Flexible protein folding by ant colony optimization

Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

An intelligent manufacturing system for heat treatment scheduling

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This research is focused on the integration problem of process planning and scheduling in steel heat treatment operations environment using artificial intelligent techniques that are capable of dealing with such problems. This work addresses the issues involved in developing a suitable methodology for scheduling heat treatment operations of steel. Several intelligent algorithms have been developed for these propose namely, Genetic Algorithm (GA), Sexual Genetic Algorithm (SGA), Genetic Algorithm with Chromosome differentiation (GACD), Age Genetic Algorithm (AGA), and Mimetic Genetic Algorithm (MGA). These algorithms have been employed to develop an efficient intelligent algorithm using Algorithm Portfolio methodology. After that all the algorithms have been tested on two types of scheduling benchmarks. To apply these algorithms on heat treatment scheduling, a furnace model is developed for optimisation proposes. Furthermore, a system that is capable of selecting the optimal heat treatment regime is developed so the required metal properties can be achieved with the least energy consumption and the shortest time using Neuro-Fuzzy (NF) and Particle Swarm Optimisation (PSO) methodologies. Based on this system, PSO is used to optimise the heat treatment process by selecting different heat treatment conditions. The selected conditions are evaluated so the best selection can be identified. This work addresses the issues involved in developing a suitable methodology for developing an NF system and PSO for mechanical properties of the steel. Using the optimisers, furnace model and heat treatment system model, the intelligent system model is developed and implemented successfully. The results of this system were exciting and the optimisers were working correctly

Applying the big bang-big crunch metaheuristic to large-sized operational problems

In this study, we present an investigation of comparing the capability of a big bang-big crunch metaheuristic (BBBC) for managing operational problems including combinatorial optimization problems. The BBBC is a product of the evolution theory of the universe in physics and astronomy. Two main phases of BBBC are the big bang and the big crunch. The big bang phase involves the creation of a population of random initial solutions, while in the big crunch phase these solutions are shrunk into one elite solution exhibited by a mass center. This study looks into the BBBC’s effectiveness in assignment and scheduling problems. Where it was enhanced by incorporating an elite pool of diverse and high quality solutions; a simple descent heuristic as a local search method; implicit recombination; Euclidean distance; dynamic population size; and elitism strategies. Those strategies provide a balanced search of diverse and good quality population. The investigation is conducted by comparing the proposed BBBC with similar metaheuristics. The BBBC is tested on three different classes of combinatorial optimization problems; namely, quadratic assignment, bin packing, and job shop scheduling problems. Where the incorporated strategies have a greater impact on the BBBC's performance. Experiments showed that the BBBC maintains a good balance between diversity and quality which produces high-quality solutions, and outperforms other identical metaheuristics (e.g. swarm intelligence and evolutionary algorithms) reported in the literature

A memetic ant colony optimization algorithm for the dynamic travelling salesman problem

Copyright @ Springer-Verlag 2010.Ant colony optimization (ACO) has been successfully applied for combinatorial optimization problems, e.g., the travelling salesman problem (TSP), under stationary environments. In this paper, we consider the dynamic TSP (DTSP), where cities are replaced by new ones during the execution of the algorithm. Under such environments, traditional ACO algorithms face a serious challenge: once they converge, they cannot adapt efficiently to environmental changes. To improve the performance of ACO on the DTSP, we investigate a hybridized ACO with local search (LS), called Memetic ACO (M-ACO) algorithm, which is based on the population-based ACO (P-ACO) framework and an adaptive inver-over operator, to solve the DTSP. Moreover, to address premature convergence, we introduce random immigrants to the population of M-ACO when identical ants are stored. The simulation experiments on a series of dynamic environments generated from a set of benchmark TSP instances show that LS is beneficial for ACO algorithms when applied on the DTSP, since it achieves better performance than other traditional ACO and P-ACO algorithms.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/01 and Grant EP/E060722/02

HEDCOS: High Efficiency Dynamic Combinatorial Optimization System using Ant Colony Optimization algorithm

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonDynamic combinatorial optimization is gaining popularity among industrial practitioners due to the ever-increasing scale of their optimization problems and efforts to solve them to remain competitive. Larger optimization problems are not only more computationally intense to optimize but also have more uncertainty within problem inputs. If some aspects of the problem are subject to dynamic change, it becomes a Dynamic Optimization Problem (DOP). In this thesis, a High Efficiency Dynamic Combinatorial Optimization System is built to solve challenging DOPs with high-quality solutions. The system is created using Ant Colony Optimization (ACO) baseline algorithm with three novel developments. First, introduced an extension method for ACO algorithm called Dynamic Impact. Dynamic Impact is designed to improve convergence and solution quality by solving challenging optimization problems with a non-linear relationship between resource consumption and fitness. This proposed method is tested against the real-world Microchip Manufacturing Plant Production Floor Optimization (MMPPFO) problem and the theoretical benchmark Multidimensional Knapsack Problem (MKP). Second, a non-stochastic dataset generation method was introduced to solve the dynamic optimization research replicability problem. This method uses a static benchmark dataset as a starting point and source of entropy to generate a sequence of dynamic states. Then using this method, 1405 Dynamic Multidimensional Knapsack Problem (DMKP) benchmark datasets were generated and published using famous static MKP benchmark instances as the initial state. Third, introduced a nature-inspired discrete dynamic optimization strategy for ACO by modelling real-world ants’ symbiotic relationship with aphids. ACO with Aphids strategy is designed to solve discrete domain DOPs with event-triggered discrete dynamism. The strategy improved inter-state convergence by allowing better solution recovery after dynamic environment changes. Aphids mediate the information from previous dynamic optimization states to maximize initial results performance and minimize the impact on convergence speed. This strategy is tested for DMKP and against identical ACO implementations using Full-Restart and Pheromone-Sharing strategies, with all other variables isolated. Overall, Dynamic Impact and ACO with Aphids developments are compounding. Using Dynamic Impact on single objective optimization of MMPPFO, the fitness value was improved by 33.2% over the ACO algorithm without Dynamic Impact. MKP benchmark instances of low complexity have been solved to a 100% success rate even when a high degree of solution sparseness is observed, and large complexity instances have shown the average gap improved by 4.26 times. ACO with Aphids has also demonstrated superior performance over the Pheromone-Sharing strategy in every test on average gap reduced by 29.2% for a total compounded dynamic optimization performance improvement of 6.02 times. Also, ACO with Aphids has outperformed the Full-Restart strategy for large datasets groups, and the overall average gap is reduced by 52.5% for a total compounded dynamic optimization performance improvement of 8.99 times

Modeling of Biological Intelligence for SCM System Optimization

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms

Multi-objective optimization for time-based preventive maintenance within the transport network: a review

Preventive maintenance in transportation is essential not only to safeguard billions in business and infrastructure investment, but also to guarantee safety, reliability and efficacy within the network. Government, industry and society have been increasingly recognising the importance of keeping transport units condition well-preserved. The challenge, however, is to achieve optimal performance of the existing transport systems within acceptable costs, effective workforce use and minimum disruption. Those are generally conflicting objectives. Multi-objective optimisation approaches have served as powerful tools to assist stakeholders to properly deploy preventive maintenance in industry. In this study, we review the research conducted in the application of multi-objective optimisation for preventive maintenance in transport-related activities. We focus on time-based preventive maintenance for production, infrastructure, rail and energy providers. In our review, we are interested in aspects such as the types of problems addressed, the existing objectives, the approaches to solutions, and how the outcomes obtained support decision