With a growing concern of an infectious diseases spreading in a population, epidemiology is becoming more important for the future of public health. In the past epidemiologist used existing data of an outbreak to help them determine how an infectious disease might spread in the future. Now with computational models, they able to analysis data produced by these models to help with prevention and intervention plans. This paper looks at the design, implementation, and analysis of a computational model based on the interactions of the population between individuals. The design of the working contact model looks closely at the SEIR model used as the foundation and the two timelines of a disease. The implementation of the contact model is reviewed while looking closely at data structures. The analysis of the experiments provide evidence this contact model can be used to help epidemiologist study the spread of an infectious disease based on the contact rate of individuals.

The dengue virus has become widespread worldwide in recent decades. It has no specific treatment and affects more than 40% of the entire population in the world. In Thailand, dengue has been a health concern for more than half a century. The highest number of cases in one year was 174,285 in 1987, leading to 1,007 deaths. In the present day, dengue is distributed throughout the entire country. Therefore, dengue has become a major challenge for public health in terms of both prevention and control of outbreaks. Different methodologies and ways of dealing with dengue outbreaks have been put forward by researchers. Computational models and simulations play an important role, as they have the ability to help researchers and officers in public health gain a greater understanding of the virus's epidemic activities. In this context, this dissertation presents a new framework, Modified Agent-Based Modeling (mABM), a hybrid platform between a mathematical model and a computational model, to simulate a dengue outbreak in human and mosquito populations. This framework improves on the realism of former models by utilizing the reported data from several Thai government organizations, such as the Thai Ministry of Public Health (MoPH), the National Statistical Office, and others. Additionally, its implementation takes into account the geography of Thailand, as well as synthetic mosquito and synthetic human populations. mABM can be used to represent human behavior in a large population across variant distances by specifying demographic factors and assigning mobility patterns for weekdays, weekends, and holidays for the synthetic human population. The mosquito dynamic population model (MDP), which is a component of the mABM framework, is used for representing the synthetic mosquito population dynamic and their ecology by integrating the regional model to capture the effect of dengue outbreak. The two synthetic populations can be linked to each other for the purpose of presenting their interactions, and the Local Stochastic Contact Model for Dengue (LSCM-DEN) is utilized. For validation, the number of cases from the experiment is compared to reported cases from the Thailand Vector Borne Disease Bureau for the selected years. This framework facilitates model configuration for sensitivity analysis by changing parameters, such as travel routes and seasonal temperatures. The effects of these parameters were studied and analyzed for an improved understanding of dengue outbreak dynamics.

The contact patterns among individuals can significantly affect the progress of an infectious outbreak within a population. Gathering data about these interaction and mixing patterns is essential to assess computational modeling of infectious diseases. Various self-report approaches have been designed in different studies to collect data about contact rates and patterns. Recent advances in sensing technology provide researchers with a bilateral automated data collection devices to facilitate contact gathering overcoming the disadvantages of previous approaches. In this study, a novel unilateral wearable sensing architecture has been proposed that overcome the limitations of the bi-lateral sensing. Our unilateral wearable sensing system gather contact data using hybrid sensor arrays embedded in wearable shirt. A smartphone application has been used to transfer the collected sensors data to the cloud and apply deep learning model to estimate the number of human contacts and the results are stored in the cloud database. The deep learning model has been developed on the hand labelled data over multiple experiments. This model has been tested and evaluated, and these results were reported in the study. Sensitivity analysis has been performed to choose the most suitable image resolution and format for the model to estimate contacts and to analyze the model's consumption of computer resources.

