Phylogenetic inference's algorithms

Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016.

CLIMATE CHANGE ADAPTATION IN VULNERABLE CROP AND LIVESTOCK PRODUCTION SYSTEMS IN MGETA, TANZANIA

Increased occurrence of drought and dry spells during the growing season have resulted in increased interest in protection of tropical water catchment areas. In Mgeta, a water catchment area in the Uluguru Mountains in Tanzania, water used for vegetable and fruit production is provided through canals from the Uluguru South Forest Reserve. The clearing of forest land for cultivation in the steep slopes in the area is causing severe land degradation, which is threatening the water catchment area, livelihoods, and food security of the local communities, as well as the major population centers in the lowlands. In this paper, the economic performance of a traditional cropping-livestock system with East African (EA)-goats and pigs and extensive vegetable production is compared with a more sustainable and environmentally friendly crop-dairy goat production system. A linear programming (LP) crop-livestock model, maximizing farm income considering the environmental constraints in the area was applied for studying the economic performance of dairy goats in the production system. The model was worked out for the rainy and dry seasons and the analysis was conducted for a basic scenario representing the current situation, based on the variability in the 30 years period from 1982-2012, and in a scenario of both lower crop yields and increased crop variability due to climate change. Data obtained from a sample of 60 farmers that were interviewed using a questionnaire was used to develop and parameterize the model. The study found that in the steep slopes of the area, a crop-dairy goat system with extensive use of grass and multipurpose trees (MPTs) would do better than the traditional vegetable gardening with the EA goat production system. The crop-dairy goat system was superior both in the basic and in a climate change scenario since the yield variation of the grass and MPTs system was less affected compared to vegetable crops due to more tree cover and the use of perennial grasses. However, the goat milk production in the area was constrained by inadequate feeding and lack of an appropriate breeding program. Hence, farmers should enhance goat milk production by supplementing with more concentrate feed and by implementing goat-breeding principles. Moreover, policy measures to promote such a development are briefly discussed.

Utilização de inteligência competitiva, da gestão de riscos e da computação aplicada para ganhos de competitividade em instituição organizadora de concursos

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2015.

Numerical enclosures of the optimal cost of the Kantorovitch’s mass transportation problem

International audience

Lot production size problem and simulation of urban transport

OBJECTIVES AND STUDY METHOD: There are two subjects in this thesis: “Lot production size for a parallel machine scheduling problem with auxiliary equipment” and “Bus holding for a simulated traffic network”. Although these two themes seem unrelated, the main idea is the optimization of complex systems. The “Lot production size for a parallel machine scheduling problem with auxiliary equipment” deals with a manufacturing setting where sets of pieces form finished products. The aim is to maximize the profit of the finished products. Each piece may be processed in more than one mold. Molds must be mounted on machines with their corresponding installation setup times. The key point of our methodology is to solve the single period lot-sizing decisions for the finished products together with the piece-mold and the mold-machine assignments, relaxing the constraint that a single mold may not be used in two machines at the same time. For the “Bus holding for a simulated traffic network” we deal with One of the most annoying problems in urban bus operations is bus bunching, which happens when two or more buses arrive at a stop nose to tail. Bus bunching reflects an unreliable service that affects transit operations by increasing passenger-waiting times. This work proposes a linear mathematical programming model that establishes bus holding times at certain stops along a transit corridor to avoid bus bunching. Our approach needs real-time input, so we simulate a transit corridor and apply our mathematical model to the data generated. Thus, the inherent variability of a transit system is considered by the simulation, while the optimization model takes into account the key variables and constraints of the bus operation. CONTRIBUTIONS AND CONCLUSIONS: For the “Lot production size for a parallel machine scheduling problem with auxiliary equipment” the relaxation we propose able to find solutions more efficiently, moreover our experimental results show that most of the solutions verify that molds are non-overlapping even if they are installed on several machines. We propose an exact integer linear programming, a Relax&Fix heuristic, and a multistart greedy algorithm to solve this problem. Experimental results on instances based on real-world data show the efficiency of our approaches. The mathematical model and the algorithm for the lot production size problem, showed in this research, can be used for production planners to help in the scheduling of the manufacturing. For the “Bus holding for a simulated traffic network” most of the literature considers quadratic models that minimize passenger-waiting times, but they are harder to solve and therefore difficult to operate by real-time systems. On the other hand, our methodology reduces passenger-waiting times efficiently given our linear programming model, with the characteristic of applying control intervals just every 5 minutes.

