Subset-Based Ant Colony Optimisation for the Discovery of Gene-Gene Interactions in Genome Wide Association Studies

In this paper an ant colony optimisation approach for the discovery of gene-gene interactions in genome-wide association study (GWAS) data is proposed. The subset-based approach includes a novel encoding mechanism and tournament selection to analyse full scale GWAS data consisting of hundreds of thousands of variables to discover associations between combinations of small DNA changes and Type II diabetes. The method is tested on a large established database from the Wellcome Trust Case Control Consortium and is shown to discover combinations that are statistically significant and biologically relevant within reasonable computational time.The work contained in this paper was supported by an EPSRC First Grant (EP/J007439/1). This study makes use of data generated by the Wellcome Trust Case Control Consortium. A full list of the inves- tigators who contributed to the generation of the data is available from http://www.wtccc.org.uk. Funding for the project was provided by the Wellcome Trust under award 076113

Hybridization of Biologically Inspired Algorithms for Discrete Optimisation Problems

In the field of Optimization Algorithms, despite the popularity of hybrid designs, not enough consideration has been given to hybridization strategies. This paper aims to raise awareness of the benefits that such a study can bring. It does this by conducting a systematic review of popular algorithms used for optimization, within the context of Combinatorial Optimization Problems. Then, a comparative analysis is performed between Hybrid and Base versions of the algorithms to demonstrate an increase in optimization performance when hybridization is employed

Genetic Programming to Optimise 3D Trajectories

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial TechnologiesTrajectory optimisation is a method of finding the optimal route connecting a start and end point. The suitability of a trajectory depends on non-intersection with any obstacles as well as predefined performance metrics. In the context of UAVs, the goal is to minimise the cost of the route, in terms of energy or time, while avoiding restricted flight zones. Artificial intelligence techniques including evolutionary computation have been applied to trajectory optimisation with various degrees of success. This thesis explores the use of genetic programming (GP) to optimise trajectories in 3D space, by encoding 3D geographic trajectories as syntax trees representing a curve. A comprehensive review of the relevant literature is presented, covering the theory and techniques of GP, as well as the principles and challenges of 3D trajectory optimisation. The main contribution of this work is the development and implementation of a novel GP algorithm using function trees to encode 3D geographical trajectories. The trajectories are validated and evaluated using a realworld dataset and multiple objectives. The results demonstrate the effectiveness of the proposed algorithm, which outperforms existing methods in terms of speed, automaticity, and robustness. Finally, insights and recommendations for future research in this area are provided, highlighting the potential for GP to be applied to other complex optimisation problems in engineering and science

The multiple pheromone Ant clustering algorithm

Ant Colony Optimisation algorithms mimic the way ants use pheromones for marking paths to important locations. Pheromone traces are followed and reinforced by other ants, but also evaporate over time. As a consequence, optimal paths attract more pheromone, whilst the less useful paths fade away. In the Multiple Pheromone Ant Clustering Algorithm (MPACA), ants detect features of objects represented as nodes within graph space. Each node has one or more ants assigned to each feature. Ants attempt to locate nodes with matching feature values, depositing pheromone traces on the way. This use of multiple pheromone values is a key innovation. Ants record other ant encounters, keeping a record of the features and colony membership of ants. The recorded values determine when ants should combine their features to look for conjunctions and whether they should merge into colonies. This ability to detect and deposit pheromone representative of feature combinations, and the resulting colony formation, renders the algorithm a powerful clustering tool. The MPACA operates as follows: (i) initially each node has ants assigned to each feature; (ii) ants roam the graph space searching for nodes with matching features; (iii) when departing matching nodes, ants deposit pheromones to inform other ants that the path goes to a node with the associated feature values; (iv) ant feature encounters are counted each time an ant arrives at a node; (v) if the feature encounters exceed a threshold value, feature combination occurs; (vi) a similar mechanism is used for colony merging. The model varies from traditional ACO in that: (i) a modified pheromone-driven movement mechanism is used; (ii) ants learn feature combinations and deposit multiple pheromone scents accordingly; (iii) ants merge into colonies, the basis of cluster formation. The MPACA is evaluated over synthetic and real-world datasets and its performance compares favourably with alternative approaches

