Gene regulatory network (GRN) consists of a set of genes and regulatory relationships between the genes. As outputs of the GRN, gene expression data contain important information that can be used to reconstruct the GRN to a certain degree. However, the reverse engineer of GRNs from gene expression data is a challenging problem in systems biology. Conventional methods fail in inferring GRNs from gene expression data because of the relative less number of observations compared with the large number of the genes. The inherent noises in the data make the inference accuracy relatively low and the combinatorial explosion nature of the problem makes the inference task extremely difficult. This study aims at reconstructing the GRNs from time-course gene expression data based on GRN models using system identification and parameter estimation methods. The main content consists of three parts: (1) a review of the methods for reverse engineering of GRNs, (2) reverse engineering of GRNs based on linear models and (3) reverse engineering of GRNs based on a nonlinear model, specifically S-systems. In the first part, after the necessary background and challenges of the problem are introduced, various methods for the inference of GRNs are comprehensively reviewed from two aspects: models and inference algorithms. The advantages and disadvantages of each method are discussed. The second part focus on inferring GRNs from time-course gene expression data based on linear models. First, the statistical properties of two sparse penalties, adaptive LASSO and SCAD, with an autoregressive model are studied. It shows that the proposed methods using these two penalties can asymptotically reconstruct the underlying networks. This provides a solid foundation for these methods and their extensions. Second, the integration of multiple datasets should be able to improve the accuracy of the GRN inference. A novel method, Huber group LASSO, is developed to infer GRNs from multiple time-course data, which is also robust to large noises and outliers that the data may contain. An efficient algorithm is also developed and its convergence analysis is provided. The third part can be further divided into two phases: estimating the parameters of S-systems with system structure known and inferring the S-systems without knowing the system structure. Two methods, alternating weighted least squares (AWLS) and auxiliary function guided coordinate descent (AFGCD), have been developed to estimate the parameters of S-systems from time-course data. AWLS takes advantage of the special structure of S-systems and significantly outperforms one existing method, alternating regression (AR). AFGCD uses the auxiliary function and coordinate descent techniques to get the smart and efficient iteration formula and its convergence is theoretically guaranteed. Without knowing the system structure, taking advantage of the special structure of the S-system model, a novel method, pruning separable parameter estimation algorithm (PSPEA) is developed to locally infer the S-systems. PSPEA is then combined with continuous genetic algorithm (CGA) to form a hybrid algorithm which can globally reconstruct the S-systems.

A ocorrência de inundações nos centros urbanos acarreta diferentes transtornos sócio-econômicos. É possível minimizar os problemas quando estes eventos são previstos com antecedência. A partir de ferramentas computacionais, da modelação hidrológica e modelação hidrodinâmica, podem-se obter predições de níveis d´água. O modelo hidrológico físico CSmap e o modelo de cálculo de condutos livres CLiv são adotados neste trabalho para demonstrar a aplicação de um sistema de previsões de cheias. A partir do estudo da Bacia do Rio Ribeira de Iguape, demonstra-se que o aprimoramento destes modelos matemáticos e das técnicas de calibração pode não ser relevante quando os dados de origem são imprecisos. / Differents social and economics problems affect urbanized areas when a flood happens. These problems may be minimized by predictions made by computer´s tools, hydrological models and hydraulics algorithmics. The physical hydrologic model CSmap and open channel´s model CLiv are adopted in this research to demonstrate a flood´s prediction system application. Another analysis shows that the development of math´s models and calibration´s techniques may not be relevant when inaccurate data is utilized.

A ocorrência de inundações nos centros urbanos acarreta diferentes transtornos sócio-econômicos. É possível minimizar os problemas quando estes eventos são previstos com antecedência. A partir de ferramentas computacionais, da modelação hidrológica e modelação hidrodinâmica, podem-se obter predições de níveis d´água. O modelo hidrológico físico CSmap e o modelo de cálculo de condutos livres CLiv são adotados neste trabalho para demonstrar a aplicação de um sistema de previsões de cheias. A partir do estudo da Bacia do Rio Ribeira de Iguape, demonstra-se que o aprimoramento destes modelos matemáticos e das técnicas de calibração pode não ser relevante quando os dados de origem são imprecisos. / Differents social and economics problems affect urbanized areas when a flood happens. These problems may be minimized by predictions made by computer´s tools, hydrological models and hydraulics algorithmics. The physical hydrologic model CSmap and open channel´s model CLiv are adopted in this research to demonstrate a flood´s prediction system application. Another analysis shows that the development of math´s models and calibration´s techniques may not be relevant when inaccurate data is utilized.

