Multiple sequence alignment with affine gap by using multi-objective genetic algorithm

Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate and statistically significant multiple alignments is still a challenge. In this paper, we propose an efficient method by using multi-objective genetic algorithm (MSAGMOGA) to discover optimal alignments with affine gap in multiple sequence data. The main advantage of our approach is that a large number of tradeoff (i.e., non-dominated) alignments can be obtained by a single run with respect to conflicting objectives: affine gap penalty minimization and similarity and support maximization. To the best of our knowledge, this is the first effort with three objectives in this direction. The proposed method can be applied to any data set with a sequential character. Furthermore, it allows any choice of similarity measures for finding alignments. By analyzing the obtained optimal alignments, the decision maker can understand the tradeoff between the objectives. We compared our method with the three well-known multiple sequence alignment methods, MUSCLE, SAGA and MSA-GA. As the first of them is a progressive method, and the other two are based on evolutionary algorithms. Experiments on the BAliBASE 2.0 database were conducted and the results confirm that MSAGMOGA obtains the results with better accuracy statistical significance compared with the three well-known methods in aligning multiple sequence alignment with affine gap. The proposed method also finds solutions faster than the other evolutionary approaches mentioned above.     

Fine-Grained Parallelism in Computational Mathematics

In the paper, a systematic discussion is made of state of the art theory and applications of fine-grained (massive) parallelism, which is permanently being adopted in computational mathematics. All known models of fine-grained computations (cellular automaton, neural and cellular neural networks, statistical automata, etc.) are represented in terms of a unique formalism, the so-called parallel substitution algorithm (PSA), which made it possible, on the one hand, to highlight common properties of the models and, on the other hand, to demonstrate expressiveness capabilities of the PSA. Theoretical and experimental results of studies on applications of fine-grained algorithms to modeling of spatial dynamics of reaction–diffusion and molecular processes are presented. Promising prospects of their application are substantiated both for the creation of special processors designed for the implementation of the algorithms and for the implementation of the algorithms on multiprocessor systems.     

Analysis of DNA sequence transformations on grids

Study of the evolution of species or organisms is essential for various biological applications. Evolution is typically studied at the molecular level by analyzing the mutations of DNA sequences of organisms. Techniques have been developed for building phylogenetic or evolutionary trees for a set of sequences. Though phylogenetic trees capture the overall evolutionary relationships among the sequences, they do not reveal fine-level details of the evolution. In this work, we attempt to resolve various fine-level sequence transformation details associated with a phylogenetic tree using cellular automata. In particular, our work tries to determine the cellular automata rules for neighbor-dependent mutations of segments of DNA sequences. We also determine the number of time steps needed for evolution of a progeny from an ancestor and the unknown segments of the intermediate sequences in the phylogenetic tree. Due to the existence of vast number of cellular automata rules, we have developed a grid system that performs parallel guided explorations of the rules on grid resources. We demonstrate our techniques by conducting experiments on a grid comprising machines in three countries and obtaining potentially useful statistics regarding evolutions in three HIV sequences. In particular, our work is able to verify the phenomenon of neighbor-dependent mutations and find that certain combinations of neighbor-dependent mutations, defined by a cellular automata rule, occur with greater than 90% probability. We also find the average number of time steps for mutations for some branches of phylogenetic tree over a large number of possible transformations with standard deviations less than 2.     

A New Evolutionary Algorithm for Solving Many-Objective Optimization Problems

In this paper, we focus on the study of evolutionary algorithms for solving multiobjective optimization problems with a large number of objectives. First, a comparative study of a newly developed dynamical multiobjective evolutionary algorithm (DMOEA) and some modern algorithms, such as the indicator-based evolutionary algorithm, multiple single objective Pareto sampling, and nondominated sorting genetic algorithm II, is presented by employing the convergence metric and relative hypervolume metric. For three scalable test problems (namely, DTLZ1, DTLZ2, and DTLZ6), which represent some of the most difficult problems studied in the literature, the DMOEA shows good performance in both converging to the true Pareto-optimal front and maintaining a widely distributed set of solutions. Second, a new definition of optimality (namely, L-optimality) is proposed in this paper, which not only takes into account the number of improved objective values but also considers the values of improved objective functions if all objectives have the same importance. We prove that L-optimal solutions are subsets of Pareto-optimal solutions. Finally, the new algorithm based on L-optimality (namely, MDMOEA) is developed, and simulation and comparative results indicate that well-distributed L-optimal solutions can be obtained by utilizing the MDMOEA but cannot be achieved by applying L-optimality to make a posteriori selection within the huge Pareto nondominated solutions. We can conclude that our new algorithm is suitable to tackle many-objective problems.      

