An MO‐GVNS algorithm for solving a multiobjective hybrid flow shop scheduling problem

This paper addresses the multiobjective hybrid flow shop (MOHFS) scheduling problem. In the MOHFS problem considered here, we have a set of jobs that must be performed in a set of stages. At each stage, we have a set of unrelated parallel machines. Some jobs may skip stages. The evaluation criteria are the minimizations of makespan, the weighted sum of the tardiness, and the weighted sum of the earliness. For solving it, an algorithm based on the multiobjective general variable neighborhood search (MO‐GVNS) metaheuristic, named adapted MO‐GVNS, is proposed. This work also presents and compares the results obtained by the adapted MO‐GVNS with those of four other algorithms: multiobjective reduced variable neighborhood search, nondominated sorting genetic algorithm II (NSGA‐II), and NSGA‐III, and another MO‐GVNS from the literature. The results were evaluated based on the Hypervolume, Epsilon, and Spacing metrics, and statistically validated by the Levene test and confidence interval charts. The results showed the efficiency of the proposed algorithm for solving the MOHFS problem.     

Hybrid multiobjective artificial bee colony for multiple sequence alignment

In the bioinformatics community, it is really important to find an accurate and simultaneous alignment among diverse biological sequences which are assumed to have an evolutionary relationship. From the alignment, the sequences homology is inferred and the shared evolutionary origins among the sequences are extracted by using phylogenetic analysis. This problem is known as the multiple sequence alignment (MSA) problem. In the literature, several approaches have been proposed to solve the MSA problem, such as progressive alignments methods, consistency-based algorithms, or genetic algorithms (GAs). In this work, we propose a Hybrid Multiobjective Evolutionary Algorithm based on the behaviour of honey bees for solving the MSA problem, the hybrid multiobjective artificial bee colony (HMOABC) algorithm. HMOABC considers two objective functions with the aim of preserving the quality and consistency of the alignment: the weighted sum-of-pairs function with affine gap penalties (WSP) and the number of totally conserved (TC) columns score. In order to assess the accuracy of HMOABC, we have used the BAliBASE benchmark (version 3.0), which according to the developers presents more challenging test cases representing the real problems encountered when aligning large sets of complex sequences. Our multiobjective approach has been compared with 13 well-known methods in bioinformatics field and with other 6 evolutionary algorithms published in the literature.     

Design of multiobjective reconfigurable antenna array with discrete phase shifters using multiobjective differential evolution based on decomposition

The reconfigurable design problem is to find the element that will result in a sector pattern main beam with side lobes. The same excitation amplitudes applied to the array with zero phase should be in a high directivity, low‐side lobe pencil‐shaped main beam. This work presents a multiobjective approach to solve this problem. We consider two design objectives: the minimum value for the dual beam and the dynamic range ratio in qualify the entire array radiation pattern in order to achieve the optimal value between the antenna‐array elements. We use a recently developed and very competitive multiobjective evolutionary algorithm, called MOEA/D. This algorithm uses a decomposition approach to convert the problem of approximation of the Pareto Front into a number of single objective optimization problems. We illustrate that the best solutions obtained by the MOEA/D can outperform stat‐of‐art single objective algorithm: generalized generation‐gap model genetic algorithm (G3‐GA) and differential evolution algorithm (DE). In addition, we compare the results obtained by MOEA/D with those obtained by one of the most widely multiobjective algorithm called NSGA‐II and mutliobjective DE. © 2012 Wiley Periodicals, Inc. Int J RF and Microwave CAE 22: 675–681, 2012.     

Multiobjective model for solving resource‐leveling problem with discounted cash flows

Nowadays, executers are struggling to improve the economic and scheduling situation of projects. Construction scheduling techniques often produce schedules that cause undesirable resource fluctuations that are inefficient and costly to implement on site. The objective of the resource‐leveling problem is to reduce resource fluctuation related costs (hiring and firing costs) without violating the project deadline. In this article, minimizing the discounted costs of resource fluctuations and minimizing the project makespan are considered in a multiobjective model. The problem is formulated as an integer nonlinear programming model, and since the optimization problem is NP‐hard, we propose multiobjective evolutionary algorithms, namely nondominated sorting genetic algorithm‐II (NSGA‐II), strength Pareto evolutionary algorithm‐II (SPEA‐II), and multiobjective particle swarm optimization (MOPSO) to solve our suggested model. To evaluate the performance of the algorithms, experimental performance analysis on various instances is presented. Furthermore, in order to study the performance of these algorithms, three criteria are proposed and compared with each other to demonstrate the strengths of each applied algorithm. To validate the results obtained for the suggested model, we compared the results of the first objective function with a well‐tuned genetic algorithm and differential algorithm, and we also compared the makespan results with one of the popular algorithms for the resource constraints project scheduling problem. Finally, we can observe that the NSGA‐II algorithm presents better solutions than the other two algorithms on average.     

