Chimeh, M.K., Heywood, P., Pennisi, M. et al. (2 more authors) (2019) Parallel pair-wise interaction for multi-agent immune systems modelling. In: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 03-06 Dec 2018, Madrid, Spain. IEEE , pp. 1367-1373. ISBN 9781538654897
Abstract
Agent Based Modelling (ABM), is an approach for modelling dynamic systems and studying complex and emergent behaviour. ABM approach is a very common technique in biological domain due to high demand for a large scale analysis tool to collect and interpret information to solve biological problems. However, simulating large scale cellular level models (i.e. large number of agents/entities) require a high degree of computational power which is achievable through parallel computing methods such as Graphics Processing Units (GPUs). The use of parallel approaches in ABMs is growing rapidly specifically when modelling in continuous space system (particle based). Parallel implementation of particle based simulation within continuum space where agents contain quantities of chemicals/substances is very challenging. Pair-wise interactions are different abstraction to continuous space (particle) models which is commonly used for immune system modelling. This paper describes an approach to parallelising the key component of biological and immune system models (pair-wise interactions) within an ABM model. Our performance results demonstrate the applicability of this method to a broader class of biological systems with the same type of cell interactions and that it can be used as the basis for developing complete immune system models on parallel hardware.
Metadata
Item Type: | Proceedings Paper |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works. Reproduced in accordance with the publisher's self-archiving policy. |
Keywords: | Agent Based Modeling; GPGPU; High Performance Computing; Cellular Modelling; Computational modelling; Parallel simulation; FLAME GPU |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Computer Science (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 27 Jan 2020 15:02 |
Last Modified: | 27 Jan 2020 15:39 |
Status: | Published |
Publisher: | IEEE |
Refereed: | Yes |
Identification Number: | 10.1109/BIBM.2018.8621404 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:155215 |