A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Optimal Path Searching through Specified Routes using different Algorithms

To connect different electrical, network and data devices with the minimum cost and shortest path, is a complex job. In huge buildings, where the devices are placed at different locations on different floors and only some specific routes are available to pass the cables and buses, the shortest path search becomes more complex. The aim of this thesis project is, to develop an application which indentifies the best path to connect all objects or devices by following the specific routes.To address the above issue we adopted three algorithms Greedy Algorithm, Simulated Annealing and Exhaustive search and analyzed their results. The given problem is similar to Travelling Salesman Problem. Exhaustive search is a best algorithm to solve this problem as it checks each and every possibility and give the accurate result but it is an impractical solution because of huge time consumption. If no. of objects increased from 12 it takes hours to search the shortest path. Simulated annealing is emerged with some promising results with lower time cost. As of probabilistic nature, Simulated annealing could be non optimal but it gives a near optimal solution in a reasonable duration. Greedy algorithm is not a good choice for this problem. So, simulated annealing is proved best algorithm for this problem. The project has been implemented in C-language which takes input and store output in an Excel Workbook

A modified Intelligent Water Drops algorithm and its application to optimization problems

The Intelligent Water Drop (IWD) algorithm is a recent stochastic swarm-based method that is useful for solving combinatorial and function optimization problems. In this paper, we investigate the effectiveness of the selection method in the solution construction phase of the IWD algorithm. Instead of the fitness proportionate selection method in the original IWD algorithm, two ranking-based selection methods, namely linear ranking and exponential ranking, are proposed. Both ranking-based selection methods aim to solve the identified limitations of the fitness proportionate selection method as well as to enable the IWD algorithm to escape from local optima and ensure its search diversity. To evaluate the usefulness of the proposed ranking-based selection methods, a series of experiments pertaining to three combinatorial optimization problems, i.e., rough set feature subset selection, multiple knapsack and travelling salesman problems, is conducted. The results demonstrate that the exponential ranking selection method is able to preserve the search diversity, therefore improving the performance of the IWD algorithm. © 2014 Elsevier Ltd. All rights reserved.

Algoritmo memético com infecção viral: uma aplicação ao problema do caixeiro viajante assimétrico

The Combinatorial Optimization is a basic area to companies who look for competitive advantages in the diverse productive sectors and the Assimetric Travelling Salesman Problem, which one classifies as one of the most important problems of this area, for being a problem of the NP-hard class and for possessing diverse practical applications, has increased interest of researchers in the development of metaheuristics each more efficient to assist in its resolution, as it is the case of Memetic Algorithms, which is a evolutionary algorithms that it is used of the genetic operation in combination with a local search procedure. This work explores the technique of Viral Infection in one Memetic Algorithms where the infection substitutes the mutation operator for obtaining a fast evolution or extinguishing of species (KANOH et al, 1996) providing a form of acceleration and improvement of the solution . For this it developed four variants of Viral Infection applied in the Memetic Algorithms for resolution of the Assimetric Travelling Salesman Problem where the agent and the virus pass for a symbiosis process which favored the attainment of a hybrid evolutionary algorithms and computational viable

Avaliação de operadores de algoritmos genéticos em otimização multidimensional

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Teoria dos grafos e suas aplicações

Pós-graduação em Matemática Universitária - IGCE

Reformulações para o problema integrado de dimensionamento e sequenciamento da produção

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Algorithms for UAS insertion in civil air space

