Influenza is a public health problem that causes serious illness and deaths all over the world. Vaccination has been shown to be the most effective mean to prevent infection. The primary component of influenza vaccine is the weakened strains. Vaccination triggers the immune system to develop antibodies against those strains whose viral surface glycoprotein hemagglutinin (HA) is similar to that of vaccine strains. However, influenza vaccine must be updated annually since the antigenic structure of HA is constantly mutation. Hemagglutination inhibition (HI) assay is a laboratory procedure frequently applied to evaluate the antigenic relationships of the influenza viruses. It enables the World Health Organization (WHO) to recommend appropriate updates on strains that will most likely be protective against the circulating influenza strains. However, HI assay is labour intensive and time-consuming since it requires several controls for standardization. We use two machine-learning methods, i.e. Artificial Neural Network (ANN) and Logistic Regression, and a Mixed-Integer Optimization Model to predict antigenic variety. The ANN generalizes the input data to patterns inherent in the data, and then uses these patterns to make predictions. The logistic regression model identifies and selects the amino acid positions, which contribute most significantly to antigenic difference. The output of the logistic regression model will be used to predict the antigenic variants based on the predicted probability. The Mixed-Integer Optimization Model is formulated to find hyperplanes that enable binary classification. The performances of our models are evaluated by cross validation.

Rail track operators have traditionally used manual methods to construct train timetables. Creating a timetable can take several weeks, and so the process usually stops once the first feasible timetable has been found. It is suspected that this timetable is often far from optimal. Existing methods schedule track maintenance once the best train timetable has been determined and allow little or no adjustments to the timetable. This approach almost certainly produces suboptimal integrated solutions since the track maintenance schedule is developed with the imposition of the previously constructed train timetable. The research in this thesis considers operationally feasible methods to produce integrated train timetables and track maintenance schedules so that, when evaluated according to key performance criteria, the overall schedule is the best possible. This research was carried out as part of the Cooperative Research Centre for Railway Engineering and Technologies. We developed a method that uses a local search meta-heuristic called 'problem space search'. A fast dispatch heuristic repeatedly selects and moves a track possessor (train or maintenance task) through the network; this results in a single integrated schedule. This technique generates a collection of alternative feasible schedules by applying the dispatch heuristic to different sets of randomly perturbed data. The quality of the schedules is then evaluated. Thousands of feasible solutions can be found within minutes. We also formulated an integer programming model that selects a path for each train and maintenance task from a set of alternatives. If all possible paths are considered, then the best schedule found is guaranteed to be optimal. To reduce the size of the model, we explored a reduction technique called 'branch and price'. The method works on small example problems where paths are selected from a predetermined set, but the computation time and memory requirements mean that the method is not suitable for realistic problems. The main advantages of the problem space search method are generality and speed. We are able to model the operations of a variety of rail networks due to the representation of the problem. The generated schedules can be ranked with a user-defined objective measure. The speed at which we produce a range of feasible integrated schedules allows the method to be used in an operational setting, both to create schedules and to test different scenarios. A comparison with simulated current practice on a range of test data sets reveals improvements in total delay of up to 22%.

