Approches générales de résolution pour les problèmes multi-attributs de tournées de véhicules et confection d'horaires

Thèse réalisée en cotutelle entre l'Université de Montréal et l'Université de Technologie de Troyes

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Multi-objective assembly job shop scheduling using genetic algorithm and tabu search

Assembly job shop scheduling problem (AJSP) is one of the most complicated combinatorial optimization problem that involves simultaneously scheduling the processing and assembly operations of complex structured products. The problem becomes even more complicated if a combination of two or more optimization criteria is considered. This thesis addresses an assembly job shop scheduling problem with multiple objectives. The objectives considered are to simultaneously minimizing makespan and total tardiness. In this thesis, two approaches viz., weighted approach and Pareto approach are used for solving the problem. However, it is quite difficult to achieve an optimal solution to this problem with traditional optimization approaches owing to the high computational complexity. Two metaheuristic techniques namely, genetic algorithm and tabu search are investigated in this thesis for solving the multiobjective assembly job shop scheduling problems. Three algorithms based on the two metaheuristic techniques for weighted approach and Pareto approach are proposed for the multi-objective assembly job shop scheduling problem (MOAJSP). A new pairing mechanism is developed for crossover operation in genetic algorithm which leads to improved solutions and faster convergence. The performances of the proposed algorithms are evaluated through a set of test problems and the results are reported. The results reveal that the proposed algorithms based on weighted approach are feasible and effective for solving MOAJSP instances according to the weight assigned to each objective criterion and the proposed algorithms based on Pareto approach are capable of producing a number of good Pareto optimal scheduling plans for MOAJSP instances.

Evolving Distributed Algorithms with Genetic Programming

Distributed systems are one of the most vital components of the economy. The most prominent example is probably the internet, a constituent element of our knowledge society. During the recent years, the number of novel network types has steadily increased. Amongst others, sensor networks, distributed systems composed of tiny computational devices with scarce resources, have emerged. The further development and heterogeneous connection of such systems imposes new requirements on the software development process. Mobile and wireless networks, for instance, have to organize themselves autonomously and must be able to react to changes in the environment and to failing nodes alike. Researching new approaches for the design of distributed algorithms may lead to methods with which these requirements can be met efficiently. In this thesis, one such method is developed, tested, and discussed in respect of its practical utility. Our new design approach for distributed algorithms is based on Genetic Programming, a member of the family of evolutionary algorithms. Evolutionary algorithms are metaheuristic optimization methods which copy principles from natural evolution. They use a population of solution candidates which they try to refine step by step in order to attain optimal values for predefined objective functions. The synthesis of an algorithm with our approach starts with an analysis step in which the wanted global behavior of the distributed system is specified. From this specification, objective functions are derived which steer a Genetic Programming process where the solution candidates are distributed programs. The objective functions rate how close these programs approximate the goal behavior in multiple randomized network simulations. The evolutionary process step by step selects the most promising solution candidates and modifies and combines them with mutation and crossover operators. This way, a description of the global behavior of a distributed system is translated automatically to programs which, if executed locally on the nodes of the system, exhibit this behavior. In our work, we test six different ways for representing distributed programs, comprising adaptations and extensions of well-known Genetic Programming methods (SGP, eSGP, and LGP), one bio-inspired approach (Fraglets), and two new program representations called Rule-based Genetic Programming (RBGP, eRBGP) designed by us. We breed programs in these representations for three well-known example problems in distributed systems: election algorithms, the distributed mutual exclusion at a critical section, and the distributed computation of the greatest common divisor of a set of numbers. Synthesizing distributed programs the evolutionary way does not necessarily lead to the envisaged results. In a detailed analysis, we discuss the problematic features which make this form of Genetic Programming particularly hard. The two Rule-based Genetic Programming approaches have been developed especially in order to mitigate these difficulties. In our experiments, at least one of them (eRBGP) turned out to be a very efficient approach and in most cases, was superior to the other representations.