Performance and energy aware scheduling simulator for HPC: evaluating different resource selection methods

Today, in an energy‐aware society, job scheduling is becoming an important task for computer engineers and system analysts that may lead to a performance per Watt trade‐off of computing infrastructures. Thus, new algorithms, and a simulator of computing environments, may help information and communications technology and data center managers to make decisions with a solid experimental basis. There are several simulators that try to address performance and, somehow, estimate energy consumption, but there are none in which the energy model is based on benchmark data that have been countersigned by independent bodies such as the Standard Performance Evaluation Corporation. This is the reason why we have implemented a performance and energy‐aware scheduling (PEAS) simulator for high‐performance computing. Furthermore, to evaluate the simulator, we propose an implementation of the non‐dominated sorting genetic algorithm‐II (NSGA‐II) algorithm, a fast and elitist multiobjective genetic algorithm, for the resource selection. With the help of the PEAS simulator, we have studied if it is possible to provide an intelligent job allocation policy that may be able to save energy and time without compromising performance. The results of our simulations show a great improvement in response time and power consumption. In most of the cases, NSGA‐II performs better than other ‘intelligent’ algorithms like multiobjective heterogeneous earliest finish time and clearly outperforms the first‐fit algorithm. We demonstrate the usefulness of the simulator for this type of studies and conclude that the superior behavior of multiobjective algorithms makes them recommended for use in modern scheduling systems. Copyright © 2015 John Wiley & Sons, Ltd.     

A hybrid approach to parallelize a fast non‐dominated sorting genetic algorithm for phylogenetic inference

The field of computational biology encloses a wide range of optimization problems that show non‐deterministic polynomial‐time hard complexities. Nowadays, phylogeneticians are dealing with a growing amount of biological data that must be analyzed to explain the origins of modern species. Evolutionary relationships among organisms are often described by means of tree‐shaped structures known as phylogenetic trees. When inferring phylogenies, two main challenges must be addressed. First, the inference of reliable evolutionary trees on data sets where different optimality principles support conflicting evolutionary hypotheses. Second, the processing of enormous tree searches spaces where traditional sequential strategies cannot be applied. In this sense, phylogenetic inference can benefit from the combination of high performance computing and evolutionary computation to carry out the reconstruction of complex evolutionary histories in reduced execution times. In this paper, we introduce multiobjective phylogenetics, a hybrid OpenMP/MPI approach to parallelize a well‐known multiobjective metaheuristic, the fast non‐dominated sorting genetic algorithm (NSGA‐II). This algorithm has been designed to conduct phylogenetic analyses on multi‐core clusters in accordance with two principles: maximum parsimony and maximum likelihood. The main goal is to combine the benefits of shared‐memory and distributed‐memory programming paradigms to efficiently infer a set of high‐quality Pareto solutions. Experiments on six real nucleotide data sets and comparisons with other hybrid parallel approaches show that multiobjective phylogenetics is able to achieve significant performance in terms of parallel, multiobjective, and biological results. Copyright © 2014 John Wiley & Sons, Ltd.     

COMPARISON AND SELECTION OF OBJECTIVE FUNCTIONS IN MULTIOBJECTIVE COMMUNITY DETECTION

Detecting communities of complex networks has been an effective way to identify substructures that could correspond to important functions. Conventional approaches usually consider community detection as a single‐objective optimization problem, which may confine the solution to a particular community structure property. Recently, a new community detection paradigm is emerging: multiobjective optimization for community detection, which means simultaneously optimizing multiple criteria and obtaining a set of community partitions. The new paradigm has shown its advantages. However, an important issue is still open: what type of objectives should be optimized to improve the performance of multiobjective community detection? To exploit this issue, we first proposed a general multiobjective community detection solution (called NSGA‐Net) and then analyzed the structural characteristics of communities identified by a variety of objective functions that have been used or can potentially be used for community detection. After that, we exploited correlation relations (i.e., positively correlated, independent, or negatively correlated) between any two objective functions. Extensive experiments on both artificial and real networks demonstrate that NSGA‐Net optimizing over a pair of negatively correlated objectives usually leads to better performances compared with the single‐objective algorithm optimizing over either of the original objectives, or even to other well‐established community detection approaches.     

