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

Exploring the correlation between the folding rates of proteins and the entanglement of their native states

The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids which are in contact. Here we argue that folding kinetics can be influenced also by the entanglement that loops may undergo within the overall three dimensional protein structure. In order to explore such possibility, we introduce a novel descriptor, which we call "maximum intrachain contact entanglement". Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the $C_{\alpha}$ atoms. By analyzing experimental data sets of two-state and multistate folders, we show that also the new index is a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.Comment: 8 figures. v2: new titl

Using a unified measure function for heuristics, discretization, and rule quality evaluation in Ant-Miner

Ant-Miner is a classification rule discovery algorithm that is based on Ant Colony Optimization (ACO) meta-heuristic. cAnt-Miner is the extended version of the algorithm that handles continuous attributes on-the-fly during the rule construction process, while ?Ant-Miner is an extension of the algorithm that selects the rule class prior to its construction, and utilizes multiple pheromone types, one for each permitted rule class. In this paper, we combine these two algorithms to derive a new approach for learning classification rules using ACO. The proposed approach is based on using the measure function for 1) computing the heuristics for rule term selection, 2) a criteria for discretizing continuous attributes, and 3) evaluating the quality of the constructed rule for pheromone update as well. We explore the effect of using different measure functions for on the output model in terms of predictive accuracy and model size. Empirical evaluations found that hypothesis of different functions produce different results are acceptable according to Friedman’s statistical test