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 authors in @cite_2 have shown that the differential evolution algorithm converges to better solutions when the initial population is created by using trained neural networks. The neural networks were trained successfully using the reinforcement learning method, by knowing only the fitness function of the class of optimization problems.
@cite_2
2021442909 2073240809 2023131636 2110988848
As one of the popular evolutionary algorithms, differential evolution (DE) shows outstanding convergence rate on continuous optimization problems. But prematurity probably still occurs in classical DE when using relatively small population, which is discussed in this paper. Considering that large population may significantly raise the computational effort, we propose a modified DE using smaller population (DESP) by introducing extra disturbance to its mutation operation. In addition, an adaptive adjustment scheme is designed to control the disturbance intensity according to the improvement during the evolution. To test the performance of DESP, two groups of experiments are conducted. The results show that DESP outperforms DE in terms of convergence rate and accuracy. Many real-world optimization problems are difficult to solve as they do not possess the nice mathematical properties required by the exact algorithms. Evolutionary algorithms are proven to be appropriate for such problems. In this paper, we propose an improved differential evolution algorithm that uses a mix of different mutation operators. In addition, the algorithm is empowered by a covariance adaptation matrix evolution strategy algorithm as a local search. To judge the performance of the algorithm, we have solved well-known benchmark as well as a variety of real-world optimization problems. The real-life problems were taken from different sources and disciplines. According to the results obtained, the algorithm shows a superior performance in comparison with other algorithms that also solved these problems. Evolutionary computation techniques have had limited capabilities in solving large-scale problems due to the large search space demanding large memory and much longer training times. In the work presented here, a genetic programming like rich encoding scheme has been constructed to identify building blocks of knowledge in a learning classifier system. The fitter building blocks from the learning system trained against smaller problems have been utilized in a higher complexity problem in the domain to achieve scalable learning. The proposed system has been examined and evaluated on four different Boolean problem domains: 1) multiplexer, 2) majority-on, 3) carry, and 4) even-parity problems. The major contribution of this paper is to successfully extract useful building blocks from smaller problems and reuse them to learn more complex large-scale problems in the domain, e.g., 135-bit multiplexer problem, where the number of possible instances is 2 135 ≈ 4 × 10 40 , is solved by reusing the extracted knowledge from the learned lower level solutions in the domain. Autonomous scaling is, for the first time, shown to be possible in learning classifier systems. It improves effectiveness and reduces the number of training instances required in large problems, but requires more time due to its sequential build-up of knowledge. Many real-world optimization problems have to be solved under the presence of uncertainties. A significant number of these uncertainty problems falls into the dynamic optimization category in which the fitness function varies through time. For this class of problems, an evolutionary algorithm is expected to perform satisfactorily in spite of different degrees and frequencies of change in the fitness landscape. In addition, the dynamic evolutionary algorithm should warrant an acceptable performance improvement to justify the additional computational cost. Effective reuse of previous evolutionary information is a must as it facilitates a faster convergence after a change has occurred. This paper proposes a new dynamic evolutionary algorithm that uses variable relocation to adapt already converged or currently evolving individuals to the new environmental condition. The proposed algorithm relocates those individuals based on their change in function value due to the change in the environment and the average sensitivities of their decision variables to the corresponding change in the objective space. The relocation occurs during the transient stage of the evolutionary process, and the algorithm reuses as much information as possible from the previous evolutionary history. As a result, the algorithm shows improved adaptation and convergence. The newly adapted population is shown to be fitter to the new environment than the original or most randomly generated population. The algorithm has been tested by several dynamic benchmark problems and has shown competitive results compared to some chosen state-of-the-art dynamic evolutionary approaches.