A multiple minima genetic algorithm for protein structure prediction

Protein structure prediction (PSP) has a large potential for valuable biotechnological applications. However the prediction itself encompasses a difficult optimization problem with thousands of degrees of freedom and is associated with extremely complex energy landscapes. In this work a simplified three-dimensional protein model (hydrophobic-polar model, HP in a cubic lattice) was used in order to allow for the fast development of a robust and efficient genetic algorithm based methodology. The new methodology employs a phenotype based crowding mechanism for the maintenance of useful diversity within the populations, which resulted in increased performance and granted the algorithm multiple solutions capabilities. Tests against several benchmark HP sequences and comparative results showed that the proposed genetic algorithm is superior to other evolutionary algorithms. The proposed algorithm was then successfully adapted to an all-atom protein model and tested on poly-alanines. The native structure, an alpha helix, was found in all test cases as a local or a global minimum, in addition to other conformations with similar energies. The results showed that optimization strategies with multiple solutions capability present two advantages for PSP applications. The first one is a more efficient investigation of complex energy landscapes; the second one is an increase in the probability of finding native structures, even when they are not at the global optimum.     

A novel classification method: A hybrid approach based on extension of the UTADIS with polynomial and PSO-GA algorithm

In this study, a new multi-criteria classification technique for nominal and ordinal groups is developed by expanding the UTilites Additives DIScriminantes (UTADIS) method with a polynomial of degree T which is used as the utility function rather than using a piecewise linear function as an approximation of the utility function of each attribute. We called this method as PUTADIS. The objective is calculating the coefficients of the polynomial and the threshold limit of classes and weight of attributes such that it minimizes the number of misclassification error. Estimation of unknown parameters of the problem is calculated by using a hybrid algorithm which is a combination of particle swarm optimization algorithm (PSO) and Genetic Algorithm (GA). The results obtained by implementing the model on different datasets and comparing its performance with other previous methods show the high efficiency of the proposed method.     

改进的蚁群算法求解蛋白质折叠问题

针对蛋白质折叠问题的二维格点模型(2DHP)提出了一种改进的蚁群算法(ACO).受链生长型算法Pruned-Enriched Rosenbluth Mvthod(PERM)的启发,在计算迹的时候增加了一个新的信息量,使得改进后的蚁群算法具有较快的收敛速度,同时采用基于极值动力学的优化方法(EO)进行局部搜索.求解基准实例的结果表明,该算法能够在保证解质量的前提下能大大缩短计算时间.     

Gene selection using hybrid particle swarm optimization and genetic algorithm

Selecting high discriminative genes from gene expression data has become an important research. Not only can this improve the performance of cancer classification, but it can also cut down the cost of medical diagnoses when a large number of noisy, redundant genes are filtered. In this paper, a hybrid Particle Swarm Optimization (PSO) and Genetic Algorithm (GA) method is used for gene selection, and Support Vector Machine (SVM) is adopted as the classifier. The proposed approach is tested on three benchmark gene expression datasets: Leukemia, Colon and breast cancer data. Experimental results show that the proposed method can reduce the dimensionality of the dataset, and confirm the most informative gene subset and improve classification accuracy.     

An improved GA and a novel PSO-GA-based hybrid algorithm

Inspired by the natural features of the variable size of the population, we present a variable population-size genetic algorithm (VPGA) by introducing the “dying probability” for the individuals and the “war/disease process” for the population. Based on the VPGA and the particle swarm optimization (PSO) algorithms, a novel PSO-GA-based hybrid algorithm (PGHA) is also proposed in this paper. Simulation results show that both VPGA and PGHA are effective for the optimization problems.     

