A review of estimation of distribution algorithms in bioinformatics

Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain.

PSO and neural networks: Optimal combination to solve non linear complex problems

Swarm colonies reproduce social habits. Working together in a group to reach a predefined goal is a social behaviour occurring in nature. Linear optimization problems have been approached by different techniques based on natural models. In particular, Particles Swarm optimization is a meta-heuristic search technique that has proven to be effective when dealing with complex optimization problems. This paper presents and develops a new method based on different penalties strategies to solve complex problems. It focuses on the training process of the neural networks, the constraints and the election of the parameters to ensure successful results and to avoid the most common obstacles when searching optimal solutions.

Thermal food processing optimization: Algorithms and software

The algorithms and graphic user interface software package ?OPT-PROx? are developed to meet food engineering needs related to canned food thermal processing simulation and optimization. The adaptive random search algorithm and its modification coupled with penalty function?s approach, and the finite difference methods with cubic spline approximation are utilized by ?OPT-PROx? package (http://tomakechoice. com/optprox/index.html). The diversity of thermal food processing optimization problems with different objectives and required constraints are solvable by developed software. The geometries supported by the ?OPT-PROx? are the following: (1) cylinder, (2) rectangle, (3) sphere. The mean square error minimization principle is utilized in order to estimate the heat transfer coefficient of food to be heated under optimal condition. The developed user friendly dialogue and used numerical procedures makes the ?OPT-PROx? software useful to food scientists in research and education, as well as to engineers involved in optimization of thermal food processing.

Robustness and Recoverability in Transport Logistics

Abstract Transport is the foundation of any economy: it boosts economic growth, creates wealth, enhances trade, geographical accessibility and the mobility of people. Transport is also a key ingredient for a high quality of life, making places accessible and bringing people together. The future prosperity of our world will depend on the ability of all of its regions to remain fully and competitively integrated in the world economy. Efficient transport is vital in making this happen. Operations research can help in efficiently planning the design and operating transport systems. Planning and operational processes are fields that are rich in combinatorial optimization problems. These problems can be analyzed and solved through the application of mathematical models and optimization techniques, which may lead to an improvement in the performance of the transport system, as well as to a reduction in the time required for solving these problems. The latter aspect is important, because it increases the flexibility of the system: the system can adapt in a faster way to changes in the environment (i.e.: weather conditions, crew illness, failures, etc.). These disturbing changes (called disruptions) often enforce the schedule to be adapted. The direct consequences are delays and cancellations, implying many schedule adjustments and huge costs. Consequently, robust schedules and recovery plans must be developed in order to fight against disruptions. This dissertation makes contributions to two different fields: rail and air applications. Robust planning and recovery methods are presented. In the field of railway transport we develop several mathematical models which answer to RENFE’s (the major railway operator in Spain) needs: 1. We study the rolling stock assignment problem: here, we introduce some robust aspects in order to ameliorate some operations which are likely to fail. Once the rolling stock assignment is known, we propose a robust routing model which aims at identifying the train units’ sequences while minimizing the expected delays and human resources needed to perform the sequences. 2. It is widely accepted that the sequential solving approach produces solutions that are not global optima. Therefore, we develop an integrated and robust model to determine the train schedule and rolling stock assignment. We also propose an integrated model to study the rolling stock circulations. Circulations are determined by the rolling stock assignment and routing of the train units. 3. Although our aim is to develop robust plans, disruptions will be likely to occur and recovery methods will be needed. Therefore, we propose a recovery method which aims to recover the train schedule and rolling stock assignment in an integrated fashion all while considering the passenger demand. In the field of air transport we develop several mathematical models which answer to IBERIA’s (the major airline in Spain) needs: 1. We look at the airline-scheduling problem and develop an integrated approach that optimizes schedule design, fleet assignment and passenger use so as to reduce costs and create fewer incompatibilities between decisions. Robust itineraries are created to ameliorate misconnected passengers. 2. Air transport operators are continuously facing competition from other air operators and different modes of transport (e.g., High Speed Rail). Consequently, airline profitability is critically influenced by the airline’s ability to estimate passenger demands and construct profitable flight schedules. We consider multi-modal competition including airline and rail, and develop a new approach that estimates the demand associated with a given schedule; and generates airline schedules and fleet assignments using an integrated schedule design and fleet assignment optimization model that captures the impacts of schedule decisions on passenger demand.