Rail track operators have traditionally used manual methods to construct train timetables. Creating a timetable can take several weeks, and so the process usually stops once the first feasible timetable has been found. It is suspected that this timetable is often far from optimal. Existing methods schedule track maintenance once the best train timetable has been determined and allow little or no adjustments to the timetable. This approach almost certainly produces suboptimal integrated solutions since the track maintenance schedule is developed with the imposition of the previously constructed train timetable. The research in this thesis considers operationally feasible methods to produce integrated train timetables and track maintenance schedules so that, when evaluated according to key performance criteria, the overall schedule is the best possible. This research was carried out as part of the Cooperative Research Centre for Railway Engineering and Technologies. We developed a method that uses a local search meta-heuristic called 'problem space search'. A fast dispatch heuristic repeatedly selects and moves a track possessor (train or maintenance task) through the network; this results in a single integrated schedule. This technique generates a collection of alternative feasible schedules by applying the dispatch heuristic to different sets of randomly perturbed data. The quality of the schedules is then evaluated. Thousands of feasible solutions can be found within minutes. We also formulated an integer programming model that selects a path for each train and maintenance task from a set of alternatives. If all possible paths are considered, then the best schedule found is guaranteed to be optimal. To reduce the size of the model, we explored a reduction technique called 'branch and price'. The method works on small example problems where paths are selected from a predetermined set, but the computation time and memory requirements mean that the method is not suitable for realistic problems. The main advantages of the problem space search method are generality and speed. We are able to model the operations of a variety of rail networks due to the representation of the problem. The generated schedules can be ranked with a user-defined objective measure. The speed at which we produce a range of feasible integrated schedules allows the method to be used in an operational setting, both to create schedules and to test different scenarios. A comparison with simulated current practice on a range of test data sets reveals improvements in total delay of up to 22%.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (p. 132-136).

Many applications in engineering, computer science and economics involve mixed-integer optimal control problems. Solving these problems in real-time is a challenging task because of the explosion of integer combinations to evaluate. This thesis focuses on the development of new algorithms for mixed-integer programming with an emphasis on optimal control problems of fast dynamical systems with discrete controls. The first part proposes two reformulations to reduce the computational complexity. The first reformulation avoids integer variables altogether. By considering a sequence of switched dynamics, we analyze the switching time optimization problem. Even though it is a continuous smooth problem, it is non-convex and the cost function and derivatives are hard to compute. We develop a new efficient method to compute the cost function and its derivatives. Our technique brings up to two orders of magnitude speedups with respect to state-of-the-art tools. The second approach reduces the number of integer decisions. In hybrid model predictive control (MPC) the computational complexity grows exponentially with the horizon length. Using approximate dynamic programming (ADP) we reduce the horizon length while maintaining good control performance by approximating the tail cost offline. This approach allows, for the first time, the application of such control techniques to fast dynamical systems with sampling times of only a few microseconds. The second part investigates embedded branch-and-bound algorithms for mixed-integer quadratic programs (MIQPs). A core component of these methods is the solution of continuous quadratic programs (QPs). We develop OSQP, a new robust and efficient general-purpose QP solver based on the alternating direction method of multipliers (ADMM) and able, for the first time, to detect infeasible problems. We include OSQP into a custom branch-and-bound algorithm suitable for embedded systems. Our extension requires only a single matrix factorization and exploits warm-starting, thereby greatly reducing the number of ADMM iterations required. Numerical examples show that our algorithm solves small to medium scale MIQPs more quickly than commercial solvers.

This research aims to understand the different requirements of civilian multiple autonomous vehicle systems in order to propose an adequate solution for the resource allocation problem. A new classification of unmanned system applications is presented with focus on unmanned aerial vehicles (UAVs). The main resource allocation systems requirements in each category are presented and discussed. A novel dynamic resource allocation model is introduced for efficient sharing of services provided by ad hoc assemblies of heterogeneous autonomous vehicles. A key contribution is the provision of capability to dynamically select sensors and platforms within constraints imposed by time dependencies, refuelling, and transportation services. The resource allocation problem is modelled as a connected network of nodes and formulated as an Integer Linear Program (ILP). Solution fitness is prioritized over computation time. Simulation results of an illustrative scenario are used to demonstrate the ability of the model to plan for sensor selection, refuelling, collaboration and cooperation between heterogeneous resources. Prioritization of operational cost leads to missions that use cheaper resources but take longer to complete. Prioritization of completion time leads to shorter missions at the expense of increased overall resource cost. Missions can be successfully re-planned through dynamic reallocation of new requests during a mission. Monte Carlo studies on systems of increasing complexity show that good solutions can be obtained using low time resolutions, with small time windows at a relatively low computational cost. In comparison with other approaches, the developed ILP model provides provably optimal solutions at the expense of longer computation time. Flight test procedures were developed for performing low cost experiments on a small scale, using commercial off the shelf equipment, with ability to infer conclusions on the large-scale implementation. Flight test experiments were developed and performed that assessed the performance of the developed ILP model and successfully demonstrated its main capabilities.