An efficient hybrid particle swarm optimization algorithm in a rolling horizon framework for the aircraft landing problem

This paper proposes a hybrid particle swarm optimization algorithm in a rolling horizon framework to solve the aircraft landing problem (ALP). ALP is an important optimization problem in air traffic control and is well known as NP-hard. The problem consists of allocating the arriving aircrafts to runways at an airport and assigning a landing time to each aircraft. Each aircraft has an optimum target landing time determined based on its most fuel-efficient airspeed and a deviation from it incurs a penalty which is proportional to the amount of deviation. The landing time of each aircraft is constrained within a specified time window and must satisfy minimum separation time requirement with its preceding aircrafts. The objective is to minimize the total penalty cost due to deviation of landing times of aircrafts from the respective target landing times. The performance of the proposed algorithm is evaluated on a set of benchmark instances involving upto 500 aircrafts and 5 runways. Computational results reveal that the proposed algorithm is effective in solving the problem in short computational time.     

An efficient dynamical evolutionary algorithm for global optimization

In this paper, we introduce a new dynamical evolutionary algorithm (DEA) that aims to find the global optimum and give the theoretical explanation from statistical mechanics. The algorithm has been evaluated numerically using a wide set of test functions which are nonlinear, multimodal and multidimensional. The numerical results show that it is possible to obtain global optimum or more accurate solutions than other methods for the investigated hard problems.     

An effective hybrid particle swarm optimization algorithm for multi-objective flexible job-shop scheduling problem

Flexible job-shop scheduling problem (FJSP) is an extension of the classical job-shop scheduling problem. Although the traditional optimization algorithms could obtain preferable results in solving the mono-objective FJSP. However, they are very difficult to solve multi-objective FJSP very well. In this paper, a particle swarm optimization (PSO) algorithm and a tabu search (TS) algorithm are combined to solve the multi-objective FJSP with several conflicting and incommensurable objectives. PSO which integrates local search and global search scheme possesses high search efficiency. And, TS is a meta-heuristic which is designed for finding a near optimal solution of combinatorial optimization problems. Through reasonably hybridizing the two optimization algorithms, an effective hybrid approach for the multi-objective FJSP has been proposed. The computational results have proved that the proposed hybrid algorithm is an efficient and effective approach to solve the multi-objective FJSP, especially for the problems on a large scale.     

一种动态分级的混合粒子群优化算法

针对粒子群算法早熟收敛和搜索精度不高的问题,提出一种动态分级的混合粒子群优化算法．该算法采取３种级别的并行粒子群算法,分别用于全局搜索和局部搜索及二者的结合,并根据搜索阶段动态调整各种级别中并行变量的数目．在全局搜索中,将混沌机制引入算法中以增强算法的全局搜索能力;在局部搜索中,采用单纯形法对适应度最优解进行局部寻优．仿真实验表明,该算法比其他优化算法具有更好的性能．     

A novel parallel hybrid intelligence optimization algorithm for a function approximation problem

A novel parallel hybrid intelligence optimization algorithm (PHIOA) is proposed based on combining the merits of particle swarm optimization with genetic algorithms. The PHIOA uses the ideas of selection, crossover and mutation from genetic algorithms (GAs) and the update velocity and situation of particle swarm optimization (PSO) under the independence of PSO and GAs. The proposed algorithm divides the individuals into two equation groups according to their fitness values. The subgroup of the top fitness values is evolved by GAs and the other subgroup is evolved by the PSO algorithm. The optimal number is selected as a global optimum at every circulation which shows better results than both PSO and GAs, then improves the overall performance of the algorithm. The PHIOA is used to optimize the structure and parameters of the fuzzy neural network. Finally, the experimental results have demonstrated the superiority of the proposed PHIOA to search the global optimal solution. The PHIOA can improve the error accuracy while speeding up the convergence process, and effectively avoid the premature convergence to compare with the existing methods.     