La sabiduría como competencia gerencial

Aunque el concepto de sabiduría ha sido ampliamente estudiado por expertos de áreas como la filosofía, la religión y la psicología, aún enfrenta limitaciones en cuanto a su definición y evaluación. Por esto, el presente trabajo tiene como objetivo, formular una definición del concepto de sabiduría que permita realizar una propuesta de evaluación del concepto como competencia en los gerentes. Para esto, se realizó un análisis documental de tipo cualitativo. De esta manera, se analizaron diversos textos sobre la historia, las definiciones y las metodologías para evaluar tanto la sabiduría como las competencias; diferenciando la sabiduría de otros constructos y analizando la diferencia entre las competencias generales y las gerenciales para posteriormente, definir la sabiduría como una competencia gerencial. Como resultado de este análisis se generó un prototipo de prueba denominado SAPIENS-O, a través del cuál se busca evaluar la sabiduría como competencia gerencial. Como alcances del instrumento se pueden identificar la posibilidad de medir la sabiduría como competencia en los gerentes, la posibilidad de dar un nuevo panorama a las dificultades teóricas y empíricas sobre la sabiduría y la posibilidad de facilitar el estudio de la sabiduría en ambientes reales, más específicamente en ambientes organizacionales.

Estado situacional de los algoritmos genéticos en los negocios internacionales

La computación evolutiva y muy especialmente los algoritmos genéticos son cada vez más empleados en las organizaciones para resolver sus problemas de gestión y toma de decisiones (Apoteker & Barthelemy, 2000). La literatura al respecto es creciente y algunos estados del arte han sido publicados. A pesar de esto, no hay un trabajo explícito que evalúe de forma sistemática el uso de los algoritmos genéticos en problemas específicos de los negocios internacionales (ejemplos de ello son la logística internacional, el comercio internacional, el mercadeo internacional, las finanzas internacionales o estrategia internacional). El propósito de este trabajo de grado es, por lo tanto, realizar un estado situacional de las aplicaciones de los algoritmos genéticos en los negocios internacionales.

The multiple team formation problem using sociometry

The Team Formation problem (TFP) has become a well-known problem in the OR literature over the last few years. In this problem, the allocation of multiple individuals that match a required set of skills as a group must be chosen to maximise one or several social positive attributes. Speci�cally, the aim of the current research is two-fold. First, two new dimensions of the TFP are added by considering multiple projects and fractions of people's dedication. This new problem is named the Multiple Team Formation Problem (MTFP). Second, an optimization model consisting in a quadratic objective function, linear constraints and integer variables is proposed for the problem. The optimization model is solved by three algorithms: a Constraint Programming approach provided by a commercial solver, a Local Search heuristic and a Variable Neighbourhood Search metaheuristic. These three algorithms constitute the first attempt to solve the MTFP, being a variable neighbourhood local search metaheuristic the most effi�cient in almost all cases. Applications of this problem commonly appear in real-life situations, particularly with the current and ongoing development of social network analysis. Therefore, this work opens multiple paths for future research.

Busca heurística através de algoritmo genético e memético com construção de vocábulos para o problema de atribuição de localidades a anéis Sonet

Telecommunications play a key role in contemporary society. However, as new technologies are put into the market, it also grows the demanding for new products and services that depend on the offered infrastructure, making the problems of planning telecommunications networks, despite the advances in technology, increasingly larger and complex. However, many of these problems can be formulated as models of combinatorial optimization, and the use of heuristic algorithms can help solving these issues in the planning phase. In this project it was developed two pure metaheuristic implementations Genetic algorithm (GA) and Memetic Algorithm (MA) plus a third hybrid implementation Memetic Algorithm with Vocabulary Building (MA+VB) for a problem in telecommunications that is known in the literature as Problem SONET Ring Assignment Problem or SRAP. The SRAP arises during the planning stage of the physical network and it consists in the selection of connections between a number of locations (customers) in order to meet a series of restrictions on the lowest possible cost. This problem is NP-hard, so efficient exact algorithms (in polynomial complexity ) are not known and may, indeed, even exist

