In the context of telecommunication networks, the user attribution problem refers to the challenge faced in recognizing communication traffic as belonging to a given user when information needed to identify the user is missing. This is analogous to trying to recognize a nameless face in a crowd. This problem worsens as users move across many mobile networks (complex networks) owned and operated by different providers. The traditional approach of using the source IP address, which indicates where a packet comes from, does not work when used to identify mobile users. Recent efforts to address this problem by exclusively relying on web browsing behavior to identify users were limited to a small number of users (28 and 100 users). This was due to the inability of solutions to link up multiple user sessions together when they rely exclusively on the web sites visited by the user. This study has tackled this problem by utilizing behavior based identification while accounting for time and the sequential order of web visits by a user. Hierarchical Temporal Memories (HTM) were used to classify historical navigational patterns for different users. Each layer of an HTM contains variable order Markov chains of connected nodes which represent clusters of web sites visited in time order by the user (user sessions). HTM layers enable inference "generalization" by linking Markov chains within and across layers and thus allow matching longer sequences of visited web sites (multiple user sessions). This approach enables linking multiple user sessions together without the need for a tracking identifier such as the source IP address. Results are promising. HTMs can provide high levels of accuracy using synthetic data with 99% recall accuracy for up to 500 users and good levels of recall accuracy of 95 % and 87% for 5 and 10 users respectively when using cellular network data. This research confirmed that the presence of long tail web sites (rarely visited) among many repeated destinations can create unique differentiation. What was not anticipated prior to this research was the very high degree of repetitiveness of some web destinations found in real network data.

Open-source software becomes increasingly popular nowadays. Many startup companies and small business owners choose to adopt open source software packages to meet their daily office computing needs or to build their IT infrastructure. Unlike proprietary software systems, open source software systems usually have a loosely-organized developer collaboration structure. Developers work on their "assignments" on a voluntary basis. Many developers do not physically meet their "co-workers." This unique developer collaboration pattern leads to unique software development process, and hence unique structure of software products. It is those unique characteristics of open source software that motivate this dissertation study. Our research follows the framework of the four key elements of software engineering: Project, People, Process and Product (Jacobson, Booch et al. 1999). This dissertation studies three of the four P's: People, Process and Product. Due to the large sizes and high complexities of many open source software packages, the traditional analysis methods and measures in software engineering can not be readily leveraged to analyze those software packages. In this dissertation, we adopt complex network theory to perform our analysis on open source software packages, software development process, and the collaboration among software developers. We intend to discover some common characteristics that are shared by different open source software packages, and provide a possible explanation of the development process of those software products. Specifically we represent real world entities, such as open source software source code or developer collaborations, with networks composed of inter-connected vertices. We then leverage the topological metrics that have been established in complex network theory to analyze those networks. We also propose our own random network growth model to illustrate open source software development processes. Our research results can be potentially used by software practitioners who are interested to develop high quality software products and reduce the risks in the development process. Chapter 1 is an introduction of the dissertation's structure and research scope. We aim at studying open source software with complex networks. The details of the 4-P framework will be introduced in that chapter. Chapter 2 analyzes five C-language based open source software packages by leveraging function dependency networks. That chapter calculates the topological measures of the dependency networks extracted from software source code. Chapter 3 analyzes the collaborative relationship among open source software developers. We extract developer's co-working data out of two software bug fixing data sets. Again by leveraging complex network theory, we find out a number of topological characteristics of the software developer networks, such as the scale-free property. We also realize the topological differences between from the bug side and from the developer side for the extracted bipartite networks. Chapter 4 is to compare two widely adopted clustering coefficient definitions, the one proposed by Watts and Strogatz, the other by Newman. The analytical similarities and differences between the two clustering coefficient definitions provide useful guidance to the proposal of the random network growth model that is presented in the next chapter. Chapter 5 aims to characterize the open source software development process. We propose a two-phase network growth model to illustrate the software development process. Our model describes how different software source code units interconnect as the size of the software grows. A case study was performed by using the same five open source software packages that have been adopted in Chapter 2. The empirical results demonstrate that our model provides a possible explanation on the process of how open source software products are developed. Chapter 6 concludes the dissertation and highlights the possible future research directions.

