Biologically Inspired Non-Mendelian Repair for Constraint Handling in Evolutionary Algorithms

This paper examines a repair technique that enables evolutionary algorithms to handle constraints. This repair technique, known as GeneRepair, repairs invalid individuals so that all problem constraints are met by every individual in the population. GeneRepair is based on the repair technique used by the Arabidopsis thaliana plant which was proposed by Lolle et al in 2005. This controversial repair method uses information inherited from ancestors previous to the parent (non-Mendelian inheritance) as a repair template to fix errors or invalidities in the current population. We compare the use of three different ancestors as repair templates and investigate the effects of various biological parameters on the choice of repair template to use

Gene ordering in partitive clustering using microarray expressions

A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering and ordering the genes using gene expression data into homogeneous groups was shown to be useful in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on gene ordering in hierarchical clustering framework for gene expression analysis, there is no work addressing and evaluating the importance of gene ordering in partitive clustering framework, to the best knowledge of the authors. Outside the framework of hierarchical clustering, different gene ordering algorithms are applied on the whole data set, and the domain of partitive clustering is still unexplored with gene ordering approaches. A new hybrid method is proposed for ordering genes in each of the clusters obtained from partitive clustering solution, using microarry gene expressions. Two existing algorithms for optimally ordering cities in travelling salesman problem (TSP), namely, FRAG_GALK and Concorde, are hybridized individually with self organizing MAP to show the importance of gene ordering in partitive clustering framework. We validated our hybrid approach using yeast and fibroblast data and showed that our approach improves the result quality of partitive clustering solution, by identifying subclusters within big clusters, grouping functionally correlated genes within clusters, minimization of summation of gene expression distances, and the maximization of biological gene ordering using MIPS categorization. Moreover, the new hybrid approach, finds comparable or sometimes superior biological gene order in less computation time than those obtained by optimal leaf ordering in hierarchical clustering solution

Solving Dynamic Traveling Salesman Problem Using Dynamic Gaussian Process Regression

This paper solves the dynamic traveling salesman problem (DTSP) using dynamic Gaussian Process Regression (DGPR) method. The problem of varying correlation tour is alleviated by the nonstationary covariance function interleaved with DGPR to generate a predictive distribution for DTSP tour. This approach is conjoined with Nearest Neighbor (NN) method and the iterated local search to track dynamic optima. Experimental results were obtained on DTSP instances. The comparisons were performed with Genetic Algorithm and Simulated Annealing. The proposed approach demonstrates superiority in finding good traveling salesman problem (TSP) tour and less computational time in nonstationary conditions

Imperialist Competitive Algorithm with Independence and Constrained Assimilation for Solving 0-1 Multidimensional Knapsack Problem

The multidimensional knapsack problem is a well-known constrained optimization problem with many real-world engineering applications. In order to solve this NP-hard problem, a new modified Imperialist Competitive Algorithm with Constrained Assimilation (ICAwICA) is presented. The proposed algorithm introduces the concept of colony independence, a free will to choose between classical ICA assimilation to empires imperialist or any other imperialist in the population. Furthermore, a constrained assimilation process has been implemented that combines classical ICA assimilation and revolution operators, while maintaining population diversity. This work investigates the performance of the proposed algorithm across 101 Multidimensional Knapsack Problem (MKP) benchmark instances. Experimental results show that the algorithm is able to obtain an optimal solution in all small instances and presents very competitive results for large MKP instances

Developing Programming Tools to Handle Traveling Salesman Problem by the Three Object-Oriented Languages

The traveling salesman problem (TSP) is one of the most famous problems. Many applications and programming tools have been developed to handle TSP. However, it seems to be essential to provide easy programming tools according to state-of-theart algorithms. Therefore, we have collected and programmed new easy tools by the three object-oriented languages. In this paper, we present ADT (abstract data type) of developed tools at first; then we analyze their performance by experiments. We also design a hybrid genetic algorithm (HGA) by developed tools. Experimental results show that the proposed HGA is comparable with the recent state-of-the-art applications

Imperialist Competitive Algorithm with Independence and Constrained Assimilation

Autonomous Supply Chai

Genetic operators for combinatorial optimization in TSP and microarray gene ordering

This paper deals with some new operators of genetic algorithms and[-27pc] demonstrates their effectiveness to the traveling salesman problem (TSP) and microarray gene ordering. The new operators developed are nearest fragment operator based on the concept of nearest neighbor heuristic, and a modified version of order crossover operator. While these result in faster convergence of Genetic Algorithm (GAs) in finding the optimal order of genes in microarray and cities in TSP, the nearest fragment operator can augment the search space quickly and thus obtain much better results compared to other heuristics. Appropriate number of fragments for the nearest fragment operator and appropriate substring length in terms of the number of cities/genes for the modified order crossover operator are determined systematically. Gene order provided by the proposed method is seen to be superior to other related methods based on GAs, neural networks and clustering in terms of biological scores computed using categorization of the genes

New local search in the space of infeasible solutions framework for the routing of vehicles

