83 research outputs found

    Maximising overlap score in DNA sequence assembly problem by Stochastic Diffusion Search

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    This paper introduces a novel study on the performance of Stochastic Diffusion Search (SDS)—a swarm intelligence algorithm—to address DNA sequence assembly problem. This is an NP-hard problem and one of the primary problems in computational molecular biology that requires optimisation methodologies to reconstruct the original DNA sequence. In this work, SDS algorithm is adapted for this purpose and several experiments are run in order to evaluate the performance of the presented technique over several frequently used benchmarks. Given the promising results of the newly proposed algorithm and its success in assembling the input fragments, its behaviour is further analysed, thus shedding light on the process through which the algorithm conducts the task. Additionally, the algorithm is applied to overlap score matrices which are generated from the raw input fragments; the algorithm optimises the overlap score matrices to find better results. In these experiments real-world data are used and the performance of SDS is compared with several other algorithms which are used by other researchers in the field, thus demonstrating its weaknesses and strengths in the experiments presented in the paper

    The mining game: a brief introduction to the Stochastic Diffusion Search metaheuristic

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    Generative Music with Stochastic Diffusion Search

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    Exploration and exploitation zones in a minimalist swarm optimiser

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    The trade off between exploration and exploitation is one of the key challenges in evolutionary and swarm optimisers which are led by guided and stochastic search. This work investigates the exploration and exploitation balance in a minimalist swarm optimiser in order to offer insights into the population’s behaviour. The minimalist and vector-stripped nature of the algorithm—dispersive flies optimisation or DFO—reduces the challenges of understanding particles’ oscillation around constantly changing centres, their influence on one another, and their trajectory. The aim is to examine the population’s dimensional behaviour in each iteration and each defined exploration-exploitation zone, and to subsequently offer improvements to the working of the optimiser. The derived variants, titled unified DFO or uDFO, are successfully applied to an extensive set of test functions, as well as high-dimensional tomographic reconstruction, which is an important inverse problem in medical and industrial imaging

    Creative or Not? Birds and Ants Draw with Muscle

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    In this work, a novel approach of merging two swarm intelligence algorithms is considered – one mimicking the behaviour of ants foraging (Stochastic Diffusion Search [5]) and the other algorithm simulating the behaviour of birds flocking (Particle Swarm Optimisation [17]). This hybrid algorithm is assisted by a mechanism inspired from the behaviour of skeletal muscles activated by motor neurons. The operation of the swarm intelligence algorithms is first introduced via metaphor before the new hybrid algorithm is defined. Next, the novel behaviour of the hybrid algorithm is reflected through a cooperative attempt to make a drawing, followed by a discussion about creativity in general and the ’computational creativity’ of the swarm

    Penguins Huddling Optimisation

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    Cooperation of Nature and Physiologically Inspired Mechanism in Visualisation

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    A novel approach of integrating two swarm intelligence algorithms is considered, one simulating the behaviour of birds flocking (Particle Swarm Optimisation) and the other one (Stochastic Diffusion Search) mimics the recruitment behaviour of one species of ants – Leptothorax acervorum. This hybrid algorithm is assisted by a biological mechanism inspired by the behaviour of blood flow and cells in blood vessels, where the concept of high and low blood pressure is utilised. The performance of the nature-inspired algorithms and the biologically inspired mechanisms in the hybrid algorithm is reflected through a cooperative attempt to make a drawing on the canvas. The scientific value of the marriage between the two swarm intelligence algorithms is currently being investigated thoroughly on many benchmarks and the results reported suggest a promising prospect (al-Rifaie, Bishop & Blackwell, 2011). We also discuss whether or not the ‘art works’ generated by nature and biologically inspired algorithms can possibly be considered as ‘computationally creative’
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