Le développement des technologies de séquençage et de génotypage haut-débit permet de mesurer, pour un individu, une grande quantité d’information génomique.L’objectif de ce travail est, dans le cadre de la sélection génomique animale,de sélectionner un sous-ensemble de marqueurs génétiques pertinents permettant de prédire un caractère quantitatif, dans un contexte où le nombre d’animaux génotypés est largement inférieur au nombre de marqueurs étudiées.Ce manuscrit présente un état de l’art des méthodes actuelles permettant de répondre à la problématique. Nous proposons ensuite de répondre à notre problématique de sélection de variables en régression en grande dimension en combinant approches d’optimisation combinatoire et modèles statistiques. Nous commençons par paramétrer expérimentalement deux méthodes d’optimisation combinatoire, la recherche locale itérée et l’algorithme génétique, combinées avec une régression linéaire multiple et nous évaluons leur pertinence. Dans le contexte de la génomique animale les relations familiales entre animaux sont connues et peuvent constituer une information importante. Notre approche étant flexible, nous proposons une adaptation permettant de prendre en considération ces relations familiales via l’utilisation d’un modèle mixte. Le problème du sur-apprentissage étant particulièrement présent sur nos données dû au déséquilibre important entre le nombre de variables étudiées et le nombre d’animaux disponibles, nous proposons également une amélioration de notre approche permettant de diminuer ce sur-apprentissage.Les différentes approches proposées sont validées sur des données de la littérature ainsi que sur des données réelles de Gènes Diffusion. / Advances in high-throughput sequencing and genotyping technologies allow tomeasure large amounts of genomic information.The aim of this work is dedicated to the animal genomic selection is to select asubset of relevant genetic markers to predict a quantitative trait, in a context wherethe number of genotyped animals is widely lower than the number of markersstudied. This thesis introduces a state-of-the-art of existing methods to address the problem.We then suggest to deal with the variable selection in high dimensional regressionproblem combining combinatorial optimization methods and statistical models.We start by experimentally set two combinatorial optimization methods, theiterated local search and the genetic algorithm, combined with a linear multipleregression and we evaluate their relevance. In the context of animal genomic, familyrelationships between animals are known and can be an important information.As our approach is flexible we suggest an adaptation to consider these familialrelationships through the use of a mixed model. Moreover, the problem of overfittingis particularly present in such data due to the large imbalance between thenumber of variables studied and the number of animals available, so we suggest animprovement of our approach in order to reduce this over-fitting.The different suggested approaches are validated on data from the literature as wellas on real data of Gènes Diffusion.

Ph.D. (Computer Science) / The development of software systems is a relatively recent field of human endeavour. Even so, it has followed a steady progression of dominant paradigms which have incrementally improved the ease with which developers are able to express the logic and structure of their systems. The initially unstructured era of free-form spaghetti code gave way to structured programming in which the entry and exit points of functional units were well defined through the creation of abstractions such as procedures, sub-routines and functions. The problem of correctly associating data with the set of operations which are legal on this data was addressed through the concept of encapsulation with the onset of object-oriented programming. Object orientation also introduced a set of abstractions for safe code reuse through inheritance and dynamic polymorphism as well as composition/aggregation and delegation. The agent-oriented software development paradigm, when viewed as an extension of object orientation, adds the capacity of agent autonomy to an object, which allows it to select for itself which of its operations it will execute at any point in time. In addition, the separation between an agent and the environment within which it is embedded must be well defined. Agent autonomy allows for the modelling and development of loosely coupled systems with the capacity for complex emergent behaviour. The mapping of a given set of environmental percepts to an agent's operation selection defines its agent function and hence its emergent behaviour. Furthermore, agents may also be embedded into a shared environment together with other agents forming a multi-agent system. The emergent characteristics of such systems are defined not only through changes in environment state but also via agent to agent interactions. Multi-agent systems are categorised into cooperative or competitive based on whether all the agents within the system share a common goal. An argument is presented that even within cooperative multi-agent systems selfishness will emerge as a direct consequence of computational intractability. The core of the argument centres on the finite nature of the computational resources available to an agent which must be divided between the evaluation of the usefulness of other agent's knowledge and intentions towards improving the collective utility of the system and directly acting upon its own. As a direct result of the halting problem it is impossible for an agent to ascertain in general whether another agent's plans are even feasible (i.e. will result in the system reaching a goal state). As a direct consequence of such a limitation agents will in general favour their own courses of action over those of others and hence an emergent selfishness occurs even in ostensibly cooperative systems...