The SR-GCWS hybrid algorithm for solving the capacitated vehicle routing problem

The capacitated vehicle routing problem (CVRP) is a well known problem which has long been tackled by researchers for several decades now, not only because of its potential applications but also due to the fact that CVRP can be used to test the efficiency of new algorithms and optimization methods. The objective of our work is to present SR-GCWS, a hybrid algorithm that combines a CVRP classical heuristic with Monte Carlo simulation using state-of-the-art random number generators. The resulting algorithm is tested against some well-known benchmarks. In most cases, our approach is able to compete or even outperform much more complex algorithms, which is especially interesting if we consider that our algorithm does not require any previous parameter fine-tuning or set-up process. Moreover, our algorithm has been able to produce high-quality solutions almost in real-time for most tested instances. Another important feature of the algorithm worth mentioning is that it uses a randomized constructive heuristic, capable of generating hundreds or even thousands of alternative solutions with different properties. These alternative solutions, in turn, can be really useful for decision-makers in order to satisfy their utility functions, which are usually unknown by the modeler. The presented methodology may be a fine framework for the development of similar algorithms for other complex combinatorial problems in the routing arena as well as in some other research fields.     

A diversity control mechanism in many objective optimizations

Multi-objective evolutionary optimization algorithms are among the best optimizers for solving problems in control systems, engineering and industrial planning. The performance of these algorithms degrades severely due to the loss of selection pressure exerted by the Pareto dominance relation which will cause the algorithm to act randomly. Various recent methods tried to provide more selection pressure but this would cause the population to converge to a specific region which is not desirable. Diversity reduction in high dimensional problems which decreases the capabilities of these approaches is a decisive factor in the overall performance of these algorithms. The novelty of this paper is to propose a new diversity measure and a diversity control mechanism which can be used in combination to remedy the mentioned problem. This measure is based on shortest Hamiltonian path for capturing an order of the population in any dimension. In order to control the diversity of population, we designed an adaptive framework which adjusts the selection operator according to diversity variation in the population using different diversity measures as well as our proposed one. This study incorporates the proposed framework in MOEA/D, an efficient widely used evolutionary algorithm. The obtained results validate the motivation on the basis of diversity and performance measures in comparison with the state-of-the-art algorithms and demonstrate the applicability of our algorithm/method in handling many-objective problems. Moreover, an extensive comparison with several diversity measure algorithms reveals the competitiveness of our proposed measure.     

Two effective hybrid metaheuristic algorithms for minimization of multimodal functions

Global optimization problems naturally arise from many applications. We propose two hybrid metaheuristic algorithms for finding a global optimum of a continuous function. Our proposed algorithms are hybridizations of genetic algorithm (GA) and variable neighbourhood search (VNS). To increase the efficiency of our algorithms, for smooth functions we present an effective locally improving line search procedure, and for non-smooth functions, we use the simplex method proposed by Nelder and Mead. By use of the recently adopted non-parametric statistical tests of Kruskal–Wallis and Mann–Whitney for analysing the behaviour of evolutionary algorithms, we compare both the efficiency and the effectiveness of our proposed algorithms with efficiently representative metaheuristic algorithms such as the multiagent GA proposed by Liang et al., the ant colony algorithm proposed by Toksari, and the VNS of Toksari and Güner on a variety of standard test functions. Computational experiments demonstrate that our proposed algorithms are efficiently effective.     