Multiple sequence alignment using the Hidden Markov Model trained by an improved quantum-behaved particle swarm optimization

Multiple sequence alignment (MSA) is an NP-complete and important problem in bioinformatics. For MSA, Hidden Markov Models (HMMs) are known to be powerful tools. However, the training of HMMs is computationally hard so that metaheuristic methods such as simulated annealing (SA), evolutionary algorithms (EAs) and particle swarm optimization (PSO), have been employed to tackle the training problem. In this paper, quantum-behaved particle swarm optimization (QPSO), a variant of PSO, is analyzed mathematically firstly, and then an improved version is proposed to train the HMMs for MSA. The proposed method, called diversity-maintained QPSO (DMQPO), is based on the analysis of QPSO and integrates a diversity control strategy into QPSO to enhance the global search ability of the particle swarm. To evaluate the performance of the proposed method, we use DMQPSO, QPSO and other algorithms to train the HMMs for MSA on three benchmark datasets. The experiment results show that the HMMs trained with DMQPSO and QPSO yield better alignments for the benchmark datasets than other most commonly used HMM training methods such as Baum–Welch and PSO.     

Multiple Sequence Alignment with Evolutionary Computation

In this paper we provide a brief review of current work in the area of multiple sequence alignment (MSA) for DNA and protein sequences using evolutionary computation (EC). We detail the strengths and weaknesses of EC techniques for MSA. In addition, we present two novel approaches for inferring MSA using genetic algorithms. Our first novel approach utilizes a GA to evolve an optimal guide tree in a progressive alignment algorithm and serves as an alternative to the more traditional heuristic techniques such as neighbor-joining. The second novel approach facilitates the optimization of a consensus sequence with a GA using a vertically scalable encoding scheme in which the number of iterations needed to find the optimal solution is approximately the same regardless the number of sequences being aligned. We compare both of our novel approaches to the popular progressive alignment program Clustal W. Experiments have confirmed that EC constitutes an attractive and promising alternative to traditional heuristic algorithms for MSA.     

Performance analysis of computational approaches to solve Multiple Sequence Alignment

In the biotechnology field, the deployment of the Multiple Sequence Alignment (MSA) problem, which is a high performance computing demanding process, is one of the new challenges to address on the new parallel systems. The aim of this problem is to find similar regions on biological sequences. Furthermore, the goal of MSA applications is to align as much sequences as possible with a level of quality that makes the alignment biologically meaningful. An efficiency study of different MSA implementations, based on T-Coffee (one of the most used MSA aligners), has been performed in order to find new optimizations that may improve the average execution time on multi-core systems. We found that the current parallel implementations have some performance issues, affecting negatively the scalability of the process. Finally, the proposed implementation based on the usage of threads in conjunction with a message-passing library is presented, with the aim to optimize the execution of the MSA problem in multi-core-based clusters.     

On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures

In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the problem has been conclusively shown to be computationally complex, we employ divisible load paradigm (also, referred to as divisible load theory, DLT) to handle such large number of sequences. We design an efficient computational engine that is capable of conducting MSAs by exploiting the underlying parallelism embedded in the computational steps of multiple sequence algorithms. Specifically, we consider the standard Smith–Waterman (SW) algorithm in our implementation, however, our approach is by no means restrictive to SW class of algorithms alone. The treatment used in this paper is generic to a class of similar dynamic programming problems. Our approach is recursive in the sense that the quality of solutions can be refined continuously till an acceptable level of quality is achieved. After first phase of computation, we design a heuristic scheme that renders the final solution for MSA. We conduct rigorous simulation experiments using several hundreds of homologous protein sequences derived from the Rattus Norvegicus and Mus Musculus databases of olfactory receptors. We quantify the performance based on speed-up metric. We compare our algorithms to serial or single machine processing approaches. We testify our findings by comparing with conventional equal load partitioning (ELP) strategy that is commonly used in the parallel processing literature. Based on our extensive simulation study, we observe that DLT paradigm offers an excellent speed-up characteristics and provides avenues for its use in several other biological sequence processing related problem. This study is a first time attempt in using the DLT paradigm to devise efficient strategies to handle large scale multiple protein sequence alignment problem on mesh-based multiprocessor systems.     