Variable screening techniques are fast and crude techniques to scan high-dimensional data and conduct dimension reduction before a refined variable selection method is applied. Its marginal analysis feature makes the method computationally feasible for ultra-high dimensional problems. However, most existing screening methods for classification problems are designed only for binary classification problems. There is lack of a comprehensive study on variable screening for multi-class classification problems. This research aims to fill the gap by developing variable screening for multi-class problems, to meet the need of high dimensional classification. The work has useful applications in cancer study, medicine, engineering and biology. In this research, we propose and investigate new and effective screening methods for multi-class classification problems. We consider two types of screening methods. The first one conducts screening for multiple binary classification problems separately and then aggregates the selected variables. The second one conducts screening for multi-class classification problems directly. In particular, for each method we investigate important issues such as choices of classification algorithms, variable ranking, and model size determination. We implement various selection criteria and compare their performance. We conduct extensive simulation studies to evaluate and compare the proposed screening methods with existing ones, which show that the new methods are promising. Furthermore, we apply the proposed methods to four cancer studies. R code has been developed for each method.

Esta tese é resultado de pesquisa que teve o objetivo de compreender o processo de desenvolvimento do Território Bico do Papagaio, no estado do Tocantins (TBP-TO), com base na implantação de projetos PROINFs, vinculados aos Programas PRONAT e PTC, visando explicitar efeitos, avanços e limites das políticas públicas territoriais em regiões com baixos índices de desenvolvimento. Nesta pesquisa utilizou-se de múltiplas estratégias para a coleta e análise de dados, seguindo os princípios e técnicas da triangulação, que constitui uma das formas de combinar métodos qualitativos entre si e de articular métodos quantitativos e qualitativos. Foi realizada, por meio de estudo de caso, em sete projetos implantados no TBP-TO. Uma questão importante, do ponto de vista metodológico, foi a oportunidade de fazer uma imersão no contexto investigado, observando e participando diretamente com os atores envolvidos na implantação e execução dos projetos PROINFs no referido território. Lançou-se mão de informações obtidas por observações, entrevistas, participação em reuniões, seminários, conversa com diferentes atores territoriais, moradores e membros do colegiado, gestores e beneficiários destes projetos. Os resultados levaram a uma compreensão das diferentes dimensões do desenvolvimento territorial e seus efeitos na vida dos beneficiários e na região. Os indicadores de desenvolvimento territorial, do ponto de vista econômico, foram avaliados entre ruins e críticos, dando a entender que a operacionalização da política territorial no TBP-TO reflete a própria história das relações de poder e dominação já existentes. Por outro lado, do ponto de vista social, foi observado o empoderamento da sociedade civil, especialmente nos casos das duas Escolas Família Agrícola (EFAs). Nesse sentido, esta tese contribuiu, não só para entender as dimensões do desenvolvimento territorial, seus desafios e possibilidades, mas para demonstrar que se não houver maior diálogo entre poder público (nas esferas municipal, estadual e federal), sociedade civil e os beneficiários dos projetos, o desenvolvimento territorial pode ficar comprometido. Diante dos resultados da pesquisa conclui-se que, nesse momento de retrocesso da política de desenvolvimento territorial, é necessário repensá-la, especialmente em relação ao exercício do poder e à autonomia dos Colegiados Territoriais. A organização dos colegiados territoriais e a união de seus membros em torno de objetivos comuns podem ser consideradas o motor propulsor da consolidação das EFAs, possibilitando a educação profissional de seus jovens. Esta organização é o maior indicador de desenvolvimento, na dimensão social, observado na pesquisa. / This thesis is the result of research that aims to understand the development process of the Parrot´s Beak Territory in the State of Tocantins (PBT-TO), based on the implantation of PROINFs projects, linked to PRONAT and PTC programs with the goal of clarifying effects, advances and limits of territorial public policies in regions with low levels of development. In this research, it was used multiple strategies for data collection and analysis, following the principles and techniques of triangulation, which is one of the ways to combine qualitative methods among themselves and to articulate quantitative and qualitative methods. The research was done through the case study in seven projects implanted in PBT-TO. An important thing, from the methodological point of view, was the opportunity to do an immersion in the context investigated by observing and participating directly with the actors involved in the implementation and execution of the projects PROINFs, in that territory. It was used the information obtained by observations, interviews, participation in meetings, seminars, talking with different territorial actors, residents and members of the board, managers and beneficiaries of these projects. The results led to an understanding of the different dimensions of territorial development and its effects on the lives of beneficiaries and in the region. The indicators of territorial development, from an economic point of view, were evaluated between bad and critical, implying that the operationalization of territorial policy in the PBT-TO reflect the history of the relationships of power and domination that exists. On the other hand, from the social point of view, it was observed the empowerment of civil society, especially in the cases of the Escolas Família Agrícola (EFAs). In this sense, this thesis has contributed not only to understand the dimensions of territorial development, its challenges and opportunities, but to demonstrate that if there is no greater dialogue between public authorities (in all spheres: Municipal, State and Federal), civil society and the beneficiaries of the projects, the territorial development may be compromised. On the research results it is concluded that, in this moment of backsliding of territorial development policy, it is necessary to rethink it, especially in relation to the exercise of power and the autonomy of Territorial governance bodies. The Organization of territorial governance bodies and the Union of its members around common goals, can be considered the impeller motor on consolidation of EFAs enabling professional education of their young. This organization is the greatest indicator of development in the social dimension, observed in the survey.