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-10-17T18:29:55Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) phd_efsb_FINAL_BIBLIOTECA.pdf: 7882904 bytes, checksum: df094c44eb4ce5be12596263047790ed (MD5) / Made available in DSpace on 2016-10-17T18:29:55Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) phd_efsb_FINAL_BIBLIOTECA.pdf: 7882904 bytes, checksum: df094c44eb4ce5be12596263047790ed (MD5) Previous issue date: 2016-08-29 / FACEPE / Context: In Software Engineering, technology transfer has been treated as a problem that concernsonly two agents (innovation and adoption agents) working together to fill the knowledge gap between them. In this scenario, the transfer is carried out in a “peer-to-peer” fashion, not changing the reality of individuals and organizations around them. This approach works well when one is just seeking the adoption of a technology by a“specific client”. However, it can not solve a common problem that is the adoption of new technologies by a large mass of potential new users. In a wider context like this, it no longer makes sense to focus on “peer-to-peer” transfer. A new way of looking at the problem is necessary. It makes more sense to approach it as diffusion of innovations, where there is an information spreading in a community, similar to that observed in epidemics. Objective: This thesis proposes a paradigm shift to show the adoption of programming languages can be formally addressed as an epidemic. This focus shift allows the dynamics of programming language adoption to be mathematically modelled as such, and besides finding models that explain the community’s behaviour when adopting programming languages, it allows some predictions to be made, helping both individuals who wish to adopt a new language that might seem to be a new industry standard, and language designers to understand in real time the adoption of a particular language by a community. Method: After a proof of concept with data from Sourceforge (2000 to 2009), data from GitHub (2009 to January 2016), a well-known open source software repository, and Stack Overflow (2008 to March 2016), a popular Q&A system for software developers, were obtained and preprocessed. Using cumulative biological growth functions, often used in epidemiological contexts, we obtained adjusted models to the data. Once with the adjusted models, we evaluated their predictive capabilities through repeated applications of hypothesis testing and statistical calculations in different versions of the models obtained after adjusting the functions to samples of different time frames from the repositories. Results: We show that programming language adoption can be formally considered an epidemiological phenomenon by adjusting a well-known mathematical function used to describe such phenomena. We also show that, using the models found, it is possible to forecast programming languages adoption. We also show that it is possible to have similar insights by observing user data, as well as data from the community itself, not using software developers as susceptible individuals. Limitations: The forecast of the adoption outcome (asymptote) needs to be taken with care because it varies depending on the sample size, which also influences the quality of forecasts in general. Unfortunately, we not always have control over the sample size, because it depends on the population under analysis. The forecast of programming language adoption is only valid for the analysed population; generalizations should be made with caution. Conclusion: Addressing programming languages adoption as an epidemiological phenomenon allows us to perform analyses not possible otherwise. We can have an overview of a population in real time regarding the use of a programming language, which allows us, as innovation agents, to adjust our technology if it is not achieving the desired “penetration”; as adoption agents, we may decide, ahead of our competitors, to adopt a seemingly promising technology that may ultimately become a standard. / Contexto: Em Engenharia de Software, transferência de tecnologia tem sido tratada como um problema pontual, um processo que diz respeito a dois agentes (os agentes de inovação e adoção) trabalhando juntos para preencher uma lacuna no conhecimento entre estes dois. Neste cenário, a transferência é realizada “ponto a ponto”, envolvendo e tendo efeito apenas nos indivíduos que participam do processo. Esta abordagem funciona bem quando se está buscando apenas a adoção da tecnologia por um “cliente” específico. No entanto, ela não consegue resolver um problema bastante comum que é a adoção de novas tecnologias por uma grande massa de potenciais novos usuários. Neste contexto mais amplo, não faz mais sentido focar em transferência ponto a ponto, faz-se necessária uma nova maneira de olhar para o problema. É mais interessante abordá-lo como difusão de inovações, onde existe um espalhamento da informação em uma comunidade, de maneira semelhante ao que se observa em epidemias. Objetivo: Esta tese de doutorado mostra que a adoção de linguagens de programação pode ser tratada formalmente como uma epidemia. Esta mudança conceitual na maneira de olhar para o fenômeno permite que a dinâmica da adoção de linguagens de programação seja modelada matematicamente como tal, e além de encontrar modelos que expliquem o comportamento da comunidade quando da adoção de uma linguagem de programação, permite que algumas previsões sejam realizadas, ajudando tanto indivíduos que desejem adotar uma nova linguagem que parece se apresentar como um novo padrão industrial, quanto ajudando projetistas de linguagens a entender em tempo real a adoção de uma determinada linguagem pela comunidade. Método: Após uma prova de conceito com dados do Sourceforge (2000 a 2009), dados do GitHub (2009 a janeiro de 2016) um repositório de projetos software de código aberto, e Stack Overflow (2008 a março de 2016) um popular sistema de perguntas e respostas para desenvolvedores de software, from obtidos e pré processados. Utilizando uma função de crescimento biológico cumulativo, frequentemente usada em contextos epidemiológicos, obtivemos modelos ajustados aos dados. Uma vez com os modelos ajustados, realizamos avaliações de sua precisão. Avaliamos suas capacidades de previsão através de repetidas aplicações de testes de hipóteses e cálculos de estatísticas em diferentes versões dos modelos, obtidas após ajustes das funções a amostras de diferentes tamanhos dos dados obtidos. Resultados: Mostramos que a adoção de linguagens de programação pode ser considerada formalmente um fenômeno epidemiológico através do ajuste de uma função matemática reconhecidamente útil para descrever tais fenômenos. Mostramos também que é possível, utilizando os modelos encontrados, realizar previsões da adoção de linguagens de programação em uma determinada comunidade. Ainda, mostramos que é possível obter conclusões semelhantes observando dados de usuários e dados da comunidade apenas, não usando desenvolvedores de software como indivíduos suscetíveis. Limitações: A previsão do limite superior da adoção (assíntota) não é confiável, variando muito dependendo do tamanho da amostra, que também influencia na qualidade das previsões em geral. Infelizmente, nem sempre teremos controle sob o tamanho da amostra, pois ela depende da população em análise. A adoção da linguagem de programação só é válida para a população em análise; generalizações devem ser realizadas com cautela. Conclusão: Abordar o fenômeno de adoção de linguagens de programação como um fenômeno epidemiológico nos permite realizar análises que não são possíveis de outro modo. Podemos ter uma visão geral de uma população em tempo real no que diz respeito ao uso de uma linguagem de programação, o que nos permite, com agentes de inovação, ajustar a tecnologia caso ela não esteja alcançando o alcance desejado; como agentes de adoção, podemos decidir por adotar uma tecnologia aparentemente promissora que pode vir a se tornar um padrão.

Many infectious diseases are spread through interactions between susceptible and infectious individuals. Keeping track of where each exposure to the disease took place, when it took place, and which individuals were involved in the exposure can give public health officials important information that they may use to formulate their interventions. Further, knowing which individuals in the population are at the highest risk of becoming infected with the disease may prove to be a useful tool for public health officials trying to curtail the spread of the disease. Epidemiological models are needed to allow epidemiologists to study the population dynamics of transmission of infectious agents and the potential impact of infectious disease control programs. While many agent-based computational epidemiological models exist in the literature, they focus on the spread of disease rather than exposure risk. These models are designed to simulate very large populations, representing individuals as agents, and using random experiments and probabilities in an attempt to more realistically guide the course of the modeled disease outbreak. The work presented in this thesis focuses on tracking exposure risk to chickenpox in an elementary school setting. This setting is chosen due to the high level of detailed information realistically available to school administrators regarding individuals' schedules and movements. Using an agent-based approach, contacts between individuals are tracked and analyzed with respect to both individuals and locations. The results are then analyzed using a combination of tools from computer science and geographic information science.