A novel ACO–GA hybrid algorithm for feature selection in protein function prediction

Protein function prediction is an important problem in functional genomics. Typically, protein sequences are represented by feature vectors. A major problem of protein datasets that increase the complexity of classification models is their large number of features. Feature selection (FS) techniques are used to deal with this high dimensional space of features. In this paper, we propose a novel feature selection algorithm that combines genetic algorithms (GA) and ant colony optimization (ACO) for faster and better search capability. The hybrid algorithm makes use of advantages of both ACO and GA methods. Proposed algorithm is easily implemented and because of use of a simple classifier in that, its computational complexity is very low. The performance of proposed algorithm is compared to the performance of two prominent population-based algorithms, ACO and genetic algorithms. Experimentation is carried out using two challenging biological datasets, involving the hierarchical functional classification of GPCRs and enzymes. The criteria used for comparison are maximizing predictive accuracy, and finding the smallest subset of features. The results of experiments indicate the superiority of proposed algorithm.     

An effective hybrid PSO-based algorithm for flow shop scheduling with limited buffers

In this paper, an effective hybrid algorithm based on particle swarm optimization (HPSO) is proposed for permutation flow shop scheduling problem (PFSSP) with the limited buffers between consecutive machines to minimize the maximum completion time (i.e., makespan). First, a novel encoding scheme based on random key representation is developed, which converts the continuous position values of particles in PSO to job permutations. Second, an efficient population initialization based on the famous Nawaz–Enscore–Ham (NEH) heuristic is proposed to generate an initial population with certain quality and diversity. Third, a local search strategy based on the generalization of the block elimination properties, named block-based local search, is probabilistically applied to some good particles. Moreover, simulated annealing (SA) with multi-neighborhood guided by an adaptive meta-Lamarckian learning strategy is designed to prevent the premature convergence and concentrate computing effort on promising solutions. Simulation results and comparisons demonstrate the effectiveness of the proposed HPSO. Furthermore, the effects of some parameters are discussed.     

A hybrid algorithm based on particle swarm and chemical reaction optimization

In this paper, a hybrid method for optimization is proposed, which combines the two local search operators in chemical reaction optimization with global search ability of for global optimum. This hybrid technique incorporates concepts from chemical reaction optimization and particle swarm optimization, it creates new molecules (particles) either operations as found in chemical reaction optimization or mechanisms of particle swarm optimization. Moreover, some technical bound constraint handling has combined when the particle update in particle swarm optimization. The effects of model parameters like InterRate, γ, Inertia weight and others parameters on performance are investigated in this paper. The experimental results tested on a set of twenty-three benchmark functions show that a hybrid algorithm based on particle swarm and chemical reaction optimization can outperform chemical reaction optimization algorithm in most of the experiments. Experimental results also indicate average improvement and deviate over chemical reaction optimization in the most of experiments.     

一种克服粒子群早熟的混合优化算法

针对粒子群优化算法在寻优时容易出现早熟现象,提出在粒子群收敛停滞时,从种群中随机选择粒子进行共轭梯度法计算,通过引入共轭梯度算法计算的信息来影响粒子速度的更新,以保持群体的活性,从而打破群体信息陷入局部最优的状况.不同于传统的粒子群算法,该算法有机地结合了粒子群的全局搜索能力和共轭梯度法的强大局部搜索能力,从而在一定程度上有效地克服了粒子群早熟的缺点.仿真计算结果表明,该改进粒子群的方法对于不同维数的非线性函数具有很好的寻优效果.     

An improved hybrid firefly algorithm for capacitated vehicle routing problem

Firefly algorithm (FA) is a new meta-heuristic which is successfully applied to solve several optimization problems. However, it suffers from a drawback of easily getting stuck at local optima. This paper proposes a new hybrid FA, called CVRP-FA, to solve capacitated vehicle routing problem. In CVRP-FA, FA is integrated with two types of local search and genetic operators to enhance the solution’s quality and accelerate the convergence. The experiments are conducted over 82 benchmark instances. The results demonstrate that CVRP-FA has fast convergence rate and high computational accuracy. It significantly outperforms the other state-of-the-art FA variants in majority of the tested instances.     

