A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media

We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in $D$ dimensions. Within this representation we can easily track the evolution in the configuration space of the alignment through local moves of low computational cost. At variance with other probabilistic algorithms proposed to solve this problem, our approach allows for the creation and deletion of gaps without extra computational cost. The algorithm was tested aligning proteins from the kinases family. When D=3 the results are consistent with those obtained using a complete algorithm. For $D>3$ where the complete algorithm fails, we show that our algorithm still converges to reasonable alignments. Moreover, we study the space of solutions obtained and show that depending on the number of sequences aligned the solutions are organized in different ways, suggesting a possible source of errors for progressive algorithms.Comment: 7 pages and 11 figure

Improving the multi-objective evolutionary optimization algorithm for hydropower reservoir operations in the California Oroville-Thermalito complex

This study demonstrates the application of an improved Evolutionary optimization Algorithm (EA), titled Multi-Objective Complex Evolution Global Optimization Method with Principal Component Analysis and Crowding Distance Operator (MOSPD), for the hydropower reservoir operation of the Oroville-Thermalito Complex (OTC) - a crucial head-water resource for the California State Water Project (SWP). In the OTC's water-hydropower joint management study, the nonlinearity of hydropower generation and the reservoir's water elevation-storage relationship are explicitly formulated by polynomial function in order to closely match realistic situations and reduce linearization approximation errors. Comparison among different curve-fitting methods is conducted to understand the impact of the simplification of reservoir topography. In the optimization algorithm development, techniques of crowding distance and principal component analysis are implemented to improve the diversity and convergence of the optimal solutions towards and along the Pareto optimal set in the objective space. A comparative evaluation among the new algorithm MOSPD, the original Multi-Objective Complex Evolution Global Optimization Method (MOCOM), the Multi-Objective Differential Evolution method (MODE), the Multi-Objective Genetic Algorithm (MOGA), the Multi-Objective Simulated Annealing approach (MOSA), and the Multi-Objective Particle Swarm Optimization scheme (MOPSO) is conducted using the benchmark functions. The results show that best the MOSPD algorithm demonstrated the best and most consistent performance when compared with other algorithms on the test problems. The newly developed algorithm (MOSPD) is further applied to the OTC reservoir releasing problem during the snow melting season in 1998 (wet year), 2000 (normal year) and 2001 (dry year), in which the more spreading and converged non-dominated solutions of MOSPD provide decision makers with better operational alternatives for effectively and efficiently managing the OTC reservoirs in response to the different climates, especially drought, which has become more and more severe and frequent in California

Research on the time optimization model algorithm of Customer Collaborative Product Innovation

Purpose: To improve the efficiency of information sharing among the innovation agents of customer collaborative product innovation and shorten the product design cycle, an improved genetic annealing algorithm of the time optimization was presented. Design/methodology/approach: Based on the analysis of the objective relationship between the design tasks, the paper takes job shop problems for machining model and proposes the improved genetic algorithm to solve the problems, which is based on the niche technology and thus a better product collaborative innovation design time schedule is got to improve the efficiency. Finally, through the collaborative innovation design of a certain type of mobile phone, the proposed model and method were verified to be correct and effective. Findings and Originality/value: An algorithm with obvious advantages in terms of searching capability and optimization efficiency of customer collaborative product innovation was proposed. According to the defects of the traditional genetic annealing algorithm, the niche genetic annealing algorithm was presented. Firstly, it avoided the effective gene deletions at the early search stage and guaranteed the diversity of solution; Secondly, adaptive double point crossover and swap mutation strategy were introduced to overcome the defects of long solving process and easily converging local minimum value due to the fixed crossover and mutation probability; Thirdly, elite reserved strategy was imported that optimal solution missing was avoided effectively and evolution speed was accelerated. Originality/value: Firstly, the improved genetic simulated annealing algorithm overcomes some defects such as effective gene easily lost in early search. It is helpful to shorten the calculation process and improve the accuracy of the convergence value. Moreover, it speeds up the evolution and ensures the reliability of the optimal solution. Meanwhile, it has obvious advantages in efficiency of information sharing among the innovation agents of customer collaborative product innovation. So, the product design cycle could be shortened.Peer Reviewe