A Comparison of three evolutionary strategies for multiobjective genetic programming

We report what we believe to be the first comparative study of multi-objective genetic programming (GP) algorithms on benchmark symbolic regression and machine learning problems. We compare the Strength Pareto Evolutionary Algorithm (SPEA2), the Non-dominated Sorting Genetic Algorithm (NSGA-II) and the Pareto Converging Genetic Algorithm (PCGA) evolutionary paradigms. As well as comparing the quality of the final solutions, we also examine the speed of convergence of the three evolutionary algorithms. Based on our observations, the SPEA2-based algorithm appears to have problems controlling tree bloat—that is, the uncontrolled growth in the size of the chromosomal tree structures. The NSGA-II-based algorithm on the other hand seems to experience difficulties in locating low error solutions. Overall, the PCGA-based algorithm gives solutions with the lowest errors and the lowest mean complexity.     

Multiobjective structural optimization using a microgenetic algorithm

In this paper, we present a genetic algorithm with a very small population and a reinitialization process (a microgenetic algorithm) for solving multiobjective optimization problems. Our approach uses three forms of elitism, including an external memory (or secondary population) to keep the nondominated solutions found along the evolutionary process. We validate our proposal using several engineering optimization problems taken from the specialized literature and compare our results with respect to two other algorithms (NSGA-II and PAES) using three different metrics. Our results indicate that our approach is very efficient (computationally speaking) and performs very well in problems with different degrees of complexity.     

Hybrid strategy for selecting compact set of clustering partitions

The selection of the most appropriate clustering algorithm is not a straightforward task, given that there is no clustering algorithm capable of determining the actual groups present in any dataset. A potential solution is to use different clustering algorithms to produce a set of partitions (solutions) and then select the best partition produced according to a specified validation measure; these measures are generally biased toward one or more clustering algorithms. Nevertheless, in several real cases, it is important to have more than one solution as the output. To address these problems, we present a hybrid partition selection algorithm, HSS, which accepts as input a set of base partitions potentially generated from clustering algorithms with different biases and aims, to return a reduced and yet diverse set of partitions (solutions). HSS comprises three steps: (i) the application of a multiobjective algorithm to a set of base partitions to generate a Pareto Front (PF) approximation; (ii) the division of the solutions from the PF approximation into a certain number of regions; and (iii) the selection of a solution per region by applying the Adjusted Rand Index. We compare the results of our algorithm with those of another selection strategy, ASA. Furthermore, we test HSS as a post-processing tool for two clustering algorithms based on multiobjective evolutionary computing: MOCK and MOCLE. The experiments revealed the effectiveness of HSS in selecting a reduced number of partitions while maintaining their quality.     

Spectral learning of weighted automata

In recent years we have seen the development of efficient provably correct algorithms for learning Weighted Finite Automata (WFA). Most of these algorithms avoid the known hardness results by defining parameters beyond the number of states that can be used to quantify the complexity of learning automata under a particular distribution. One such class of methods are the so-called spectral algorithms that measure learning complexity in terms of the smallest singular value of some Hankel matrix. However, despite their simplicity and wide applicability to real problems, their impact in application domains remains marginal to this date. One of the goals of this paper is to remedy this situation by presenting a derivation of the spectral method for learning WFA that—without sacrificing rigor and mathematical elegance—puts emphasis on providing intuitions on the inner workings of the method and does not assume a strong background in formal algebraic methods. In addition, our algorithm overcomes some of the shortcomings of previous work and is able to learn from statistics of substrings. To illustrate the approach we present experiments on a real application of the method to natural language parsing.     

Chaos-based multi-objective immune algorithm with a fine-grained selection mechanism

In this paper, we propose a chaos-based multi-objective immune algorithm (CMIA) with a fine-grained selection mechanism based on the clonal selection principle. Taking advantage of the ergodic and stochastic properties of chaotic sequence, a novel mutation operator, named as chaos-based mutation (CM) operator, is proposed. Moreover, the information of diversity estimation is also adopted in the CM operator for nondominated solutions to adjust mutation steps adaptively, which encourages searching less-crowded regions with relative large step sizes. When comparing with polynomial mutation operator that is used in many state-of-the-art multi-objective optimization evolutionary algorithms, simulations show that it is effective to enhance the search performance. On the other hand, in order to increase the population diversity, a fine-grained selection mechanism is proposed in this paper, which seems to be remarkably effective in two-objective benchmark functions. When comparing with two state-of-the-art multi-objective evolutionary algorithms (NSGA-II and SPEA-2) and a new multi-objective immune algorithm (NNIA), simulation results of CMIA indicate the effectiveness of the fine-grained selection mechanism and the remarkable performance in finding the true Pareto-optimal front, especially on some benchmark functions with many local Pareto-optimal fronts.     