The effect of boundary conditions in the numerical solution of 3-D thermoelastic problems

After the extensive research on the capabilities of the Boundary Integral Equation Method produced during the past years the versatility of its applications has been well founded. Maybe the years to come will see the in-depth analysis of several conflictive points, for example, adaptive integration, solution of the system of equations, etc. This line is clear in academic research. In this paper we comment on the incidence of the manner of imposing the boundary conditions in 3-D coupled problems. Here the effects are particularly magnified: in the first place by the simple model used (constant elements) and secondly by the process of solution, i.e. first a potential problem is solved and then the results are used as data for an elasticity problem. The errors add to both processes and small disturbances, unimportant in separated problems, can produce serious errors in the final results. The specific problem we have chosen is especially interesting. Although more general cases (i.e. transient)can be treated, here the domain integrals can be converted into boundary ones and the influence of the manner in which boundary conditions are applied will reflect the whole importance of the problem.

Optimal boundary geometry in an elasticity problem: a systematic adjoint approach

In different problems of Elasticity the definition of the optimal gcometry of the boundary, according to a given objective function, is an issue of great interest. Finding the shape of a hole in the middle of a plate subjected to an arbitrary loading such that the stresses along the hole minimizes some functional or the optimal middle curved concrete vault for a tunnel along which a uniform minimum compression are two typical examples. In these two examples the objective functional depends on the geometry of the boundary that can be either a curve (in case of 2D problems) or a surface boundary (in 3D problems). Typically, optimization is achieved by means of an iterative process which requires the computation of gradients of the objective function with respect to design variables. Gradients can by computed in a variety of ways, although adjoint methods either continuous or discrete ones are the more efficient ones when they are applied in different technical branches. In this paper the adjoint continuous method is introduced in a systematic way to this type of problems and an illustrative simple example, namely the finding of an optimal shape tunnel vault immersed in a linearly elastic terrain, is presented.

Distributed Estimation of Distribution Algorithms for continuous optimization: how does the exchanged information influence their behavior?

One of the most promising areas in which probabilistic graphical models have shown an incipient activity is the field of heuristic optimization and, in particular, in Estimation of Distribution Algorithms. Due to their inherent parallelism, different research lines have been studied trying to improve Estimation of Distribution Algorithms from the point of view of execution time and/or accuracy. Among these proposals, we focus on the so-called distributed or island-based models. This approach defines several islands (algorithms instances) running independently and exchanging information with a given frequency. The information sent by the islands can be either a set of individuals or a probabilistic model. This paper presents a comparative study for a distributed univariate Estimation of Distribution Algorithm and a multivariate version, paying special attention to the comparison of two alternative methods for exchanging information, over a wide set of parameters and problems ? the standard benchmark developed for the IEEE Workshop on Evolutionary Algorithms and other Metaheuristics for Continuous Optimization Problems of the ISDA 2009 Conference. Several analyses from different points of view have been conducted to analyze both the influence of the parameters and the relationships between them including a characterization of the configurations according to their behavior on the proposed benchmark.