Pessoas com deficiências possuem muitas dificuldades em participar do mercado de trabalho, possuindo uma taxa de desemprego bem maior do que a média populacional. Isso motiva o estudo de novos modos de produção que permitam incluir essas pessoas com baixo custo operacional. Neste trabalho é feito um estudo sobre a inclusão de pessoas com deficiências em flow shops com o objetivo de minimizar o makespan. Como flow shops normalmente possuem poucas máquinas, o foco do estudo é na inserção de um e dois trabalhadores. O problema é definido, são propostos modelos matemáticos e uma solução heurística para resolvê-lo, assim como instâncias de teste realistas. Nos testes computacionais a performance dos modelos e da heurística é avaliada e a utilidade prática deste modelo de inclusão é analisada. Nós concluímos que o problema pode ser resolvido de forma satisfatória e que a inclusão de trabalhadores com deficiêcia emn flow shops é economicamente viável. / Persons with disabilities have severe problems participating in the job market and their unemployment rate is usually much higher than the average of the population. This motivates the research of new modes of production which allow to include these persons at a low overhead. In this work we study the inclusion of persons with disabilities into flow shops with the objective of minimizing the makespan. Since flow shops usually have only a few machines, we focus on the inclusion of one and two workers. We define the problem, propose mathematical models and a heuristic solution, as well as realistic test instances. In computational tests we evaluate the performance of the models and the heuristic, and assess the utility of such a model of inclusion. We conclude that the problem can be solved satisfactorily, and that including workers with disabilities into flow shops is economically feasible.

We have proposed a method by which the topology of a network might be discovered through an algorithm like the distributed Bellman-Ford algorithm. We have explored the inner workings of two methods to automate power distribution network reconfiguration, the ILP Solver and the Heuristic Solver. We have seen how networks of different shapes can be translated into a flattened topology, which is necessary preprocessing to find a power assignment solution for a network. We have also seen some experimental results comparing the performance of the ILP Solver and the Heuristic Solver. The Heuristic Solver is a very fast, efficient algorithm to reconfigure power distribution, which is important in the case of an emergency. It performs consistently with near perfect results at a speed that is orders of magnitude quicker than the ILP Solver in almost all cases. In an application where a network is small and time is not an important constraint, the ILP Solver could possibly be preferable, but in any context where time is sensitive and near-perfect results are as acceptable as perfect results, the Heuristic Solver is much preferable. There is always room for improvement. Future tests should perhaps allow for non-integer capacity units, or loads that require other values than unit capacity. Optimizing each algorithm by rewriting them in C could give more optimized tests, though this may not be necessary to make judgments about implementing one or the other. There may be some ways to improve the Heuristic Solver, such as arranging the ordered_links in some way that could be more optimal. The algorithm could also be improved by taking advantage of the fact that once there are no more sources with capacity to provide any loads, the process of trying to assign loads to them for power supply can cease. Perhaps this method could be combined with other methods that do not presently account for load priorities or place as much value on fast execution.