Estratégias de aplicações sequenciais e paralelas da metaheurística otimização por enxame de partículas ao problema do caixeiro viajante

Particle Swarm Optimization is a metaheuristic that arose in order to simulate the behavior of a number of birds in flight, with its random movement locally, but globally determined. This technique has been widely used to address non-liner continuous problems and yet little explored in discrete problems. This paper presents the operation of this metaheuristic, and propose strategies for implementation of optimization discret problems as form of execution parallel as sequential. The computational experiments were performed to instances of the TSP, selected in the library TSPLIB contenct to 3038 nodes, showing the improvement of performance of parallel methods for their sequential versions, in executation time and results

Metaheurísticas evolutivas para o problema de roteamento de unidades móveis de pistoneio

This paper presents metaheuristic strategies based on the framework of evolutionary algorithms (Genetic and Memetic) with the addition of Technical Vocabulary Building for solving the Problem of Optimizing the Use of Multiple Mobile Units Recovery of Oil (MRO units). Because it is an NP-hard problem, a mathematical model is formulated for the problem, allowing the construction of test instances that are used to validate the evolutionary metaheuristics developed

Algoritmo Q-learning como estratégia de exploração e/ou explotação para metaheurísticas GRASP e algoritmo genético

Techniques of optimization known as metaheuristics have achieved success in the resolution of many problems classified as NP-Hard. These methods use non deterministic approaches that reach very good solutions which, however, don t guarantee the determination of the global optimum. Beyond the inherent difficulties related to the complexity that characterizes the optimization problems, the metaheuristics still face the dilemma of xploration/exploitation, which consists of choosing between a greedy search and a wider exploration of the solution space. A way to guide such algorithms during the searching of better solutions is supplying them with more knowledge of the problem through the use of a intelligent agent, able to recognize promising regions and also identify when they should diversify the direction of the search. This way, this work proposes the use of Reinforcement Learning technique - Q-learning Algorithm - as exploration/exploitation strategy for the metaheuristics GRASP (Greedy Randomized Adaptive Search Procedure) and Genetic Algorithm. The GRASP metaheuristic uses Q-learning instead of the traditional greedy-random algorithm in the construction phase. This replacement has the purpose of improving the quality of the initial solutions that are used in the local search phase of the GRASP, and also provides for the metaheuristic an adaptive memory mechanism that allows the reuse of good previous decisions and also avoids the repetition of bad decisions. In the Genetic Algorithm, the Q-learning algorithm was used to generate an initial population of high fitness, and after a determined number of generations, where the rate of diversity of the population is less than a certain limit L, it also was applied to supply one of the parents to be used in the genetic crossover operator. Another significant change in the hybrid genetic algorithm is the proposal of a mutually interactive cooperation process between the genetic operators and the Q-learning algorithm. In this interactive/cooperative process, the Q-learning algorithm receives an additional update in the matrix of Q-values based on the current best solution of the Genetic Algorithm. The computational experiments presented in this thesis compares the results obtained with the implementation of traditional versions of GRASP metaheuristic and Genetic Algorithm, with those obtained using the proposed hybrid methods. Both algorithms had been applied successfully to the symmetrical Traveling Salesman Problem, which was modeled as a Markov decision process

Aplicaçaõ das técnicas Path-relinking e Vocabulary buiding na melhoria de performance do algoritmo memético para o problema do caixeiro viajante assimétrico

The present essay shows strategies of improvement in a well succeded evolutionary metaheuristic to solve the Asymmetric Traveling Salesman Problem. Such steps consist in a Memetic Algorithm projected mainly to this problem. Basically this improvement applied optimizing techniques known as Path-Relinking and Vocabulary Building. Furthermore, this last one has being used in two different ways, in order to evaluate the effects of the improvement on the evolutionary metaheuristic. These methods were implemented in C++ code and the experiments were done under instances at TSPLIB library, being possible to observe that the procedures purposed reached success on the tests done