This thesis presents an investigation into Gyrodactylus species recognition, making use of machine learning classification and feature selection techniques, and explores image feature extraction to demonstrate proof of concept for an envisaged rapid, consistent and secure initial identification of pathogens by field workers and non-expert users. The design of the proposed cognitively inspired framework is able to provide confident discrimination recognition from its non-pathogenic congeners, which is sought in order to assist diagnostics during periods of a suspected outbreak. Accurate identification of pathogens is a key to their control in an aquaculture context and the monogenean worm genus Gyrodactylus provides an ideal test-bed for the selected techniques. In the proposed algorithm, the concept of classification using a single model is extended to include more than one model. In classifying multiple species of Gyrodactylus, experiments using 557 specimens of nine different species, two classifiers and three feature sets were performed. To combine these models, an ensemble based majority voting approach has been adopted. Experimental results with a database of Gyrodactylus species show the superior performance of the ensemble system. Comparison with single classification approaches indicates that the proposed framework produces a marked improvement in classification performance. The second contribution of this thesis is the exploration of image processing techniques. Active Shape Model (ASM) and Complex Network methods are applied to images of the attachment hooks of several species of Gyrodactylus to classify each species according to their true species type. ASM is used to provide landmark points to segment the contour of the image, while the Complex Network model is used to extract the information from the contour of an image. The current system aims to confidently classify species, which is notifiable pathogen of Atlantic salmon, to their true class with high degree of accuracy. Finally, some concluding remarks are made along with proposal for future work.

Um dos padrões mais importantes que ocorrem em ecossistemas é a relação espécie-área, que relaciona o número de espécies em um ecossistema com a sua área disponível. O estudo dessa relação é fundamental para entender-se a biodiversidade e o impacto de políticas ambientais de preservação de espécies, de modo que é possível analisar desde os tamanhos das reservas necessários para a conservação das espécies e até verificar o impacto da intervenção humana em habitats naturais. Assim sendo, várias estratégias matemáticas e computacionais foram desenvolvidas para prever e entender esse padrão ecológico em modelos ecológicos. Todavia, muitas abordagens são simuladas em ambientes homogêneos e regulares, porém, sabe-se que, em cada ecossistema, há regiões com acidentes geográficos, variações de altitudes, vegetação e clima. Dessa forma, nesse trabalho, estamos interessados em estudar a influência de diferentes ambientes no processo de evolução das espécies. Para isso, consideramos modelos ecológicos que utilizam características geográficas para colonização e, comportamentos individuais como dispersão, mutação, acasalamento. Com isso, foi possível simular a propagação das espécies em diferentes topologias e analisar como ocorreu a dinâmica em cada uma delas. Assim, verificamos que a topologia regular e a dispersão homogênea dos indivíduos são duas características que maximizam a diversidade de espécies. E por outro lado, a formação de regiões mais densas e interações heterogêneas, contribuem para a diminuição da quantidade de espécies, apesar de em alguns casos, ajudarem na velocidade de propagação e colonização. / One of the most important patterns that occur in ecosystems is the species-area relationship, which says that the number of species increases with the sampled area. There is a great interest among ecologists about this pattern, since it is possible to verify the human impact on the environment and the area of reserves necessary to maintain species. Thus, motivated by the explanation of such behavior, some mathematical and computational strategies have been developed over the years. However, most approaches are simulated in homogeneous and regular scenarios, however, in the ecosystem, there are regions with landforms, different climates and vegetation. Thus, in this work, we are interested in studying the influence of different environments in the evolution process of the species. We consider ecological models that use geographical characteristics for colonization and individual behaviors such as dispersion, mutation, and mating. Thereby, it was possible to simulate the propagation of the species in different topologies and to analyze how the dynamics occurred in each case. Therefore, we verified that the regular topology and the homogeneous dispersion of the individuals are two characteristics that maximize the diversity of species. On the other hand, denser regions and heterogeneous interactions, contribute to the decrease the number of species, even when in some cases, they help in the speed of propagation and colonization.