Esta tese é resultado de pesquisa que teve o objetivo de compreender o processo de desenvolvimento do Território Bico do Papagaio, no estado do Tocantins (TBP-TO), com base na implantação de projetos PROINFs, vinculados aos Programas PRONAT e PTC, visando explicitar efeitos, avanços e limites das políticas públicas territoriais em regiões com baixos índices de desenvolvimento. Nesta pesquisa utilizou-se de múltiplas estratégias para a coleta e análise de dados, seguindo os princípios e técnicas da triangulação, que constitui uma das formas de combinar métodos qualitativos entre si e de articular métodos quantitativos e qualitativos. Foi realizada, por meio de estudo de caso, em sete projetos implantados no TBP-TO. Uma questão importante, do ponto de vista metodológico, foi a oportunidade de fazer uma imersão no contexto investigado, observando e participando diretamente com os atores envolvidos na implantação e execução dos projetos PROINFs no referido território. Lançou-se mão de informações obtidas por observações, entrevistas, participação em reuniões, seminários, conversa com diferentes atores territoriais, moradores e membros do colegiado, gestores e beneficiários destes projetos. Os resultados levaram a uma compreensão das diferentes dimensões do desenvolvimento territorial e seus efeitos na vida dos beneficiários e na região. Os indicadores de desenvolvimento territorial, do ponto de vista econômico, foram avaliados entre ruins e críticos, dando a entender que a operacionalização da política territorial no TBP-TO reflete a própria história das relações de poder e dominação já existentes. Por outro lado, do ponto de vista social, foi observado o empoderamento da sociedade civil, especialmente nos casos das duas Escolas Família Agrícola (EFAs). Nesse sentido, esta tese contribuiu, não só para entender as dimensões do desenvolvimento territorial, seus desafios e possibilidades, mas para demonstrar que se não houver maior diálogo entre poder público (nas esferas municipal, estadual e federal), sociedade civil e os beneficiários dos projetos, o desenvolvimento territorial pode ficar comprometido. Diante dos resultados da pesquisa conclui-se que, nesse momento de retrocesso da política de desenvolvimento territorial, é necessário repensá-la, especialmente em relação ao exercício do poder e à autonomia dos Colegiados Territoriais. A organização dos colegiados territoriais e a união de seus membros em torno de objetivos comuns podem ser consideradas o motor propulsor da consolidação das EFAs, possibilitando a educação profissional de seus jovens. Esta organização é o maior indicador de desenvolvimento, na dimensão social, observado na pesquisa. / This thesis is the result of research that aims to understand the development process of the Parrot´s Beak Territory in the State of Tocantins (PBT-TO), based on the implantation of PROINFs projects, linked to PRONAT and PTC programs with the goal of clarifying effects, advances and limits of territorial public policies in regions with low levels of development. In this research, it was used multiple strategies for data collection and analysis, following the principles and techniques of triangulation, which is one of the ways to combine qualitative methods among themselves and to articulate quantitative and qualitative methods. The research was done through the case study in seven projects implanted in PBT-TO. An important thing, from the methodological point of view, was the opportunity to do an immersion in the context investigated by observing and participating directly with the actors involved in the implementation and execution of the projects PROINFs, in that territory. It was used the information obtained by observations, interviews, participation in meetings, seminars, talking with different territorial actors, residents and members of the board, managers and beneficiaries of these projects. The results led to an understanding of the different dimensions of territorial development and its effects on the lives of beneficiaries and in the region. The indicators of territorial development, from an economic point of view, were evaluated between bad and critical, implying that the operationalization of territorial policy in the PBT-TO reflect the history of the relationships of power and domination that exists. On the other hand, from the social point of view, it was observed the empowerment of civil society, especially in the cases of the Escolas Família Agrícola (EFAs). In this sense, this thesis has contributed not only to understand the dimensions of territorial development, its challenges and opportunities, but to demonstrate that if there is no greater dialogue between public authorities (in all spheres: Municipal, State and Federal), civil society and the beneficiaries of the projects, the territorial development may be compromised. On the research results it is concluded that, in this moment of backsliding of territorial development policy, it is necessary to rethink it, especially in relation to the exercise of power and the autonomy of Territorial governance bodies. The Organization of territorial governance bodies and the Union of its members around common goals, can be considered the impeller motor on consolidation of EFAs enabling professional education of their young. This organization is the greatest indicator of development in the social dimension, observed in the survey.