NURBS-Based Geometry Parameterization for Aerodynamic Shape Optimization

La motivación de esta tesis es el desarrollo de una herramienta de optimización automática para la mejora del rendimiento de formas aerodinámicas enfocado en la industria aeronáutica. Este trabajo cubre varios aspectos esenciales, desde el empleo de Non-Uniform Rational B-Splines (NURBS), al cálculo de gradientes utilizando la metodología del adjunto continuo, el uso de b-splines volumétricas como parámetros de diseño, el tratamiento de la malla en las intersecciones, y no menos importante, la adaptación de los algoritmos de la dinámica de fluidos computacional (CFD) en arquitecturas hardware de alto paralelismo, como las tarjetas gráficas, para acelerar el proceso de optimización. La metodología adjunta ha posibilitado que los métodos de optimización basados en gradientes sean una alternativa prometedora para la mejora de la eficiencia aerodinámica de los aviones. La formulación del adjunto permite calcular los gradientes de una función de coste, como la resistencia aerodinámica o la sustentación, independientemente del número de variables de diseño, a un coste computacional equivalente a una simulación CFD. Sin embargo, existen problemas prácticos que han imposibilitado su aplicación en la industria, que se pueden resumir en: integrabilidad, rendimiento computacional y robustez de la solución adjunta. Este trabajo aborda estas contrariedades y las analiza en casos prácticos. Como resumen, las contribuciones de esta tesis son: • El uso de NURBS como variables de diseño en un bucle de automático de optimización, aplicado a la mejora del rendimiento aerodinámico de alas en régimen transónico. • El desarrollo de algoritmos de inversión de punto, para calcular las coordenadas paramétricas de las coordenadas espaciales, para ligar los vértices de malla a las NURBS. • El uso y validación de la formulación adjunta para el calculo de los gradientes, a partir de las sensibilidades de la solución adjunta, comparado con diferencias finitas. • Se ofrece una estrategia para utilizar la geometría CAD, en forma de parches NURBS, para tratar las intersecciones, como el ala-fuselaje. • No existen muchas alternativas de librerías NURBS viables. En este trabajo se ha desarrollado una librería, DOMINO NURBS, y se ofrece a la comunidad como código libre y abierto. • También se ha implementado un código CFD en tarjeta gráfica, para realizar una valoración de cómo se puede adaptar un código sobre malla no estructurada a arquitecturas paralelas. • Finalmente, se propone una metodología, basada en la función de Green, como una forma eficiente de paralelizar simulaciones numéricas. Esta tesis ha sido apoyada por las actividades realizadas por el Área de Dinámica da Fluidos del Instituto Nacional de Técnica Aeroespacial (INTA), a través de numerosos proyectos de financiación nacional: DOMINO, SIMUMAT, y CORESFMULAERO. También ha estado en consonancia con las actividades realizadas por el departamento de Métodos y Herramientas de Airbus España y con el grupo Investigación y Tecnología Aeronáutica Europeo (GARTEUR), AG/52. ABSTRACT The motivation of this work is the development of an automatic optimization strategy for large scale shape optimization problems that arise in the aeronautics industry to improve the aerodynamic performance; covering several aspects from the use of Non-Uniform Rational B-Splines (NURBS), the calculation of the gradients with the continuous adjoint formulation, the development of volumetric b-splines parameterization, mesh adaptation and intersection handling, to the adaptation of Computational Fluid Dynamics (CFD) algorithms to take advantage of highly parallel architectures in order to speed up the optimization process. With the development of the adjoint formulation, gradient-based methods for aerodynamic optimization become a promising approach to improve the aerodynamic performance of aircraft designs. The adjoint methodology allows the evaluation the gradients to all design variables of a cost function, such as drag or lift, at the equivalent cost of more or less one CFD simulation. However, some practical problems have been delaying its full implementation to the industry, which can be summarized as: integrability, computer performance, and adjoint robustness. This work tackles some of these issues and analyse them in well-known test cases. As summary, the contributions comprises: • The employment of NURBS as design variables in an automatic optimization loop for the improvement of the aerodynamic performance of aircraft wings in transonic regimen. • The development of point inversion algorithms to calculate the NURBS parametric coordinates from the space coordinates, to link with the computational grid vertex. • The use and validation of the adjoint formulation to calculate the gradients from the surface sensitivities in an automatic optimization loop and evaluate its reliability, compared with finite differences. • This work proposes some algorithms that take advantage of the underlying CAD geometry description, in the form of NURBS patches, to handle intersections and mesh adaptations. • There are not many usable libraries for NURBS available. In this work an open source library DOMINO NURBS has been developed and is offered to the community as free, open source code. • The implementation of a transonic CFD solver from scratch in a graphic card, for an assessment of the implementability of conventional CFD solvers for unstructured grids to highly parallel architectures. • Finally, this research proposes the use of the Green's function as an efficient paralellization scheme of numerical solvers. The presented work has been supported by the activities carried out at the Fluid Dynamics branch of the National Institute for Aerospace Technology (INTA) through national founding research projects: DOMINO, SIMUMAT, and CORESIMULAERO; in line with the activities carried out by the Methods and Tools and Flight Physics department at Airbus and the Group for Aeronautical Research and Technology in Europe (GARTEUR) action group AG/52.