One of the most interesting challenge of the next years will be the Air Space Systems automation. This process will involve different aspects as the Air Traffic Management, the Aircrafts and Airport Operations and the Guidance and Navigation Systems. The use of UAS (Uninhabited Aerial System) for civil mission will be one of the most important steps in this automation process. In civil air space, Air Traffic Controllers (ATC) manage the air traffic ensuring that a minimum separation between the controlled aircrafts is always provided. For this purpose ATCs use several operative avoidance techniques like holding patterns or rerouting. The use of UAS in these context will require the definition of strategies for a common management of piloted and piloted air traffic that allow the UAS to self separate. As a first employment in civil air space we consider a UAS surveillance mission that consists in departing from a ground base, taking pictures over a set of mission targets and coming back to the same ground base. During all mission a set of piloted aircrafts fly in the same airspace and thus the UAS has to self separate using the ATC avoidance as anticipated. We consider two objective, the first consists in the minimization of the air traffic impact over the mission, the second consists in the minimization of the impact of the mission over the air traffic. A particular version of the well known Travelling Salesman Problem (TSP) called Time-Dependant-TSP has been studied to deal with traffic problems in big urban areas. Its basic idea consists in a cost of the route between two clients depending on the period of the day in which it is crossed. Our thesis supports that such idea can be applied to the air traffic too using a convenient time horizon compatible with aircrafts operations. The cost of a UAS sub-route will depend on the air traffic that it will meet starting such route in a specific moment and consequently on the avoidance maneuver that it will use to avoid that conflict. The conflict avoidance is a topic that has been hardly developed in past years using different approaches. In this thesis we purpose a new approach based on the use of ATC operative techniques that makes it possible both to model the UAS problem using a TDTSP framework both to use an Air Traffic Management perspective. Starting from this kind of mission, the problem of the UAS insertion in civil air space is formalized as the UAS Routing Problem (URP). For this reason we introduce a new structure called Conflict Graph that makes it possible to model the avoidance maneuvers and to define the arc cost function of the departing time. Two Integer Linear Programming formulations of the problem are proposed. The first is based on a TDTSP formulation that, unfortunately, is weaker then the TSP formulation. Thus a new formulation based on a TSP variation that uses specific penalty to model the holdings is proposed. Different algorithms are presented: exact algorithms, simple heuristics used as Upper Bounds on the number of time steps used, and metaheuristic algorithms as Genetic Algorithm and Simulated Annealing. Finally an air traffic scenario has been simulated using real air traffic data in order to test our algorithms. Graphic Tools have been used to represent the Milano Linate air space and its air traffic during different days. Such data have been provided by ENAV S.p.A (Italian Agency for Air Navigation Services).

Product warranty logistics: Issues and challenges

Warranty is an important element of marketing new products. The servicing of warranty results in additional costs to the manufacturer. Warranty logistics deals with various issues relating to the servicing of warranty. Proper management of warranty logistics is needed not only to reduce the warranty servicing cost but also to ensure customer satisfaction as customer dissatisfaction has a negative impact on sales and revenue. Unfortunately, warranty logistics has received very little attention. The paper links the literature on warranty and on logistics and then discusses the different issues in warranty logistics. It highlights the challenges and identifies some research topics of potential interest to operational researchers. (C) 2003 Elsevier B.V. All rights reserved.

A study on the deployment of GA in a grid computing framework

Dissertação de Mestrado, Engenharia Informática, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

An ensemble of intelligent water drop algorithms and its application to optimization problems

Crown Copyright © 2015 Published by Elsevier Inc. All rights reserved. The Intelligent Water Drop (IWD) algorithm is a recent stochastic swarm-based method that is useful for solving combinatorial and function optimization problems. In this paper, we propose an IWD ensemble known as the Master-River, Multiple-Creek IWD (MRMC-IWD) model, which serves as an extension of the modified IWD algorithm. The MRMC-IWD model aims to improve the exploration capability of the modified IWD algorithm. It comprises a master river which cooperates with multiple independent creeks to undertake optimization problems based on the divide-and-conquer strategy. A technique to decompose the original problem into a number of sub-problems is first devised. Each sub-problem is then assigned to a creek, while the overall solution is handled by the master river. To empower the exploitation capability, a hybrid MRMC-IWD model is introduced. It integrates the iterative improvement local search method with the MRMC-IWD model to allow a local search to be conducted, therefore enhancing the quality of solutions provided by the master river. To evaluate the effectiveness of the proposed models, a series of experiments pertaining to two combinatorial problems, i.e., the travelling salesman problem (TSP) and rough set feature subset selection (RSFS), are conducted. The results indicate that the MRMC-IWD model can satisfactorily solve optimization problems using the divide-and-conquer strategy. By incorporating a local search method, the resulting hybrid MRMC-IWD model not only is able to balance exploration and exploitation, but also to enable convergence towards the optimal solutions, by employing a local search method. In all seven selected TSPLIB problems, the hybrid MRMC-IWD model achieves good results, with an average deviation of 0.021% from the best known optimal tour lengths. Compared with other state-of-the-art methods, the hybrid MRMC-IWD model produces the best results (i.e. the shortest and uniform reducts of 20 runs) for all13 selected RSFS problems.

