento de novas metodologias, particularmente no campo de análise visual. Nosso método permite a análise automática de um sinal definido nos vértices de uma rede, tornando possível a detecção de propriedades da rede. Especificamente, usamos uma aproximação da transformada wavelet em grafo para obter um conjunto de coeficientes wavelet, que são então usados para identificar padrões de atividade em redes de grande porte, incluindo a sua recorrência temporal. Os coeficientes wavelet naturalmente codificam variações espaciais e temporais do sinal, criando uma representação eficiente e com significado expressivo. Esse método permite explorar a evolução estrutural da rede e seus padrões ao longo do tempo. A eficácia da nossa abordagem é demonstrada usando diferentes cenários e comparações envolvendo redes dinâmicas reais.

A rápida evolução dos recursos computacionais vem permitindo que grandes conjuntos de dados sejam armazenados e recuperados. No entanto, a exploração, compreensão e extração de informação útil ainda são um desafio. Com relação às ferramentas computacionais que visam tratar desse problema, a Visualização de Informação possibilita a análise de conjuntos de dados por meio de representações gráficas e a Mineração de Dados fornece processos automáticos para a descoberta e interpretação de padrões. Apesar da recente popularidade dos métodos de visualização de informação, um problema recorrente é a baixa escalabilidade visual quando se está analisando grandes conjuntos de dados, resultando em perda de contexto e desordem visual. Com intuito de representar grandes conjuntos de dados reduzindo a perda de informação relevante, o processo de agregação visual de dados vem sendo empregado. A agregação diminui a quantidade de dados a serem representados, preservando a distribuição e as tendências do conjunto de dados original. Quanto à mineração de dados, visualização de informação vêm se tornando ferramental essencial na interpretação dos modelos computacionais e resultados gerados, em especial das técnicas não-supervisionados, como as de agrupamento. Isso porque nessas técnicas, a única forma do usuário interagir com o processo de mineração é por meio de parametrização, limitando a inserção de conhecimento de domínio no processo de análise de dados. Nesta dissertação, propomos e desenvolvemos uma metáfora visual baseada na TableLens que emprega abordagens baseadas no conceito de agregação para criar representações mais escaláveis para a interpretação de dados tabulares. Como aplicação, empregamos a metáfora desenvolvida na análise de resultados de técnicas de agrupamento. O ferramental resultante não somente suporta análise de grandes bases de dados com reduzida perda de contexto, mas também fornece subsídios para entender como os atributos dos dados contribuem para a formação de agrupamentos em termos da coesão e separação dos grupos formados. / The rapid evolution of computing resources has enabled large datasets to be stored and retrieved. However, exploring, understanding and extracting useful information is still a challenge. Among the computational tools to address this problem, information visualization techniques enable the data analysis employing the human visual ability by making a graphic representation of the data set, and data mining provides automatic processes for the discovery and interpretation of patterns. Despite the recent popularity of information visualization methods, a recurring problem is the low visual scalability when analyzing large data sets resulting in context loss and visual disorder. To represent large datasets reducing the loss of relevant information, the process of aggregation is being used. Aggregation decreases the amount of data to be represented, preserving the distribution and trends of the original dataset. Regarding data mining, information visualization has become an essential tool in the interpretation of computational models and generated results, especially of unsupervised techniques, such as clustering. This occurs because, in these techniques, the only way the user interacts with the mining process is through parameterization, limiting the insertion of domain knowledge in the process. In this thesis, we propose and develop the new visual metaphor based on the TableLens that employs approaches based on the concept of aggregation to create more scalable representations of tabular data. As application, we use the developed metaphor in the analysis of the results of clustering techniques. The resulting framework does not only support large database analysis but also provides insights into how data attributes contribute to clustering regarding cohesion and separation of the composed groups