Profit maximization of TSP through a hybrid algorithm

Here a new model of Traveling Salesman Problem (TSP) with uncertain parameters is formulated and solved using a hybrid algorithm. For this TSP, there are some fixed number of cities and the costs and time durations for traveling from one city to another are known. Here a Traveling Salesman (TS) visits and spends some time in each city for selling the company’s product. The return and expenditure at each city are dependent on the time spent by the TS at that city and these are given in functional forms of t. The total time limit for the entire tour is fixed and known. Now, the problem for the TS is to identify a tour program and also to determine the stay time at each city so that total profit out of the system is maximum. Here the model is solved by a hybrid method combining the Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO). The problem is divided into two subproblems where ACO and PSO are used successively iteratively in a generation using one’s result for the other. Numerical experiments are performed to illustrate the models. Some behavioral studies of the models and convergences of the proposed hybrid algorithm with respect to iteration numbers and cost matrix sizes are presented.     

Comparison of genetic algorithm to particle swarm for constrained simulation-based optimization of a geothermal power plant

The performance of a genetic algorithm is compared with that of particle swarm optimization for the constrained, non-linear, simulation-based optimization of a double flash geothermal power plant. Particle swarm optimization converges to better (higher) objective function values. The genetic algorithm is shown to converge more quickly and more tightly, resulting in a loss of solution diversity. Particle swarm optimization obtains solutions within 0.1% and 0.5% of the best known optimum in significantly fewer objective function evaluations than the genetic algorithm.     

Genetic algorithm with advanced mechanisms applied to the protein structure prediction in a hydrophobic-polar model and cubic lattice

This paper presents a genetic algorithm applied to the protein structure prediction in a hydrophobic-polar model on a cubic lattice. The proposed genetic algorithm is extended with crowding, clustering, repair, local search and opposition-based mechanisms. The crowding is responsible for maintaining the good solutions to the end of the evolutionary process while the clustering is used to divide a whole population into a number of subpopulations that can locate different good solutions. The repair mechanism transforms infeasible solutions to feasible solutions that do not occupy the lattice point for more than one monomer. In order to improve convergence speed the algorithm uses local search. This mechanism improves the quality of conformations with the local movement of one or two consecutive monomers through the entire conformation. The opposition-based mechanism is introduced to transform conformations to the opposite direction. In this way the algorithm easily improves good solutions on both sides of the sequence. The proposed algorithm was tested on a number of well-known hydrophobic-polar sequences. The obtained results show that the mechanisms employed improve the algorithm's performance and that our algorithm is superior to other state-of-the-art evolutionary and swarm algorithms.     

一种混合粒子群优化算法的研究

结合粒子群优化算法和拟牛顿法的优点,提出了一种混合粒子群优化算法。该算法首先运行粒子群优化算法,到进化到一定程度时,把当代的最好点作为拟牛顿法的初始点,再利用拟牛顿法,对其进行二次优化。算法充分发挥了粒子群优化算法的全局搜索性和拟牛顿法的局部精细搜索性,同时也克服了粒子群算法后期搜索效率低和拟牛顿法对初始点敏感的缺陷。数值实验结果表明,该算法具有很高的收敛速度和求解精度。     

A hybrid algorithm based on particle swarm and chemical reaction optimization for multi-object problems

Over the past decade, the particle swarm optimization (PSO) has been an effective algorithm for solving single and multi-object optimization problems. Recently, the chemical reaction optimization (CRO) algorithm is emerging as a new algorithm used to efficiently solve single-object optimization.In this paper, we present HP-CRO (hybrid of PSO and CRO) a new hybrid algorithm for multi-object optimization. This algorithm has features of CRO and PSO, HP-CRO creates new molecules (particles) not only used by CRO operations as found in CRO algorithm but also by mechanisms of PSO. The balancing of CRO and PSO operators shows that the method can be used to avoid premature convergence and explore more in the search space.This paper proposes a model with modified CRO operators and also adding new saving molecules into the external population to increase the diversity. The experimental results of the HP-CRO algorithm compared to some meta-heuristics algorithms such as FMOPSO, MOPSO, NSGAII and SPEA2 show that there is improved efficiency of the HP-CRO algorithm for solving multi-object optimization problems.