Optimization models for a short sea fuel oil distribution problem

O transporte marítimo e o principal meio de transporte de mercadorias em todo o mundo. Combustíveis e produtos petrolíferos representam grande parte das mercadorias transportadas por via marítima. Sendo Cabo Verde um arquipelago o transporte por mar desempenha um papel de grande relevância na economia do país. Consideramos o problema da distribuicao de combustíveis em Cabo Verde, onde uma companhia e responsavel por coordenar a distribuicao de produtos petrolíferos com a gestão dos respetivos níveis armazenados em cada porto, de modo a satisfazer a procura dos varios produtos. O objetivo consiste em determinar políticas de distribuicão de combustíveis que minimizam o custo total de distribuiçao (transporte e operacões) enquanto os n íveis de armazenamento sao mantidos nos n íveis desejados. Por conveniencia, de acordo com o planeamento temporal, o prob¬lema e divido em dois sub-problemas interligados. Um de curto prazo e outro de medio prazo. Para o problema de curto prazo sao discutidos modelos matemáticos de programacao inteira mista, que consideram simultaneamente uma medicao temporal cont ínua e uma discreta de modo a modelar multiplas janelas temporais e taxas de consumo que variam diariamente. Os modelos sao fortalecidos com a inclusão de desigualdades validas. O problema e então resolvido usando um "software" comercial. Para o problema de medio prazo sao inicialmente discutidos e comparados varios modelos de programacao inteira mista para um horizonte temporal curto assumindo agora uma taxa de consumo constante, e sao introduzidas novas desigualdades validas. Com base no modelo escolhido sao compara¬das estrategias heurísticas que combinam três heur ísticas bem conhecidas: "Rolling Horizon", "Feasibility Pump" e "Local Branching", de modo a gerar boas soluçoes admissíveis para planeamentos com horizontes temporais de varios meses. Finalmente, de modo a lidar com situaçoes imprevistas, mas impor¬tantes no transporte marítimo, como as mas condicões meteorológicas e congestionamento dos portos, apresentamos um modelo estocastico para um problema de curto prazo, onde os tempos de viagens e os tempos de espera nos portos sao aleatórios. O problema e formulado como um modelo em duas etapas, onde na primeira etapa sao tomadas as decisões relativas as rotas do navio e quantidades a carregar e descarregar e na segunda etapa (designada por sub-problema) sao consideradas as decisoes (com recurso) relativas ao escalonamento das operacões. O problema e resolvido por um metodo de decomposto que usa um algoritmo eficiente para separar as desigualdades violadas no sub-problema.

Do cyanobacteria swim using traveling surface waves?

Bacteria that swim without the benefit of flagella might do so by generating longitudinal or transverse surface waves. For example, swimming speeds of order 25 microns/s are expected for a spherical cell propagating longitudinal waves of 0.2 micron length, 0.02 micron amplitude, and 160 microns/s speed. This problem was solved earlier by mathematicians who were interested in the locomotion of ciliates and who considered the undulations of the envelope swept out by ciliary tips. A new solution is given for spheres propagating sinusoidal waveforms rather than Legendre polynomials. The earlier work is reviewed and possible experimental tests are suggested.

An integrated scheduling problem of PCB components on sequential pick-and-place machines:mathematical models and heuristic solutions

This paper formulates several mathematical models for determining the optimal sequence of component placements and assignment of component types to feeders simultaneously or the integrated scheduling problem for a type of surface mount technology placement machines, called the sequential pick-andplace (PAP) machine. A PAP machine has multiple stationary feeders storing components, a stationary working table holding a printed circuit board (PCB), and a movable placement head to pick up components from feeders and place them to a board. The objective of integrated problem is to minimize the total distance traveled by the placement head. Two integer nonlinear programming models are formulated first. Then, each of them is equivalently converted into an integer linear type. The models for the integrated problem are verified by two commercial packages. In addition, a hybrid genetic algorithm previously developed by the authors is adopted to solve the models. The algorithm not only generates the optimal solutions quickly for small-sized problems, but also outperforms the genetic algorithms developed by other researchers in terms of total traveling distance.