Hybrid wind-diesel power plant valuation and optimization using real option theory and dynamic programming

El sistema de energía eólica-diesel híbrido tiene un gran potencial en la prestación de suministro de energía a comunidades remotas. En comparación con los sistemas tradicionales de diesel, las plantas de energía híbridas ofrecen grandes ventajas tales como el suministro de capacidad de energía extra para "microgrids", reducción de los contaminantes y emisiones de gases de efecto invernadero, y la cobertura del riesgo de aumento inesperado del precio del combustible. El principal objetivo de la presente tesis es proporcionar nuevos conocimientos para la evaluación y optimización de los sistemas de energía híbrido eólico-diesel considerando las incertidumbres. Dado que la energía eólica es una variable estocástica, ésta no puede ser controlada ni predecirse con exactitud. La naturaleza incierta del viento como fuente de energía produce serios problemas tanto para la operación como para la evaluación del valor del sistema de energía eólica-diesel híbrido. Por un lado, la regulación de la potencia inyectada desde las turbinas de viento es una difícil tarea cuando opera el sistema híbrido. Por otro lado, el bene.cio económico de un sistema eólico-diesel híbrido se logra directamente a través de la energía entregada a la red de alimentación de la energía eólica. Consecuentemente, la incertidumbre de los recursos eólicos incrementa la dificultad de estimar los beneficios globales en la etapa de planificación. La principal preocupación del modelo tradicional determinista es no tener en cuenta la incertidumbre futura a la hora de tomar la decisión de operación. Con lo cual, no se prevé las acciones operativas flexibles en respuesta a los escenarios futuros. El análisis del rendimiento y simulación por ordenador en el Proyecto Eólico San Cristóbal demuestra que la incertidumbre sobre la energía eólica, las estrategias de control, almacenamiento de energía, y la curva de potencia de aerogeneradores tienen un impacto significativo sobre el rendimiento del sistema. En la presente tesis, se analiza la relación entre la teoría de valoración de opciones y el proceso de toma de decisiones. La opción real se desarrolla con un modelo y se presenta a través de ejemplos prácticos para evaluar el valor de los sistemas de energía eólica-diesel híbridos. Los resultados muestran que las opciones operacionales pueden aportar un valor adicional para el sistema de energía híbrida, cuando esta flexibilidad operativa se utiliza correctamente. Este marco se puede aplicar en la optimización de la operación a corto plazo teniendo en cuenta la naturaleza dependiente de la trayectoria de la política óptima de despacho, dadas las plausibles futuras realizaciones de la producción de energía eólica. En comparación con los métodos de valoración y optimización existentes, el resultado del caso de estudio numérico muestra que la política de operación resultante del modelo de optimización propuesto presenta una notable actuación en la reducción del con- sumo total de combustible del sistema eólico-diesel. Con el .n de tomar decisiones óptimas, los operadores de plantas de energía y los gestores de éstas no deben centrarse sólo en el resultado directo de cada acción operativa, tampoco deberían tomar decisiones deterministas. La forma correcta es gestionar dinámicamente el sistema de energía teniendo en cuenta el valor futuro condicionado en cada opción frente a la incertidumbre. ABSTRACT Hybrid wind-diesel power systems have a great potential in providing energy supply to remote communities. Compared with the traditional diesel systems, hybrid power plants are providing many advantages such as providing extra energy capacity to the micro-grid, reducing pollution and greenhouse-gas emissions, and hedging the risk of unexpected fuel price increases. This dissertation aims at providing novel insights for assessing and optimizing hybrid wind-diesel power systems considering the related uncertainties. Since wind power can neither be controlled nor accurately predicted, the energy harvested from a wind turbine may be considered a stochastic variable. This uncertain nature of wind energy source results in serious problems for both the operation and value assessment of the hybrid wind-diesel power system. On the one hand, regulating the uncertain power injected from wind turbines is a difficult task when operating the hybrid system. On the other hand, the economic profit of a hybrid wind-diesel system is achieved directly through the energy delivered to the power grid from the wind energy. Therefore, the uncertainty of wind resources has increased the difficulty in estimating the total benefits in the planning stage. The main concern of the traditional deterministic model is that it does not consider the future uncertainty when making the dispatch decision. Thus, it does not provide flexible operational actions in response to the uncertain future scenarios. Performance analysis and computer simulation on the San Cristobal Wind Project demonstrate that the wind power uncertainty, control strategies, energy storage, and the wind turbine power curve have a significant impact on the performance of the system. In this dissertation, the relationship between option pricing theory and decision making process is discussed. A real option model is developed and presented through practical examples for assessing the value of hybrid wind-diesel power systems. Results show that operational options can provide additional value to the hybrid power system when this operational flexibility is correctly utilized. This framework can be applied in optimizing short term dispatch decisions considering the path-dependent nature of the optimal dispatch policy, given the plausible future realizations of the wind power production. Comparing with the existing valuation and optimization methods, result from numerical example shows that the dispatch policy resulting from the proposed optimization model exhibits a remarkable performance in minimizing the total fuel consumption of the wind-diesel system. In order to make optimal decisions, power plant operators and managers should not just focus on the direct outcome of each operational action; neither should they make deterministic decisions. The correct way is to dynamically manage the power system by taking into consideration the conditional future value in each option in response to the uncertainty.