Rough‐fuzzy quadratic minimum spanning tree problem

A quadratic minimum spanning tree problem determines a minimum spanning tree of a network whose edges are associated with linear and quadratic weights. Linear weights represent the edge costs whereas the quadratic weights are the interaction costs between a pair of edges of the graph. In this study, a bi‐objective rough‐fuzzy quadratic minimum spanning tree problem has been proposed for a connected graph, where the linear and the quadratic weights are represented as rough‐fuzzy variables. The proposed model is formulated by using rough‐fuzzy chance‐constrained programming technique. Subsequently, three related theorems are also proposed for the crisp transformation of the proposed model. The crisp equivalent models are solved with a classical multi‐objective solution technique, the epsilon‐constraint method and two multi‐objective evolutionary algorithms: (a) nondominated sorting genetic algorithm II (NSGA‐II) and (b) multi‐objective cross‐generational elitist selection, heterogeneous recombination, and cataclysmic mutation (MOCHC) algorithm. A numerical example is provided to illustrate the proposed model when solved with different methodologies. A sensitivity analysis of the example is also performed at different confidence levels. The performance of NSGA‐II and MOCHC are analysed on five randomly generated instances of the proposed model. Finally, a numerical illustration of an application of the proposed model is also presented in this study.     

Multiobjective approach for detecting communities in heterogeneous networks

Online social networks have a strong potential to be divided into a number of dense substructures, called communities. In such heterogeneous networks, the communities refer not only to dense parts of links but also to clusters present among other dimensions such as users' profiles, comments, and information flows. To find communities in these networks, researchers have developed a number of methods; however, to the best of the authors' knowledge, these methods are limited in taking only 2 dimensions into account, and they are also not able to give a sense of how users behave in their communities. To deal with these issues, this paper proposes a multiobjective optimization model in which a specific objective function has been used for each considered dimension in a given network. Because of the NP‐hardness of the studied problem, an efficient and effective multiobjective metaheuristic algorithm has been developed. By juxtaposing the nondominated solutions obtained, the proposed algorithm can demonstrate how users behave in their communities. To illustrate the effectiveness of the algorithm, a set of experiments with a comprehensive evaluation method is provided. The results show the superiority and the stability of the proposed algorithm.     

A new Multiobjective Artificial Bee Colony algorithm to solve a real-world frequency assignment problem

Artificial bee colony (ABC) is a recently introduced algorithm that models the behavior of honey bee swarm to address a multiobjective version for ABC, named Multiobjective Artificial Bee Colony algorithm (MO-ABC). We describe the methodology and results obtained when applying the new MO-ABC metaheuristic, which was developed to solve a real-world frequency assignment problem (FAP) in GSM networks. A precise mathematical formulation for this problem was used, where the frequency plans are evaluated using accurate interference information taken from a real GSM network. In this paper, our work is divided into two stages: In the first one, we have accurately tuned the algorithm parameters. Then, in the second step, we have compared the MO-ABC with previous versions of distinct multiobjective algorithms already developed to the same instances of the problem. As we will see, results show that this approach is able to obtain reasonable frequency plans when solving a real-world FAP. In the results analysis, we consider as complementary metrics the hypervolume indicator to measure the quality of the solutions to this problem as well as the coverage relation information.     

Fuzzy resource‐constrained project scheduling using taboo search algorithm

This paper proposes a mathematical model to deal with project scheduling problem under vagueness and a framework of a heuristic approach to fuzzy resource‐constrained project scheduling problem (F‐RCPSP) using heuristic and metaheuristic scheduling methods. Our approach is very simple to apply, and it does not require knowing the explicit form of the membership functions of the fuzzy activity times. We first identify two typical activity priority rules, namely, resource over time and minimum slack priority rules. They are used in the F‐RCPS problem and in the initial solution of Taboo search (TS) method. We improved the TS algorithm method for the solution of F‐RCPSP. Our objective is to check the performance of these rules and metaheuristic method in minimizing the project completion time for the F‐RCPS problems. In our study, we use trapezoidal fuzzy numbers (TraFNs) for activity times and activity‐on‐nodes (AON) representation and compute several project characteristics such as earliest, latest, and slack times in terms of TraFNs. The computational experiment shows that the performance of the proposed TS is better than the evaluation and light beam search algorithms in the literature. © 2012 Wiley Periodicals, Inc.     