Em sistemas biológicos, o estudo da estabilidade das redes de regulação gênica é visto como uma contribuição importante que a Matemática pode proporcionar a pesquisas sobre câncer e outras doenças genéticas. Neste trabalho, utilizamos o conceito de ``canalização\'\' como sinônimo de estabilidade em uma rede biológica. Como as características de uma rede de regulação canalizada ainda são superficialmente compreendidas, estudamos esse conceito sob o ponto de vista computacional: propomos um modelo matemático simplificado para descrever o fenômeno e realizamos algumas análises sobre o mesmo. Mais especificamente, a estabilidade da maior bacia de atração das redes Booleanas - um clássico paradigma para a modelagem de redes de regulação - é analisada. Os resultados indicam que a estabilidade da maior bacia de atração está relacionada com dados biológicos sobre o crescimento de colônias de leveduras e que considerações sobre a interação entre as funções Booleanas e a topologia da rede devem ser realizadas conjuntamente na análise de redes estáveis. / In biological systems, the study of gene regulatory networks stability is seen as an important contribution that Mathematics can make to cancer research and that of other genetic diseases. In this work, we consider the concept of ``canalization\'\' as a consequence of stability in gene regulatory networks. The characteristics of canalized regulatory networks are superficially understood. Hence, we study the canalization concept under a computational framework: a simplified model is proposed to describe the phenomenon using Boolean Networks - a classical paradigm to modeling regulatory networks. Specifically, the stability of the largest basin of attraction in gene regulatory networks is analyzed. Our results indicate that the stability of the largest basin of attraction is related to biological data on growth of yeast colonies, and that thoughts about the interaction between Boolean functions and network topologies must be given in the analysis of stable networks.

Imagens multiespectrais estão presentes na grande maioria de dispositivos de imageamento atuais, desde câmeras pessoais até microscópios, telescópios e satélites. No entanto, grande parte dos trabalhos em análise de texturas e afins propõem abordagens monocromáticas, que muitas vezes consideram apenas níveis de cinza. Nesse contexto e considerando o aumento da capacidade dos computadores atuais, o uso da informação espectral deve ser considerada na construção de modelos melhores. Ultimamente redes neurais convolucionais profundas pré-treinadas tem sido usadas em imagens coloridas de 3 canais, porém são limitadas a apenas esse formato e computam muitas convoluções, o que demanda por hardware específico (GPU). Esses fatos motivaram esse trabalho, que propõem técnicas para a modelagem e caracterização de imagens multiespectrais baseadas em redes complexas, que tem se mostrado uma ferramenta eficiente em trabalhos anteriores e possui complexidade computacional similar à métodos tradicionais. São introduzidas duas abordagens para aplicação em imagens coloridas de três canais, denominadas Rede Multicamada (RM) e Rede Multicamada Direcionada (RMD). Esses métodos modelam todos os canais da imagem de forma conjunta, onde as redes possuem conexões intra e entre canais, de forma parecida ao processamento oponente de cor do sistema visual humano. Experimentos em cinco bases de textura colorida mostram a proposta RMD supera vários métodos da literatura no geral, incluindo redes convolucionais e métodos tradicionais integrativos. Além disso, as propostas demonstraram alta robustez a diferentes espaços de cor (RGB, LAB, HSV e I1I2I3), enquanto que outros métodos oscilam de base para base. Também é proposto um método para caracterizar imagens multiespectrais de muitos canais, denominado Rede Direcionada de Similaridade Angular (RDSA). Nessa proposta, cada pixel multiespectral é considerado como um vetor de dimensão equivalente à quantidade de canais da imagem e o peso das arestas representa sua similaridade do cosseno, apontando para o pixel de maior valor absoluto. Esse método é aplicado em um conjunto de imagens de microscopia por fluorescência de 32 canais, em um experimento para identificar variações na estrutura foliar do espécime Jacaranda Caroba submetidos à diferentes condições. O método RDSA obtém as maiores taxas de acerto de classificação nesse conjunto de dados, com 91, 9% usando o esquema de validação cruzada Leave-one-out e 90, 5(±1, 1)% com 10-pastas, contra 81, 8% e 84, 7(±2, 2) da rede convolucional VGG16. / Multispectral images are present in the vast majority of current imaging devices, from personal cameras to microscopes, telescopes and satellites. However, much of the work in texture analysis and the like proposes monochromatic approaches, which often consider only gray levels. In this context and considering the performance increase of current computers, the use of the spectral information must be considered in the construction of better models. Lately, pre-trained deep convolutional neural networks have been used in 3-channel color images, however they are limited to just this format and compute many convolutions, which demands specific hardware (GPU). These facts motivated this work, which propose techniques for the modeling and characterization of multispectral images based on complex networks, which has proved to be an efficient tool in previous works and has computational complexity similar to traditional methods. Two approaches are introduced for application in 3-channel color images, called Multilayer Network (RM) and Directed Multilayer Network (RMD). These methods model all channels of the image together, where the networks have intra- and inter-channel connections, similar to the opponent color processing of the human visual system. Experiments in five color texture datasets shows that the RMD proposal overcomes several methods of the literature in general, including convolutional networks and traditional integrative methods. In addition, the proposals have demonstrated high robustness to different color spaces (RGB, LAB, HSV and I1I2I3), while other methods oscillate from dataset to dataset. Moreover it is proposed a new method to characterize multispectral images of many channels, called Directed Network of Angular Similarity (RDSA). In this proposal, each multispectral pixel is considered as a vector of dimensions equivalent to the number of channels of the image and the weight of the edges represents its cosine similarity, pointing to the pixel of greatest absolute value. This method is applied to a set of fluorescence microscopy images of 32 channels in an experiment to identify variations in the leaf structure of the Jacaranda Caroba specimen under different conditions. The RDSA method obtains the highest classification rates in this dataset, with 91.9% with the Leave-one-out cross-validation scheme and 90.5(±1.1)% with 10-folds, against 81.8% and 84.7(±2.2) of the convolutional network VGG16.