Large scale evolutionary optimization using cooperative coevolution

Evolutionary algorithms (EAs) have been applied with success to many numerical and combinatorial optimization problems in recent years. However, they often lose their effectiveness and advantages when applied to large and complex problems, e.g., those with high dimensions. Although cooperative coevolution has been proposed as a promising framework for tackling high-dimensional optimization problems, only limited studies were reported by decomposing a high-dimensional problem into single variables (dimensions). Such methods of decomposition often failed to solve nonseparable problems, for which tight interactions exist among different decision variables. In this paper, we propose a new cooperative coevolution framework that is capable of optimizing large scale nonseparable problems. A random grouping scheme and adaptive weighting are introduced in problem decomposition and coevolution. Instead of conventional evolutionary algorithms, a novel differential evolution algorithm is adopted. Theoretical analysis is presented in this paper to show why and how the new framework can be effective for optimizing large nonseparable problems. Extensive computational studies are also carried out to evaluate the performance of newly proposed algorithm on a large number of benchmark functions with up to 1000 dimensions. The results show clearly that our framework and algorithm are effective as well as efficient for large scale evolutionary optimisation problems. We are unaware of any other evolutionary algorithms that can optimize 1000-dimension nonseparable problems as effectively and efficiently as we have done.     

Estimation of distribution and differential evolution cooperation for large scale economic load dispatch optimization of power systems

Economic Load Dispatch (ELD) is an important and difficult optimization problem in power system planning. This article aims at addressing two practically important issues related to ELD optimization: (1) analyzing the ELD problem from the perspective of evolutionary optimization; (2) developing effective algorithms for ELD problems of large scale. The first issue is addressed by investigating the fitness landscape of ELD problems with the purpose of estimating the expected performance of different approaches. To address the second issue, a new algorithm named “Estimation of Distribution and Differential Evolution Cooperation” (ED-DE) is proposed, which is a serial hybrid of two effective evolutionary computation (EC) techniques: estimation of distribution and differential evolution. The advantages of ED-DE over the previous ELD optimization algorithms are experimentally testified on ELD problems with the number of generators scaling from 10 to 160. The best solution records of classical 13 and 40-generator ELD problems with valve points, and the best solution records of 10, 20, 40, 80 and 160-generator ELD problems with both valve points and multiple fuels are updated in this work. To further evaluate the efficiency and effectiveness of ED-DE, we also compare it with other state-of-the-art evolutionary algorithms (EAs) on typical function optimization tasks.     

How evolutionary algorithms are applied to statistical natural language processing

Statistical natural language processing (NLP) and evolutionary algorithms (EAs) are two very active areas of research which have been combined many times. In general, statistical models applied to deal with NLP tasks require designing specific algorithms to be trained and applied to process new texts. The development of such algorithms may be hard. This makes EAs attractive since they offer a general design, yet providing a high performance in particular conditions of application. In this article, we present a survey of many works which apply EAs to different NLP problems, including syntactic and semantic analysis, grammar induction, summaries and text generation, document clustering and machine translation. This review finishes extracting conclusions about which are the best suited problems or particular aspects within those problems to be solved with an evolutionary algorithm.     

A Multiobjective Optimization-Based Evolutionary Algorithm for Constrained Optimization

A considerable number of constrained optimization evolutionary algorithms (COEAs) have been proposed due to increasing interest in solving constrained optimization problems (COPs) by evolutionary algorithms (EAs). In this paper, we first review existing COEAs. Then, a novel EA for constrained optimization is presented. In the process of population evolution, our algorithm is based on multiobjective optimization techniques, i.e., an individual in the parent population may be replaced if it is dominated by a nondominated individual in the offspring population. In addition, three models of a population-based algorithm-generator and an infeasible solution archiving and replacement mechanism are introduced. Furthermore, the simplex crossover is used as a recombination operator to enrich the exploration and exploitation abilities of the approach proposed. The new approach is tested on 13 well-known benchmark functions, and the empirical evidence suggests that it is robust, efficient, and generic when handling linear/nonlinear equality/inequality constraints. Compared with some other state-of-the-art algorithms, our algorithm remarkably outperforms them in terms of the best, mean, and worst objective function values and the standard deviations. It is noteworthy that our algorithm does not require the transformation of equality constraints into inequality constraints     