A matheuristic for the discrete bilevel problem with multiple objectives at the lower level

In this paper, we solve a discrete bilevel problem with multiple objectives at the lower level and constraints at the upper level coupling variables of both levels. In the case of a multiobjective lower level, we deal with a set of Pareto‐efficient solutions rather than a single optimal lower level solution. To calculate the upper level objective function value, we need to select one solution out of a potentially large set of efficient lower level solutions. To avoid the enumeration of the whole set of Pareto solutions, we formulate an auxiliary mixed integer linear programming problem with a large number of constraints. We propose an iterative exact method to solve it. To find a near‐optimal upper level solution, we apply a metaheuristic. The method is tested on the discrete ()‐centroid problem with multiple objectives at the lower level.     

Automatic clustering using nature-inspired metaheuristics: A survey

In cluster analysis, a fundamental problem is to determine the best estimate of the number of clusters; this is known as the automatic clustering problem. Because of lack of prior domain knowledge, it is difficult to choose an appropriate number of clusters, especially when the data have many dimensions, when clusters differ widely in shape, size, and density, and when overlapping exists among groups. In the late 1990s, the automatic clustering problem gave rise to a new era in cluster analysis with the application of nature-inspired metaheuristics. Since then, researchers have developed several new algorithms in this field. This paper presents an up-to-date review of all major nature-inspired metaheuristic algorithms used thus far for automatic clustering. Also, the main components involved during the formulation of metaheuristics for automatic clustering are presented, such as encoding schemes, validity indices, and proximity measures. A total of 65 automatic clustering approaches are reviewed, which are based on single-solution, single-objective, and multiobjective metaheuristics, whose usage percentages are 3%, 69%, and 28%, respectively. Single-objective clustering algorithms are adequate to efficiently group linearly separable clusters. However, a strong tendency in using multiobjective algorithms is found nowadays to address non-linearly separable problems. Finally, a discussion and some emerging research directions are presented.     

Game-theoretic differential evolution for multiobjective optimization of green sand mould system

Many large-scale engineering problems often take a multiobjective form. Thus, several solution options to the MO problem are usually ascertained by the engineer. Then the most desirable options with respect to the industrial circumstances and online operating conditions are selected. In this work, the trade-off solutions are obtained using the weighted-sum approach. In addition the standard metaheuristic, differential evolution is improved using concepts from evolutionary game theory. These techniques are then applied to solve the industrial green sand mould development problem. The solutions are then examined and discussed from various standpoints.     

A hybrid metaheuristic for multiobjective unconstrained binary quadratic programming

The conventional unconstrained binary quadratic programming (UBQP) problem is known to be a unified modeling and solution framework for many combinatorial optimization problems. This paper extends the single-objective UBQP to the multiobjective case (mUBQP) where multiple objectives are to be optimized simultaneously. We propose a hybrid metaheuristic which combines an elitist evolutionary multiobjective optimization algorithm and a state-of-the-art single-objective tabu search procedure by using an achievement scalarizing function. Finally, we define a formal model to generate mUBQP instances and validate the performance of the proposed approach in obtaining competitive results on large-size mUBQP instances with two and three objectives.     

Solving a comprehensive model for multiobjective project portfolio selection

Any organization is routinely faced with the need to make decisions regarding the selection and scheduling of project portfolios from a set of candidate projects. We propose a multiobjective binary programming model that facilitates both obtaining efficient portfolios in line with the set of objectives pursued by the organization, as well as their scheduling regarding the optimum time to launch each project within the portfolio without the need for a priori information on the decision-maker's preferences. Resource constraints, the possibility of transferring resources not consumed in a given a period to the following one, and project interdependence have also been taken into account. Given that the complexity of this problem increases as the number of projects and the number of objectives increase, we solve it using a metaheuristic procedure based on Scatter Search that we call SS-PPS (Scatter Search for Project Portfolio Selection). The characteristics and effectiveness of this method are compared with other heuristic approaches (SPEA and a fully random procedure) using computational experiments on randomly generated instances.

Statement of scope and purpose

This paper describes a model to aid in the selection and scheduling of project portfolios within an organization. The model was designed assuming strong interdependence between projects, which therefore have to be assessed in groups, while allowing individual projects to start at different times depending on resource availability or any other strategic or political requirements, which involves timing issues. The simultaneous combination of project portfolio selection and scheduling under general conditions involves known drawbacks that we attempt to remedy. Finally, the model takes into account multiple objectives without requiring a priori specifications regarding the decision-maker's preferences.The resolution of the problem was approached using a metaheuristic procedure, which showed by computational experiments good performance compared with other heuristics.