As redes complexas surgiram como uma nova e importante maneira de representação e abstração de dados capaz de capturar as relações espaciais, topológicas, funcionais, entre outras características presentes em muitas bases de dados. Dentre as várias abordagens para a análise de dados, destacam-se a classificação e a detecção de outliers. A classificação de dados permite atribuir uma classe aos dados, baseada nas características de seus atributos e a detecção de outliers busca por dados cujas características se diferem dos demais. Métodos de classificação de dados e de detecção de outliers baseados em redes complexas ainda são pouco estudados. Tendo em vista os benefícios proporcionados pelo uso de redes complexas na representação de dados, o presente trabalho apresenta o desenvolvimento de um método baseado em redes complexas para detecção de outliers que utiliza a caminhada aleatória e um índice de dissimilaridade. Este método possibilita a identificação de diferentes tipos de outliers usando a mesma medida. Dependendo da estrutura da rede, os vértices outliers podem ser tanto aqueles distantes do centro como os centrais, podem ser hubs ou vértices com poucas ligações. De um modo geral, a medida proposta é uma boa estimadora de vértices outliers em uma rede, identificando, de maneira adequada, vértices com uma estrutura diferenciada ou com uma função especial na rede. Foi proposta também uma técnica de construção de redes capaz de representar relações de similaridade entre classes de dados, baseada em uma função de energia que considera medidas de pureza e extensão da rede. Esta rede construída foi utilizada para caracterizar mistura entre classes de dados. A caracterização de classes é uma questão importante na classificação de dados, porém ainda é pouco explorada. Considera-se que o trabalho desenvolvido é uma das primeiras tentativas nesta direção / Complex networks have emerged as a new and important way of representation and data abstraction capable of capturing the spatial relationships, topological, functional, and other features present in many databases. Among the various approaches to data analysis, we highlight classification and outlier detection. Data classification allows to assign a class to the data based on characteristics of their attributes and outlier detection search for data whose characteristics differ from the others. Methods of data classification and outlier detection based on complex networks are still little studied. Given the benefits provided by the use of complex networks in data representation, this study developed a method based on complex networks to detect outliers based on random walk and on a dissimilarity index. The method allows the identification of different types of outliers using the same measure. Depending on the structure of the network, the vertices outliers can be either those distant from the center as the central, can be hubs or vertices with few connections. In general, the proposed measure is a good estimator of outlier vertices in a network, properly identifying vertices with a different structure or a special function in the network. We also propose a technique for building networks capable of representing similarity relationships between classes of data based on an energy function that considers measures of purity and extension of the network. This network was used to characterize mixing among data classes. Characterization of classes is an important issue in data classification, but it is little explored. We consider that this work is one of the first attempts in this direction

Epidemiologists rely on human interaction networks for determining states and dynamics of disease propagations in populations. However, such networks are empirical snapshots of the past. It will greatly benefit if human interaction networks are statistically predicted and dynamically created while an epidemic is in progress. We develop an application framework for the generation of human interaction networks and running epidemiological processes utilizing research on human mobility patterns and agent-based modeling. The interaction networks are dynamically constructed by incorporating different types of Random Walks and human rules of engagements. We explore the characteristics of the created network and compare them with the known theoretical and empirical graphs. The dependencies of epidemic dynamics and their outcomes on patterns and parameters of human motion and motives are encountered and presented through this research. This work specifically describes how the types and parameters of random walks define properties of generated graphs. We show that some configurations of the system of agents in random walk can produce network topologies with properties similar to small-world networks. Our goal is to find sets of mobility patterns that lead to empirical-like networks. The possibility of phase transitions in the graphs due to changes in the parameterization of agent walks is the focus of this research as this knowledge can lead to the possibility of disruptions to disease diffusions in populations. This research shall facilitate work of public health researchers to predict the magnitude of an epidemic and estimate resources required for mitigation.