A dandelion-encoded evolutionary algorithm for the delay-constrained capacitated minimum spanning tree problem

This paper proposes an evolutionary algorithm with Dandelion-encoding to tackle the Delay-Constrained Capacitated Minimum Spanning Tree (DC-CMST) problem. This problem has been recently proposed, and consists of finding several broadcast trees from a source node, jointly considering traffic and delay constraints in trees. A version of the problem in which the source node is also included in the optimization process is considered as well in the paper. The Dandelion code used in the proposed evolutionary algorithm has been recently proposed as an effective way of encoding trees in evolutionary algorithms. Good properties of locality has been reported on this encoding, which makes it very effective to solve problems in which the solutions can be expressed in form of trees. In the paper we describe the main characteristics of the algorithm, the implementation of the Dandelion-encoding to tackled the DC-CMST problem and a modification needed to include the source node in the optimization. In the experimental section of this article we compare the results obtained by our evolutionary with that of a recently proposed heuristic for the DC-CMST, the Least Cost (LC) algorithm. We show that our Dandelion-encoded evolutionary algorithm is able to obtain better results that the LC in all the instances tackled.     

Combining convergence and diversity in evolutionary multiobjective optimization

Over the past few years, the research on evolutionary algorithms has demonstrated their niche in solving multiobjective optimization problems, where the goal is to find a number of Pareto-optimal solutions in a single simulation run. Many studies have depicted different ways evolutionary algorithms can progress towards the Pareto-optimal set with a widely spread distribution of solutions. However, none of the multiobjective evolutionary algorithms (MOEAs) has a proof of convergence to the true Pareto-optimal solutions with a wide diversity among the solutions. In this paper, we discuss why a number of earlier MOEAs do not have such properties. Based on the concept of epsilon-dominance, new archiving strategies are proposed that overcome this fundamental problem and provably lead to MOEAs that have both the desired convergence and distribution properties. A number of modifications to the baseline algorithm are also suggested. The concept of epsilon-dominance introduced in this paper is practical and should make the proposed algorithms useful to researchers and practitioners alike.     

Best practices in measuring algorithm performance for dynamic optimization problems

Dynamic optimization problems (DOPs) have attracted considerable attention due to the wide range of problems they can be applied to. Lots of efforts have been expended in modeling dynamic situations, proposing algorithms, and analyzing the results (too often in a visual way). Numeric performance measurements and their statistical validation have been however barely used in the literature. Most of works in DOPs report only the best-of-generation fitness, due to its simplicity of computation. Although this measure indicates the best algorithm in terms of fitness, it does not provide any details about the actual strength and weakness of each algorithm. In this article, we conduct a comparative study among algorithms of different search modes via several performance measures to demonstrate their relative advantages. We discuss the role of using different performance measures in drawing balanced conclusions about algorithms for DOPs.     

Biogeography-based optimisation with chaos

The biogeography-based optimisation (BBO) algorithm is a novel evolutionary algorithm inspired by biogeography. Similarly, to other evolutionary algorithms, entrapment in local optima and slow convergence speed are two probable problems it encounters in solving challenging real problems. Due to the novelty of this algorithm, however, there is little in the literature regarding alleviating these two problems. Chaotic maps are one of the best methods to improve the performance of evolutionary algorithms in terms of both local optima avoidance and convergence speed. In this study, we utilise ten chaotic maps to enhance the performance of the BBO algorithm. The chaotic maps are employed to define selection, emigration, and mutation probabilities. The proposed chaotic BBO algorithms are benchmarked on ten test functions. The results demonstrate that the chaotic maps (especially Gauss/mouse map) are able to significantly boost the performance of BBO. In addition, the results show that the combination of chaotic selection and emigration operators results in the highest performance.