ARARUNA, Arthur Rodrigues. Caminho mínimo com restrição probabilística de atraso máximo. 2013. 88 f. : Dissertação (mestrado) - Universidade Federal do Ceará, Centro de Ciências, Departamento de Computação, Fortaleza-CE, 2013. / Submitted by guaracy araujo (guaraa3355@gmail.com) on 2016-06-01T19:53:59Z No. of bitstreams: 1 2013_dis_arararuna.pdf: 2167566 bytes, checksum: cd1f84fd0b24a51bd2b955d8e18a7ea1 (MD5) / Approved for entry into archive by guaracy araujo (guaraa3355@gmail.com) on 2016-06-01T19:54:22Z (GMT) No. of bitstreams: 1 2013_dis_arararuna.pdf: 2167566 bytes, checksum: cd1f84fd0b24a51bd2b955d8e18a7ea1 (MD5) / Made available in DSpace on 2016-06-01T19:54:22Z (GMT). No. of bitstreams: 1 2013_dis_arararuna.pdf: 2167566 bytes, checksum: cd1f84fd0b24a51bd2b955d8e18a7ea1 (MD5) Previous issue date: 2013 / In the Probabilistic Delay Constrained Shortest Path problem we aim to consider the time factor in the design of cargo routing paths in road networks at minimum cost, considering the increasing uncertainty in travel times of these routes in real networks, and keeping in mind strategies of quality of service, in order to obtain a compromise between the travel costs and the compliance of the arrival time at the destination. We conducted a study of related problems in the literature of transport networks optimization, in order to better understand the problem to be addressed, about which we are not aware of existing works. We developed a scheme for enumerating partitions of the solution space of this problem, which uses an L decomposition to select these partitions wisely, and is aided by solutions to relaxations of the problem to obtain bounds for the optimal cost. In addition, we developed some branching and pruning strategies for a Branch-and-Bound scheme, with a pre-processing phase, in order to try and solve the problem directly. The computational results show that we are competitive with the commercial tool used for comparison in the smaller instances. For the remaining instances, this tool is more efficient in the time required for solving the problem. / No problema do Caminho Mínimo com Restrição Probabilística de Atraso Máximo visamos considerar o fator tempo no projeto de rotas de transporte de cargas em malhas viárias a custo mínimo, atentando à crescente incerteza nos tempos de percurso dessas rotas em malhas reais, e observá-lo tendo em mente estratégias de qualidade de serviço, de forma a obtermos um compromisso entre o custo de percurso e a conformidade ao prazo de chegada ao destino. Realizamos um estudo de problemas relacionados na literatura da área de otimização em redes de transporte, de forma a tentarmos conhecer melhor o problema a ser estudado, sobre o qual não tomamos conhecimento de trabalhos existentes. Desenvolvemos um esquema para enumeração de partições do espaço de soluções do problema, que utiliza uma decomposição em L para selecionar partições de forma inteligente, e que é auxiliado por soluções de relaxações do problema de forma a obter cotas para o custo ótimo. Além disso, desenvolvemos algumas estratégias de ramificação e de poda para um esquema de Branch-and-Bound, com uma fase de pré-processamento, de forma a tentar resolver o problema diretamente. Os resultados computacionais obtidos demonstram que somos competitivos com a ferramenta comercial utilizada para comparação em instâncias de menor porte para o problema. Para as demais instâncias, essa ferramenta se mostrou mais eficiente quanto ao tempo necessário para a resolução.

In this paper we proposed 0-1 integer programming formulation to model single batch processing machine. This problem deals with a set of jobs with non-identical sizes and processing times that has to be grouped to form batches according to the limited capacity of the machine. The processing time of a batch is the longest processing time of all jobs in the batch. The performance measure is the total time required to process all jobs (makespan). The formulation presented strengthens the model, i.e., it is closer to the optimal formulation than those proposed in the literature. Computational experiments demonstrate that the model is consistent and adequately represents the problem addressed. / Neste trabalho é proposta uma formulação de programação inteira 0-1 para modelar o problema de programação e dimensionamento de lotes de produção em máquina única. Este problema considera um conjunto de tarefas com diferentes tamanhos e tempos de processamento que devem ser agrupadas em lotes de acordo com a capacidade limitada da máquina. O tempo de processamento de um lote é determinado pelo maior tempo de processamento dentre todas as tarefas que compõem o lote. A medida de desempenho é o tempo total necessário para processar todas as tarefas (makespan). A formulação apresentada é mais forte, ou seja, mais próxima da formulação ideal do que aquelas propostas na literatura. Experimentos computacionais demonstram que o modelo é consistente e representa adequadamente o problema tratado.