Exact and heuristic approaches for multi-component optimisation problems

Modern real world applications are commonly complex, consisting of multiple subsystems that may interact with or depend on each other. Our case-study about wave energy converters (WEC) for the renewable energy industry shows that in such a multi-component system, optimising each individual component cannot yield global optimality for the entire system, owing to the influence of their interactions or the dependence on one another. Moreover, modelling a multi-component problem is rarely easy due to the complexity of the issues, which leads to a desire for existent models on which to base, and against which to test, calculations. Recently, the travelling thief problem (TTP) has attracted significant attention in the Evolutionary Computation community. It is intended to offer a better model for multicomponent systems, where researchers can push forward their understanding of the optimisation of such systems, especially for understanding of the interconnections between the components. The TTP interconnects with two classic NP-hard problems, namely the travelling salesman problem and the 0-1 knapsack problem, via the transportation cost that non-linearly depends on the accumulated weight of items. This non-linear setting introduces additional complexity. We study this nonlinearity through a simplified version of the TTP - the packing while travelling (PWT) problem, which aims to maximise the total reward for a given travelling tour. Our theoretical and experimental investigations demonstrate that the difficulty of a given problem instance is significantly influenced by adjusting a single parameter, the renting rate, which prompted our method of creating relatively hard instances using simple evolutionary algorithms. Our further investigations into the PWT problem yield a dynamic programming (DP) approach that can solve the problem in pseudo polynomial time and a corresponding approximation scheme. The experimental investigations show that the new approaches outperform the state-of-the-art ones. We furthermore propose three exact algorithms for the TTP, based on the DP of the PWT problem. By employing the exact DP for the underlying PWT problem as a subroutine, we create a novel indicator-based hybrid evolutionary approach for a new bi-criteria formulation of the TTP. This hybrid design takes advantage of the DP approach, along with a number of novel indicators and selection mechanisms to achieve better solutions. The results of computational experiments show that the approach is capable to outperform the state-of-the-art results.Thesis (Ph.D.) -- University of Adelaide, School of Computer Science, 201

Power transmission planning using heuristic optimisation techniques: Deterministic crowding genetic algorithms and Ant colony search methods

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The goal of transmission planning in electric power systems is a robust network which is economical, reliable, and in harmony with its environment taking into account the inherent uncertainties. For reasons of practicality, transmission planners have normally taken an incremental approach and tended to evaluate a relatively small number of expansion alternatives over a relatively short time horizon. In this thesis, two new planning methodologies namely the Deterministic Crowding Genetic Algorithm and the Ant Colony System are applied to solve the long term transmission planning problem. Both optimisation techniques consider a 'green field' approach, and are not constrained by the existing network design. They both identify the optimal transmission network over an extended time horizon based only on the expected pattern of electricity demand and generation sources. Two computer codes have been developed. An initial comparative investigation of the application of Ant Colony Optimisation and a Genetic Algorithm to an artificial test problem has been undertaken. It was found that both approaches were comparable for the artificial test problem.EPRSC and National Grid Company pl

Ant algorithm hyperheuristic approaches for scheduling problems

For decades, optimisation research has investigated methods to find optimal solutions to many problems in the fields of scheduling, timetabling and rostering. A family of abstract methods known as metaheuristics have been developed and applied to many of these problems, but their application to specific problems requires problem-specific coding and parameter adjusting to produce the best results for that problem. Such specialisation makes code difficult to adapt to new problem instances or new problems. One methodology that intended to increase the generality of state of the art algorithms is known as hyperheuristics. Hyperheuristics are algorithms which construct algorithms: using "building block" heuristics, the higher-level algorithm chooses between heuristics to move around the solution space, learning how to use the heuristics to find better solutions. We introduce a new hyperheuristic based upon the well-known ant algorithm metaheuristic, and apply it towards several real-world problems without parameter tuning, producing results that are competitive with other hyperheuristic methods and established bespoke metaheuristic techniques