Parallel Hybrid Trajectory Based Metaheuristics for Real-World Problems

G. Luque, E. Alba, Parallel Hybrid Trajectory Based Metaheuristics for Real-World Problems, In Proceedings of Intelligent Networking and Collaborative Systems, pp. 184-191, 2-4 September, 2015, Taipei, Taiwan, IEEE PressThis paper proposes a novel algorithm combining path relinking with a set of cooperating trajectory based parallel algorithms to yield a new metaheuristic of enhanced search features. Algorithms based on the exploration of the neighborhood of a single solution, like simulated annealing (SA), have offered accurate results for a large number of real-world problems in the past. Because of their trajectory based nature, some advanced models such as the cooperative one are competitive in academic problems, but still show many limitations in addressing large scale instances. In addition, the field of parallel models for trajectory methods has not deeply been studied yet (at least in comparison with parallel population based models). In this work, we propose a new hybrid algorithm which improves cooperative single solution techniques by using path relinking, allowing both to reduce the global execution time and to improve the efficacy of the method. We applied here this new model using a large benchmark of instances of two real-world NP-hard problems: DNA fragment assembly and QAP problems, with competitive results.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A Hybrid Metaheuristics based technique for Mutation Based Disease Classification

Due to recent advancements in computational biology, DNA microarray technology has evolved as a useful tool in the detection of mutation among various complex diseases like cancer. The availability of thousands of microarray datasets makes this field an active area of research. Early cancer detection can reduce the mortality rate and the treatment cost. Cancer classification is a process to provide a detailed overview of the disease microenvironment for better diagnosis. However, the gene microarray datasets suffer from a curse of dimensionality problems also the classification models are prone to be overfitted due to small sample size and large feature space. To address these issues, the authors have proposed an Improved Binary Competitive Swarm Optimization Whale Optimization Algorithm (IBCSOWOA) for cancer classification, in which IBCSO has been employed to reduce the informative gene subset originated from using minimum redundancy maximum relevance (mRMR) as filter method. The IBCSOWOA technique has been tested on an artificial neural network (ANN) model and the whale optimization algorithm (WOA) is used for parameter tuning of the model. The performance of the proposed IBCSOWOA is tested on six different mutation-based microarray datasets and compared with existing disease prediction methods. The experimental results indicate the superiority of the proposed technique over the existing nature-inspired methods in terms of optimal feature subset, classification accuracy, and convergence rate. The proposed technique has illustrated above 98% accuracy in all six datasets with the highest accuracy of 99.45% in the Lung cancer dataset

A Teaching-Learning-Based Optimization Algorithm for the Weighted Set-Covering Problem

The need to make good use of resources has allowed metaheuristics to become a tool to achieve this goal. There are a number of complex problems to solve, among which is the Set-Covering Problem, which is a representation of a type of combinatorial optimization problem, which has been applied to several real industrial problems. We use a binary version of the optimization algorithm based on teaching and learning to solve the problem, incorporating various binarization schemes, in order to solve the binary problem. In this paper, several binarization techniques are implemented in the teaching/learning based optimization algorithm, which presents only the minimum parameters to be configured such as the population and number of iterations to be evaluated. The performance of metaheuristic was evaluated through 65 benchmark instances. The results obtained are promising compared to those found in the literature

Hybrid ant colony system algorithm for static and dynamic job scheduling in grid computing

Grid computing is a distributed system with heterogeneous infrastructures. Resource management system (RMS) is one of the most important components which has great influence on the grid computing performance. The main part of RMS is the scheduler algorithm which has the responsibility to map submitted tasks to available resources. The complexity of scheduling problem is considered as a nondeterministic polynomial complete (NP-complete) problem and therefore, an intelligent algorithm is required to achieve better scheduling solution. One of the prominent intelligent algorithms is ant colony system (ACS) which is implemented widely to solve various types of scheduling problems. However, ACS suffers from stagnation problem in medium and large size grid computing system. ACS is based on exploitation and exploration mechanisms where the exploitation is sufficient but the exploration has a deficiency. The exploration in ACS is based on a random approach without any strategy. This study proposed four hybrid algorithms between ACS, Genetic Algorithm (GA), and Tabu Search (TS) algorithms to enhance the ACS performance. The algorithms are ACS(GA), ACS+GA, ACS(TS), and ACS+TS. These proposed hybrid algorithms will enhance ACS in terms of exploration mechanism and solution refinement by implementing low and high levels hybridization of ACS, GA, and TS algorithms. The proposed algorithms were evaluated against twelve metaheuristic algorithms in static (expected time to compute model) and dynamic (distribution pattern) grid computing environments. A simulator called ExSim was developed to mimic the static and dynamic nature of the grid computing. Experimental results show that the proposed algorithms outperform ACS in terms of best makespan values. Performance of ACS(GA), ACS+GA, ACS(TS), and ACS+TS are better than ACS by 0.35%, 2.03%, 4.65% and 6.99% respectively for static environment. For dynamic environment, performance of ACS(GA), ACS+GA, ACS+TS, and ACS(TS) are better than ACS by 0.01%, 0.56%, 1.16%, and 1.26% respectively. The proposed algorithms can be used to schedule tasks in grid computing with better performance in terms of makespan