Combinatorial optimisation problems (COPs) have been at the origin of the design of many optimal and heuristic solution frameworks such as branch-and-bound algorithms, branch-and-cut algorithms, classical local search methods, metaheuristics, and hyperheuristics. This thesis proposes a refined generic and parametrised infeasible local search (GPILS) algorithm for solving COPs and customises it to solve the traveling salesman problem (TSP), for illustration purposes. In addition, a rule-based heuristic is proposed to initialise infeasible local search, referred to as the parameterised infeasible heuristic (PIH), which allows the analyst to have some control over the features of the infeasible solution he/she might want to start the infeasible search with. A recursive infeasible neighbourhood search (RINS) as well as a generic patching procedure to search the infeasible space are also proposed. These procedures are designed in a generic manner, so they can be adapted to any choice of parameters of the GPILS, where the set of parameters, in fact for simplicity, refers to set of parameters, components, criteria and rules. Furthermore, a hyperheuristic framework is proposed for optimizing the parameters of GPILS referred to as HH-GPILS. Experiments have been run for both sequential (i.e. simulated annealing, variable neighbourhood search, and tabu search) and parallel hyperheuristics (i.e., genetic algorithms / GAs) to empirically assess the performance of the proposed HH-GPILS in solving TSP using instances from the TSPLIB. Empirical results suggest that HH-GPILS delivers an outstanding performance. Finally, an offline learning mechanism is proposed as a seeding technique to improve the performance and speed of the proposed parallel HH-GPILS. The proposed offline learning mechanism makes use of a knowledge-base to keep track of the best performing chromosomes and their scores. Empirical results suggest that this learning mechanism is a promising technique to initialise the GA’s population

OptPlatform: metaheuristic optimisation framework for solving complex real-world problems

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonWe optimise daily, whether that is planning a round trip that visits the most attractions within a given holiday budget or just taking a train instead of driving a car in a rush hour. Many problems, just like these, are solved by individuals as part of our daily schedule, and they are effortless and straightforward. If we now scale that to many individuals with many different schedules, like a school timetable, we get to a point where it is just not feasible or practical to solve by hand. In such instances, optimisation methods are used to obtain an optimal solution. In this thesis, a practical approach to optimisation has been taken by developing an optimisation platform with all the necessary tools to be used by practitioners who are not necessarily familiar with the subject of optimisation. First, a high-performance metaheuristic optimisation framework (MOF) called OptPlatform is implemented, and the versatility and performance are evaluated across multiple benchmarks and real-world optimisation problems. Results show that, compared to competing MOFs, the OptPlatform outperforms in both the solution quality and computation time. Second, the most suitable hardware platform for OptPlatform is determined by an in-depth analysis of Ant Colony Optimisation scaling across CPU, GPU and enterprise Xeon Phi. Contrary to the common benchmark problems used in the literature, the supply chain problem solved could not scale on GPUs. Third, a variety of metaheuristics are implemented into OptPlatform. Including, a new metaheuristic based on Imperialist Competitive Algorithm (ICA), called ICA with Independence and Constrained Assimilation (ICAwICA) is proposed. The ICAwICA was compared against two different types of benchmark problems, and results show the versatile application of the algorithm, matching and in some cases outperforming the custom-tuned approaches. Finally, essential MOF features like automatic algorithm selection and tuning, lacking on existing frameworks, are implemented in OptPlatform. Two novel approaches are proposed and compared to existing methods. Results indicate the superiority of the implemented tuning algorithms within constrained tuning budget environment

Optimal seismic retrofitting of existing RC frames through soft-computing approaches

2016 - 2017Ph.D. Thesis proposes a Soft-Computing approach capable of supporting the engineer judgement in the selection and design of the cheapest solution for seismic retrofitting of existing RC framed structure. Chapter 1 points out the need for strengthening the existing buildings as one of the main way of decreasing economic and life losses as direct consequences of earthquake disasters. Moreover, it proposes a wide, but not-exhaustive, list of the most frequently observed deficiencies contributing to the vulnerability of concrete buildings. Chapter 2 collects the state of practice on seismic analysis methods for the assessment the safety of the existing buildings within the framework of a performancebased design. The most common approaches for modeling the material plasticity in the frame non-linear analysis are also reviewed. Chapter 3 presents a wide state of practice on the retrofitting strategies, intended as preventive measures aimed at mitigating the effect of a future earthquake by a) decreasing the seismic hazard demands; b) improving the dynamic characteristics supplied to the existing building. The chapter presents also a list of retrofitting systems, intended as technical interventions commonly classified into local intervention (also known “member-level” techniques) and global intervention (also called “structure-level” techniques) that might be used in synergistic combination to achieve the adopted strategy. In particular, the available approaches and the common criteria, respectively for selecting an optimum retrofit strategy and an optimal system are discussed. Chapter 4 highlights the usefulness of the Soft-Computing methods as efficient tools for providing “objective” answer in reasonable time for complex situation governed by approximation and imprecision. In particular, Chapter 4 collects the applications found in the scientific literature for Fuzzy Logic, Artificial Neural Network and Evolutionary Computing in the fields of structural and earthquake engineering with a taxonomic classification of the problems in modeling, simulation and optimization. Chapter 5 “translates” the search for the cheapest retrofitting system into a constrained optimization problem. To this end, the chapter includes a formulation of a novel procedure that assembles a numerical model for seismic assessment of framed structures within a Soft-Computing-driven optimization algorithm capable to minimize the objective function defined as the total initial cost of intervention. The main components required to assemble the procedure are described in the chapter: the optimization algorithm (Genetic Algorithm); the simulation framework (OpenSees); and the software environment (Matlab). Chapter 6 describes step-by-step the flow-chart of the proposed procedure and it focuses on the main implementation aspects and working details, ranging from a clever initialization of the population of candidate solutions up to a proposal of tuning procedure for the genetic parameters. Chapter 7 discusses numerical examples, where the Soft-Computing procedure is applied to the model of multi-storey RC frames obtained through simulated design. A total of fifteen “scenarios” are studied in order to assess its “robustness” to changes in input data. Finally, Chapter 8, on the base of the outcomes observed, summarizes the capabilities of the proposed procedure, yet highlighting its “limitations” at the current state of development. Some possible modifications are discussed to enhance its efficiency and completeness. [edited by author]XVI n.s