A questão da justiça é tema sempre presente nas perquirições da filosofia do direito. Como tema recorrente deve ser submetido a novas investigações à luz de paradigmas teóricos alternativos e inovadores. A teoria dos sistemas de Niklas Luhmann representa um marco teórico capaz de inaugurar novos percursos investigativos no estudo da função do direito e de sua relação com a justiça, ora como função, ora como capacidade de adaptação. A ideia da autopoiese e sua elaboração na teoria dos sistemas de Luhmann torna possível observar essa relação entre direito e justiça dentro do contexto do aumento da complexidade e da contingência na sociedade moderna. A presente tese busca produzir uma investigação jusfilosófica, com inspiração interdisciplinar ao combinar-se com especulações teoréticas da sociologia jurídica de inspiração luhmanniana. Ao utilizar uma metodologia fundada na pesquisa bibliográfica primacialmente nos idiomas originais, a tese persegue a reconstrução da teoria da justiça na perspectiva do funcional-estruturalismo de Niklas Luhmann. Na consecução deste projeto, a tese utiliza a metáfora do horizonte, de matriz fenomenológica, para propor a dualidade entre justiça operativo-funcional e justiça adaptativo-mutante. Dualidade que servirá de baliza para conclusões desta tese que poderá trazer uma contribuição original à cultura jurídica nacional. / The problem of justice is an ever-present issue in the investigations of philosophy of law. As a recurring theme, it should be subjected to further investigation in the light of alternative and innovative theoretical paradigms. The systems theory of Niklas Luhmann is a theoretical framework capable of opening new routes for studies and researches on the role of law and its relation to justice, either as function either as adaptability. The idea of autopoiesis and its elaboration in Luhmann´s systems theory makes it possible to observe the relationship between law and justice within the context of the increased complexity and contingency in modern society. This thesis aims to produce an investigation in the philosophy of law with interdisciplinary inspiration when combined with theoretical speculations of legal sociology of luhmannian inspiration. Using a methodology based on a primary bibliographic research in works in their original language, the thesis pursues the reconstruction of the theory of justice from the perspective of functional-structuralism as thought by Niklas Luhmann. In pursuing this project, the thesis uses the metaphor of the horizon, in its phenomenological matrix, to propose the duality between justice as operation and adaptation (mutant). This duality will serve as a beacon for the conclusions produced in this thesis that can bring an original contribution to legal culture.

A questão da justiça é tema sempre presente nas perquirições da filosofia do direito. Como tema recorrente deve ser submetido a novas investigações à luz de paradigmas teóricos alternativos e inovadores. A teoria dos sistemas de Niklas Luhmann representa um marco teórico capaz de inaugurar novos percursos investigativos no estudo da função do direito e de sua relação com a justiça, ora como função, ora como capacidade de adaptação. A ideia da autopoiese e sua elaboração na teoria dos sistemas de Luhmann torna possível observar essa relação entre direito e justiça dentro do contexto do aumento da complexidade e da contingência na sociedade moderna. A presente tese busca produzir uma investigação jusfilosófica, com inspiração interdisciplinar ao combinar-se com especulações teoréticas da sociologia jurídica de inspiração luhmanniana. Ao utilizar uma metodologia fundada na pesquisa bibliográfica primacialmente nos idiomas originais, a tese persegue a reconstrução da teoria da justiça na perspectiva do funcional-estruturalismo de Niklas Luhmann. Na consecução deste projeto, a tese utiliza a metáfora do horizonte, de matriz fenomenológica, para propor a dualidade entre justiça operativo-funcional e justiça adaptativo-mutante. Dualidade que servirá de baliza para conclusões desta tese que poderá trazer uma contribuição original à cultura jurídica nacional. / The problem of justice is an ever-present issue in the investigations of philosophy of law. As a recurring theme, it should be subjected to further investigation in the light of alternative and innovative theoretical paradigms. The systems theory of Niklas Luhmann is a theoretical framework capable of opening new routes for studies and researches on the role of law and its relation to justice, either as function either as adaptability. The idea of autopoiesis and its elaboration in Luhmann´s systems theory makes it possible to observe the relationship between law and justice within the context of the increased complexity and contingency in modern society. This thesis aims to produce an investigation in the philosophy of law with interdisciplinary inspiration when combined with theoretical speculations of legal sociology of luhmannian inspiration. Using a methodology based on a primary bibliographic research in works in their original language, the thesis pursues the reconstruction of the theory of justice from the perspective of functional-structuralism as thought by Niklas Luhmann. In pursuing this project, the thesis uses the metaphor of the horizon, in its phenomenological matrix, to propose the duality between justice as operation and adaptation (mutant). This duality will serve as a beacon for the conclusions produced in this thesis that can bring an original contribution to legal culture.