Texto guía para docentes enfocado en el bloque de matemáticas discretas en el primero B.G.U.

El presente trabajo de titulación denominado Texto Guía para Docentes enfocado en el bloque de Matemáticas Discretas del Primero B.G.U, ha sido desarrollado con la finalidad de presentar un aporte significativoy de ayuda al docente de Matemáticas de Primero de Bachillerato, anhelando un mejor desenvolvimiento dentro del aula de clase. Este documento está elaborado en base a la legislación educativa ecuatoriana vigente y de los documentos oficiales del Ministerio de Educación, el tema propuesto corresponde al tercer bloque curricular del primer año de Bachillerato General Unificado en la asignatura de Matemáticas. Nuestro trabajo de titulación se compone de tres capítulos. En el capítulo uno, se presenta una síntesis de temas como la evolución de la educación ecuatoriana, los modelos pedagógicos, los métodos de enseñanza, didáctica de la matemática y programación lineal, considerados como base para el desarrollo de la propuesta. En el capítulo dos, se detalla la investigación estadística realizada mediante una encuesta aplicada a docentes de Matemáticas de Primer año de Bachillerato, pertenecientes a la Coordinación Zonal 6 de Educación, Distrito Norte. Los resultados encontrados cimentaron la propuesta de la implementación del texto guía para el aprendizaje de Matemáticas Discretas. En el capítulo tres se elabora la propuesta del texto guía, estructurado en seis guías didácticas, cada una corresponde al desarrollo de una destreza con criterio de desempeñopara el tema planteado. Al final de este capítulo, se detallan conclusiones y recomendaciones dirigidas para el docente de matemáticas.

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments.

Design Optimization of Nozzle Shapes for Maximum Uniformity of Exit Flow

The objective of this study is to identify the optimal designs of converging-diverging supersonic and hypersonic nozzles that perform at maximum uniformity of thermodynamic and flow-field properties with respect to their average values at the nozzle exit. Since this is a multi-objective design optimization problem, the design variables used are parameters defining the shape of the nozzle. This work presents how variation of such parameters can influence the nozzle exit flow non-uniformities. A Computational Fluid Dynamics (CFD) software package, ANSYS FLUENT, was used to simulate the compressible, viscous gas flow-field in forty nozzle shapes, including the heat transfer analysis. The results of two turbulence models, k-e and k-ω, were computed and compared. With the analysis results obtained, the Response Surface Methodology (RSM) was applied for the purpose of performing a multi-objective optimization. The optimization was performed with ModeFrontier software package using Kriging and Radial Basis Functions (RBF) response surfaces. Final Pareto optimal nozzle shapes were then analyzed with ANSYS FLUENT to confirm the accuracy of the optimization process.

Short-Term Trading for a Wind-PV Power Producer in an Electricity Market

This paper deals with the problem of coordinated trading of wind and photovoltaic systems in order to find the optimal bid to submit in a pool-based electricity market. The coordination of wind and photovoltaic systems presents uncertainties not only due to electricity market prices, but also with wind and photovoltaic power forecast. Electricity markets are characterized by financial penalties in case of deficit or excess of generation. So, the aim o this work is to reduce these financial penalties and maximize the expected profit of the power producer. The problem is formulated as a stochastic linear programming problem. The proposed approach is validated with real data of pool-based electricity market of Iberian Peninsula.