Stationarity and regularity of infinite collections of sets. Applications to infinitely constrained optimization

This article continues the investigation of stationarity and regularity properties of infinite collections of sets in a Banach space started in Kruger and López (J. Optim. Theory Appl. 154(2), 2012), and is mainly focused on the application of the stationarity criteria to infinitely constrained optimization problems. We consider several settings of optimization problems which involve (explicitly or implicitly) infinite collections of sets and deduce for them necessary conditions characterizing stationarity in terms of dual space elements—normals and/or subdifferentials.

Problems in assessing the impact of Education Division programs on girls and women for the National Advisory Council on Women's Educational Programs /

Issued October 1977.

The cross-entropy method for continuous multi-extremal optimization

In recent years, the cross-entropy method has been successfully applied to a wide range of discrete optimization tasks. In this paper we consider the cross-entropy method in the context of continuous optimization. We demonstrate the effectiveness of the cross-entropy method for solving difficult continuous multi-extremal optimization problems, including those with non-linear constraints.

Optimization of chemical plant simulation using double collocation

A method has been constructed for the solution of a wide range of chemical plant simulation models including differential equations and optimization. Double orthogonal collocation on finite elements is applied to convert the model into an NLP problem that is solved either by the VF 13AD package based on successive quadratic programming, or by the GRG2 package, based on the generalized reduced gradient method. This approach is termed simultaneous optimization and solution strategy. The objective functional can contain integral terms. The state and control variables can have time delays. Equalities and inequalities containing state and control variables can be included into the model as well as algebraic equations and inequalities. The maximum number of independent variables is 2. Problems containing 3 independent variables can be transformed into problems having 2 independent variables using finite differencing. The maximum number of NLP variables and constraints is 1500. The method is also suitable for solving ordinary and partial differential equations. The state functions are approximated by a linear combination of Lagrange interpolation polynomials. The control function can either be approximated by a linear combination of Lagrange interpolation polynomials or by a piecewise constant function over finite elements. The number of internal collocation points can vary by finite elements. The residual error is evaluated at arbitrarily chosen equidistant grid-points, thus enabling the user to check the accuracy of the solution between collocation points, where the solution is exact. The solution functions can be tabulated. There is an option to use control vector parameterization to solve optimization problems containing initial value ordinary differential equations. When there are many differential equations or the upper integration limit should be selected optimally then this approach should be used. The portability of the package has been addressed converting the package from V AX FORTRAN 77 into IBM PC FORTRAN 77 and into SUN SPARC 2000 FORTRAN 77. Computer runs have shown that the method can reproduce optimization problems published in the literature. The GRG2 and the VF I 3AD packages, integrated into the optimization package, proved to be robust and reliable. The package contains an executive module, a module performing control vector parameterization and 2 nonlinear problem solver modules, GRG2 and VF I 3AD. There is a stand-alone module that converts the differential-algebraic optimization problem into a nonlinear programming problem.

Online trendy topics detection in microblogs with selective user monitoring under cost constraints

As microblog services such as Twitter become a fast and convenient communication approach, identification of trendy topics in microblog services has great academic and business value. However detecting trendy topics is very challenging due to huge number of users and short-text posts in microblog diffusion networks. In this paper we introduce a trendy topics detection system under computation and communication resource constraints. In stark contrast to retrieving and processing the whole microblog contents, we develop an idea of selecting a small set of microblog users and processing their posts to achieve an overall acceptable trendy topic coverage, without exceeding resource budget for detection. We formulate the selection operation of these subset users as mixed-integer optimization problems, and develop heuristic algorithms to compute their approximate solutions. The proposed system is evaluated with real-time test data retrieved from Sina Weibo, the dominant microblog service provider in China. It's shown that by monitoring 500 out of 1.6 million microblog users and tracking their microposts (about 15,000 daily) with our system, nearly 65% trendy topics can be detected, while on average 5 hours earlier before they appear in Sina Weibo official trends.