On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Large neighborhood search for the most strings with few bad columns problem

In this work, we consider the following NP-hard combinatorial optimization problem from computational biology. Given a set of input strings of equal length, the goal is to identify a maximum cardinality subset of strings that differ maximally in a pre-defined number of positions. First of all, we introduce an integer linear programming model for this problem. Second, two variants of a rather simple greedy strategy are proposed. Finally, a large neighborhood search algorithm is presented. A comprehensive experimental comparison among the proposed techniques shows, first, that larger neighborhood search generally outperforms both greedy strategies. Second, while large neighborhood search shows to be competitive with the stand-alone application of CPLEX for small- and medium-sized problem instances, it outperforms CPLEX in the context of larger instances.Peer ReviewedPostprint (author's final draft

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data

Mass spectrometry (MS) data provide a promising strategy for biomarker discovery. For this purpose, the detection of relevant peakbins in MS data is currently under intense research. Data from mass spectrometry are challenging to analyze because of their high dimensionality and the generally low number of samples available. To tackle this problem, the scientific community is becoming increasingly interested in applying feature subset selection techniques based on specialized machine learning algorithms. In this paper, we present a performance comparison of some metaheuristics: best first (BF), genetic algorithm (GA), scatter search (SS) and variable neighborhood search (VNS). Up to now, all the algorithms, except for GA, have been first applied to detect relevant peakbins in MS data. All these metaheuristic searches are embedded in two different filter and wrapper schemes coupled with Naive Bayes and SVM classifiers

A generic approach to behaviour-driven biochemical model construction

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Modelling of biochemical systems has received considerable attention over the last decade from bioengineering, biochemistry, computer science, and mathematics. This thesis investigates the applications of computational techniques to computational systems biology, for the construction of biochemical models in terms of topology and kinetic rates. Due to the complexity of biochemical systems, it is natural to construct models representing the biochemical systems incrementally in a piecewise manner. Syntax and semantics of two patterns are defined for the instantiation of components which are extendable, reusable and fundamental building blocks for models composition. We propose and implement a set of genetic operators and composition rules to tackle issues of piecewise composing models from scratch. Quantitative Petri nets are evolved by the genetic operators, and evolutionary process of modelling are guided by the composition rules. Metaheuristic algorithms are widely applied in BioModel Engineering to support intelligent and heuristic analysis of biochemical systems in terms of structure and kinetic rates. We illustrate parameters of biochemical models based on Biochemical Systems Theory, and then the topology and kinetic rates of the models are manipulated by employing evolution strategy and simulated annealing respectively. A new hybrid modelling framework is proposed and implemented for the models construction. Two heuristic algorithms are performed on two embedded layers in the hybrid framework: an outer layer for topology mutation and an inner layer for rates optimization. Moreover, variants of the hybrid piecewise modelling framework are investigated. Regarding flexibility of these variants, various combinations of evolutionary operators, evaluation criteria and design principles can be taken into account. We examine performance of five sets of the variants on specific aspects of modelling. The comparison of variants is not to explicitly show that one variant clearly outperforms the others, but it provides an indication of considering important features for various aspects of the modelling. Because of the very heavy computational demands, the process of modelling is paralleled by employing a grid environment, GridGain. Application of the GridGain and heuristic algorithms to analyze biological processes can support modelling of biochemical systems in a computational manner, which can also benefit mathematical modelling in computer science and bioengineering. We apply our proposed modelling framework to model biochemical systems in a hybrid piecewise manner. Modelling variants of the framework are comparatively studied on specific aims of modelling. Simulation results show that our modelling framework can compose synthetic models exhibiting similar species behaviour, generate models with alternative topologies and obtain general knowledge about key modelling features

The development and application of metaheuristics for problems in graph theory: A computational study

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.It is known that graph theoretic models have extensive application to real-life discrete optimization problems. Many of these models are NP-hard and, as a result, exact methods may be impractical for large scale problem instances. Consequently, there is a great interest in developing e±cient approximate methods that yield near-optimal solutions in acceptable computational times. A class of such methods, known as metaheuristics, have been proposed with success. This thesis considers some recently proposed NP-hard combinatorial optimization problems formulated on graphs. In particular, the min- imum labelling spanning tree problem, the minimum labelling Steiner tree problem, and the minimum quartet tree cost problem, are inves- tigated. Several metaheuristics are proposed for each problem, from classical approximation algorithms to novel approaches. A compre- hensive computational investigation in which the proposed methods are compared with other algorithms recommended in the literature is reported. The results show that the proposed metaheuristics outper- form the algorithms recommended in the literature, obtaining optimal or near-optimal solutions in short computational running times. In addition, a thorough analysis of the implementation of these methods provide insights for the implementation of metaheuristic strategies for other graph theoretic problems