Redes complexas é uma área de estudo relativamente recente, que tem chamado a atenção da comunidade científica e vem sendo aplicada com êxito em diferentes áreas de atuação tais como redes de computadores, sociologia, medicina, física, matemática entre outras. Entretanto a literatura demonstra que poucos são os trabalhos que empregam redes complexas na extração de características de imagens para posterior analise ou classificação. Dada uma imagem é possível modela-la como uma rede, extrair características topológicas e, utilizando-se dessas medidas, construir o classificador desejado. Esse trabalho objetiva, portanto, investigar mais a fundo esse tipo de aplicação, analisando novas formas de modelar uma imagem como uma rede complexa e investigar diferentes características topológicas na caracterização de imagens. Como forma de analisar o potencial das técnicas desenvolvidas, selecionamos um grande desafio na área de visão computacional: identificação vegetal por meio de análise foliar. A identificação vegetal é uma importante tarefa em vários campos de pesquisa como biodiversidade, ecologia, botânica, farmacologia entre outros. / Complex networks is a relatively recent field of study, that has called the attention of the scientific community and has been successfully applied in different areas such as computer networking, sociology, medicine, physics, mathematics and others. However the literature shows that there are few works that employ complex networks in feature extraction of images for later analysis or classification. Given an image, it can be modeled as a network, extract topological features and, using these measures, build the classifier desired. This work aims, therefore, investigate this type of application, analyzing new forms of modeling an image as a complex network and investigate some topological features to characterize images. In order to analyze the potential of the techniques developed, we selected a major challenge in the field of computer vision: plant identification by leaf analysis. The plant identification is an important task in many research fields such as biodiversity, ecology, botany, pharmacology and others.

A Clusterização de dados em grupos oferece uma maneira de entender e extrair informações relevantes de grandes conjuntos de dados. A abordagem em relação a aspectos como a representação dos dados e medida de similaridade entre clusters, e a necessidade de ajuste de parâmetros iniciais são as principais diferenças entre os algoritmos de clusterização, influenciando na qualidade da divisão dos clusters. O uso cada vez mais comum de grandes conjuntos de dados aliado à possibilidade de melhoria das técnicas já existentes tornam a clusterização de dados uma área de pesquisa que permite inovações em diferentes campos. Nesse trabalho é feita uma revisão dos métodos de clusterização já existentes, e é descrito um novo método de clusterização de dados baseado na identificação de comunidades em redes complexas e modelos computacionais inspirados biologicamente. A técnica de clusterização proposta é composta por duas etapas: formação da rede usando os dados de entrada; e particionamento dessa rede para obtenção dos clusters. Nessa última etapa, a técnica de otimização por nuvens de partículas é utilizada a fim de identificar os clusters na rede, resultando em um algoritmo de clusterização hierárquico divisivo. Resultados experimentais revelaram como características do método proposto a capacidade de detecção de clusters de formas arbitrárias e a representação de clusters com diferentes níveis de refinamento. / DAta clustering is an important technique to understand and to extract relevant information in large datasets. Data representation and similarity measure adopted, and the need to adjust initial parameters, are the main differences among clustering algorithms, interfering on clusters quality. The crescent use of large datasets and the possibility to improve existing techniques make data clustering a research area that allows innovation in different fields. In this work is made a review of existing data clustering methods, and it is proposed a new data clustering technique based on community dectection on complex networks and bioinspired models. The proposed technique is composed by two steps: network formation to represent input data; and network partitioning to identify clusters. In the last step, particle swarm optimization technique is used to detect clusters, resulting in an hierarchical clustering algorithm. Experimental results reveal two main features of the algorithm: the ability to detect clusters in arbitrary shapes and the ability to generate clusters with different refinement degrees