Bidding and Optimization Strategies for Wind-PV Systems in Electricity Markets

The variability in non-dispatchable power generation raises important challenges to the integration of renewable energy sources into the electricity power grid. This paper provides the coordinated trading of wind and photovoltaic energy to mitigate risks due to the wind and solar power variability, electricity prices, and financial penalties arising out the generation shortfall and surplus. The problem of wind-photovoltaic coordinated trading is formulated as a linear programming problem. The goal is to obtain the optimal bidding strategy that maximizes the total profit. The wind-photovoltaic coordinated operation is modeled and compared with the uncoordinated operation. A comparison of the models and relevant conclusions are drawn from an illustrative case study of the Iberian day-ahead electricity market.

Coordinated Scheduling of Wind-Thermal Gencos in Day-Ahead Markets

This paper presents a stochastic mixed-integer linear programming approach for solving the self-scheduling problem of a price-taker thermal and wind power producer taking part in a pool-based electricity market. Uncertainty on electricity price and wind power is considered through a set of scenarios. Thermal units are modeled by variable costs, start-up costs and technical operating constraints, such as: ramp up/down limits and minimum up/down time limits. An efficient mixed-integer linear program is presented to develop the offering strategies of the coordinated production of thermal and wind energy generation, aiming to maximize the expected profit. A case study with data from the Iberian Electricity Market is presented and results are discussed to show the effectiveness of the proposed approach.

Bidding and Optimization Strategies for Wind-PV Systems in Electricity Markets Assisted by CPS

The variability in non-dispatchable power generation raises important challenges to the integration of renewable energy sources into the electricity power grid. This paper provides the coordinated trading of wind and photovoltaic energy assisted by a cyber-physical system for supporting management decisions to mitigate risks due to the wind and solar power variability, electricity prices, and financial penalties arising out the generation shortfall and surplus. The problem of wind-photovoltaic coordinated trading is formulated as a stochastic linear programming problem. The goal is to obtain the optimal bidding strategy that maximizes the total profit. The wind-photovoltaic coordinated operation is modelled and compared with the uncoordinated operation. A comparison of the models and relevant conclusions are drawn from an illustrative case study of the Iberian day-ahead electricity market.

Bidding Decision of Wind-Thermal GenCo in Day-Ahead Market

This paper deals with the self-scheduling problem of a price-taker having wind and thermal power production and assisted by a cyber-physical system for supporting management decisions in a day-ahead electric energy market. The self-scheduling is regarded as a stochastic mixed-integer linear programming problem. Uncertainties on electricity price and wind power are considered through a set of scenarios. Thermal units are modelled by start-up and variable costs, furthermore constraints are considered, such as: ramp up/down and minimum up/down time limits. The stochastic mixed-integer linear programming problem allows a decision support for strategies advantaging from an effective wind and thermal mixed bidding. A case study is presented using data from the Iberian electricity market.

Bidding strategy of wind-thermal energy producers

This paper presents a stochastic mixed-integer linear programming approach for solving the self-scheduling problem of a price-taker thermal and wind power producer taking part in a pool-based electricity market. Uncertainty on electricity price and wind power is considered through a set of scenarios. Thermal units are modelled by variable costs, start-up costs and technical operating constraints, such as: forbidden operating zones, ramp up/down limits and minimum up/down time limits. An efficient mixed-integer linear program is presented to develop the offering strategies of the coordinated production of thermal and wind energy generation, having as a goal the maximization of profit. A case study with data from the Iberian Electricity Market is presented and results are discussed to show the effectiveness of the proposed approach.

Optimal Wind Bidding Strategies in Day-Ahead Markets

This paper presents a computer application for wind energy bidding in a day-ahead electricity market to better accommodate the variability of the energy source. The computer application is based in a stochastic linear mathematical programming problem. The goal is to obtain the optimal bidding strategy in order to maximize the revenue. Electricity prices and financial penalties for shortfall or surplus energy deliver are modeled. Finally, conclusions are drawn from an illustrative case study, using data from the day-ahead electricity market of the Iberian Peninsula.