This paper presents a two-level protein folding optimization on a three-dimensional AB off-lattice model. The first level is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid positions. These conformations are forwarded to the second level, where an accurate search is performed with the aim of locating conformations with the best energy value. The optimization process switches between these two levels until the stopping condition is satisfied. An auxiliary fitness function was designed for the first level, while the original fitness function is used in the second level. The auxiliary fitness function includes expression about the quality of the hydrophobic core. This expression is crucial for leading the search process to the promising solutions that have a good hydrophobic core and, consequently, improves the efficiency of the whole optimization process. Our differential evolution algorithm was used for demonstrating the efficiency of the two-level optimization. It was analyzed on well-known amino acid sequences that are used frequently in the literature. The obtained experimental results show that the employed two-level optimization improves the efficiency of our algorithm significantly, and that the proposed algorithm is superior to other state-of-the-art algorithms.
The algorithm that combines the particle swarm optimization, genetic algorithm, and tabu search was presented in @cite_30 . Within this algorithm, the particle swarm optimization is used to generate an initial solution that is not too random, and the factor of stochastic disturbance is adopted to improve the ability of global search. The genetic algorithm was used to generate local optima in order to speed up the convergence of the algorithm, while the tabu search is used with a mutation operator to locate the global optimum.
@cite_30
2087760458 2017565019 2121957462 2111065664
A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. This paper considers a new variant of the two-dimensional bin packing problem where each rectangle is assigned a due date and each bin has a fixed processing time. Hence the objective is not only to minimize the number of bins, but also to minimize the maximum lateness of the rectangles. This problem is motivated by the cutting of stock sheets and the potential increased efficiency that might be gained by drawing on a larger pool of demand pieces by mixing orders, while also aiming to ensure a certain level of customer service. We propose a genetic algorithm for searching the solution space, which uses a new placement heuristic for decoding the gene based on the best fit heuristic designed for the strip packing problems. The genetic algorithm employs an innovative crossover operator that considers several different children from each pair of parents. Further, the dual objective is optimized hierarchically with the primary objective periodically alternating between maximum lateness and number of bins. As a result, the approach produces several non-dominated solutions with different trade-offs. Two further approaches are implemented. One is based on a previous Unified Tabu Search, suitably modified to tackle this revised problem. The other is randomized descent and serves as a benchmark for comparing the results. Comprehensive computational results are presented, which show that the Unified Tabu Search still works well in minimizing the bins, but the genetic algorithm performs slightly better. When also considering maximum lateness, the genetic algorithm is considerably better. This paper presents a new algorithm based on integrating genetic algorithms, tabu search and simulated annealing methods to solve the unit commitment problem. The core of the proposed algorithm is based on genetic algorithms. Tabu search is used to generate new population members in the reproduction phase of the genetic algorithm. A simulated annealing method is used to accelerate the convergence of the genetic algorithm by applying the simulated annealing test for all the population members. A new implementation of the genetic algorithm is introduced. The genetic algorithm solution is coded as a mix between binary and decimal representation. The fitness function is constructed from the total operating cost of the generating units without penalty terms. In the tabu search part of the proposed algorithm, a simple short-term memory procedure is used to counter the danger of entrapment at a local optimum, and the premature convergence of the genetic algorithm. A simple cooling schedule has been implemented to apply the simulated annealing test in the algorithm. Numerical results showed the superiority of the solutions obtained compared to genetic algorithms, tabu search and simulated annealing methods, and to two exact algorithms. This paper proposes an evolutionary-group-based particle-swarm-optimization (EGPSO) algorithm for fuzzy-controller (FC) design. The EGPSO uses a group-based framework to incorporate crossover and mutation operations into particle-swarm optimization. The EGPSO dynamically forms different groups to select parents in crossover operations, particle updates, and replacements. An adaptive velocity-mutated operation (AVMO) is incorporated to improve search ability. The EGPSO is applied to design all of the free parameters in a zero-order Takagi-Sugeno-Kang (TSK)-type FC. The objective of EGPSO is to improve fuzzy-control accuracy and design efficiency. Comparisons with different population-based optimizations of fuzzy-control problems demonstrate the superiority of EGPSO performance. In particular, the EGPSO-designed FC is applied to mobile-robot navigation in unknown environments. In this application, the robot learns to follow object boundaries through an EGPSO-designed FC. A simple learning environment is created to build this behavior without an exhaustive collection of input-output training pairs in advance. A behavior supervisor is proposed to combine the boundary-following behavior and the target-seeking behavior for navigation, and the problem of dead cycles is considered. Successful mobile-robot navigation in simulation and real environments verifies the EGPSO-designed FC-navigation approach.