Les flux d’information suivent aujourd’hui des chemins complexes: la propagation des informations, impliquant éditeurs on-line, chaînes d’information en continu et réseaux sociaux, emprunte alors des chemins croisés, susceptibles d’agir sur le contenu et sa perception. Ce projet de thèse étudie l’adaptation des mesures de graphes classiques aux graphes multiplexes en relation avec le domaine étudié, propose de construire des visualisations à partir de plusieurs représentations graphiques des réseaux, et de les combiner (visualisations multi-vues synchronisées, représentations hybrides, etc.). L’accent est mis sur les modes d’interaction permettant de prendre en compte l’aspect multiplexe (multicouche) des réseaux. Ces représentations et manipulations interactives s’appuient aussi sur le calcul d’indicateurs propres aux réseaux multiplexes. Ce travail est basé sur deux jeux de données principaux: l’un est une archive de 12 ans de l’émission japonaise publique quotidienne NHK News 7, de 2001 à 2013. L’autre recense les participants aux émissions de télévision/radio françaises entre 2010 et 2015. Deux systèmes de visualisation s’appuyant sur une interface Web ont été développés pour analyser des réseaux multiplexes, que nous appelons «Visual Cloud» et «Laputa». Dans le Visual Cloud, nous définissons formellement une notion de similitude entre les concepts et les groupes de concepts que nous nommons possibilité de co-occurrence (CP). Conformément à cette définition, nous proposons un algorithme de classification hiérarchique. Nous regroupons les couches dans le réseau multiplexe de documents, et intégrons cette hiérarchie dans un nuage de mots interactif. Nous améliorons les algorithmes traditionnels de disposition de mise en forme de nuages de mots de sorte à préserver les contraintes sur la hiérarchie de concepts. Le système Laputa est destiné à l’analyse complexe de réseaux temporels denses et multidimensionnels. Pour ce faire, il associe un graphe à une segmentation. La segmentation par communauté, par attribut, ou encore par tranche temporelle, forme des vues de ce graphe. Afin d’associer ces vues avec le tout global, nous utilisons des diagrammes de Sankey pour révéler l’évolution des communautés (diagrammes que nous avons augmentés avec un zoom sémantique). Cette thèse nous permet ainsi de parcourir trois aspects (3V) des plus intéressants de la donnée et du BigData appliqués aux archives multimédia: Le Volume de nos données dans l’immensité des archives, nous atteignons des ordres de grandeurs qui ne sont pas praticables pour la visualisation et l’exploitation des liens. La Vélocité à cause de la nature temporelle de nos données (par définition). La Variété qui est un corollaire de la richesse des données multimédia et de tout ce que l’on peut souhaiter vouloir y investiguer. Ce que l’on peut retenir de cette thèse c’est que la traduction de ces trois défis a pris dans tous les cas une réponse sous la forme d’une analyse de réseaux multiplexes. Nous retrouvons toujours ces structures au coeur de notre travail, que ce soit de manière plus discrète dans les critères pour filtrer les arêtes par l’algorithme Simmelian backbone, que ce soit par la superposition de tranches temporelles, ou bien que ce soit beaucoup plus directement dans la combinaison d’indices sémantiques visuels et textuels pour laquelle nous extrayons les hiérarchies permettant notre visualisation. / Nowadays, information follows complex paths: information propagation involving on-line editors, 24-hour news providers and social medias following entangled paths acting on information content and perception. This thesis studies the adaptation of classical graph measurements to multiplex graphs, to build visualizations from several graphical representations of the networks, and to combine them (synchronized multi-view visualizations, hybrid representations, etc.). Emphasis is placed on the modes of interaction allowing to take in hand the multiplex nature (multilayer) of the networks. These representations and interactive manipulations are also based on the calculation of indicators specific to multiplex networks. The work is based on two main datasets: one is a 12-year archive of the Japanese public daily broadcast NHK News 7, from 2001 to 2013. Another lists the participants in the French TV/radio shows between 2010 and 2015. Two visualization systems based on a Web interface have been developed for multiplex network analysis, which we call "Visual Cloud" and "Laputa". In the Visual Cloud, we formally define a notion of similarity between concepts and groups of concepts that we call co-occurrence possibility (CP). According to this definition, we propose a hierarchical classification algorithm. We aggregate the layers in a multiplex network of documents, and integrate that hierarchy into an interactive word cloud. Here we improve the traditional word cloud layout algorithms so as to preserve the constraints on the concept hierarchy. The Laputa system is intended for the complex analysis of dense and multidimensional temporal networks. To do this, it associates a graph with a segmentation. The segmentation by communities, by attributes, or by time slices, forms views of this graph. In order to associate these views with the global whole, we use Sankey diagrams to reveal the evolution of the communities (diagrams that we have increased with a semantic zoom). This thesis allows us to browse three aspects of the most interesting aspects of the data miming and BigData applied to multimedia archives: The Volume since our archives are immense and reach orders of magnitude that are usually not practicable for the visualization; Velocity, because of the temporal nature of our data (by definition). The Variety that is a corollary of the richness of multimedia data and of all that one may wish to want to investigate. What we can retain from this thesis is that we met each of these three challenges by taking an answer in the form of a multiplex network analysis. These structures are always at the heart of our work, whether in the criteria for filtering edges using the Simmelian backbone algorithm, or in the superposition of time slices in the complex networks, or much more directly in the combinations of visual and textual semantic indices for which we extract hierarchies allowing our visualization.

Information technology has played several important roles in group decision making, such as communication support and decision support. Little is known about how information technology can be used to persuade members of a group to reach a consensus. In this dissertation, I aim to address the issues that are related to the role of visual representation technology (VRT) for persuasion in a forecasting context. VRTs are not traditional graphical representation technologies. VRTs can select, transform, and present data in a rich visual format that facilitates exploration, comprehension, and sense-making. The first study investigates conditions under which teams are likely to increase the use of VRTs and how the use of VRTs affects teams' consensus development and decision performance. The second study evaluates the effects of influence types and information technology on a choice shift. A choice shift is the tendency of group members to shift their initial positions to a more extreme direction following discussion. A choice shift is also called group polarization. To complement my first two studies, I conduct a laboratory experiment in my third study. I explore the effect of VRTs and team composition on a choice shift in group confidence.

Irregular algorithms such as graph algorithms, sorting, and sparse matrix multiplication, present numerous programming challenges, including scalability, load balancing, and efficient memory utilization. In this age of Big Data we face additional challenges since the data is often streaming at a high velocity and we wish to make near real-time decisions for real-world events. For instance, we may wish to track Twitter for the pandemic spread of a virus. Analyzing such data sets requires combing algorithmic optimizations and utilization of massively multithreaded architectures, accelerator such as GPUs, and distributed systems. My research focuses upon designing new analytics and algorithms for the continuous monitoring of dynamic social networks. Achieving high performance computing for irregular algorithms such as Social Network Analysis (SNA) is challenging as the instruction flow is highly data dependent and requires domain expertise. The rapid changes in the underlying network necessitates understanding real-world graph properties such as the small world property, shrinking network diameter, power law distribution of edges, and the rate at which updates occur. These properties, with respect to a given analytic, can help design load-balancing techniques, avoid wasteful (redundant) computations, and create streaming algorithms. In the course of my research I have considered several parallel programming paradigms for a wide range systems of multithreaded platforms: x86, NVIDIA's CUDA, Cray XMT2, SSE-SIMD, and Plurality's HyperCore. These unique programming models require examination of the parallel programming at multiple levels: algorithmic design, cache efficiency, fine-grain parallelism, memory bandwidths, data management, load balancing, scheduling, control flow models and more. This thesis deals with these issues and more.