- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Submit a Manuscript
- Subscription Information
- Table of Contents
ISRN Artificial Intelligence
Volume 2012 (2012), Article ID 365791, 13 pages
Optimization of Swarm-Based Simulations
1Department of Computer Science, Faculty of Science, University of Calgary, Calgary, AB, Canada T2N 1N4
2Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, Canada T2N 1N4
Received 14 March 2012; Accepted 8 April 2012
Academic Editors: F. Camastra, K. W. Chau, and K. Rasheed
Copyright © 2012 Sebastian von Mammen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. von Neumann and A. W. Burks, Theory of Self-Reproducing Automata, University of Illinois Press, London, UK, 1966.
- S. A. Kauffman, “Metabolic stability and epigenesis in randomly constructed genetic nets,” Journal of Theoretical Biology, vol. 22, no. 3, pp. 437–467, 1969.
- S. A. Kauffman, The Origins of Order, Oxford University, New York, NY, USA, 1993.
- S. Wolfram, A New Kind of Science, Wolfram Media, Champaign, Ill, USA, 2002.
- M. F. Horstemeyer, “Multiscale modeling: a review,” Practical Aspects of Computational Chemistry, pp. 87–135, 2010.
- T. Eissing, L. Kuepfer, C. Becker et al., “A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks,” Frontiers in Physiology, vol. 2, no. 4, pp. 1–10, 2011.
- J. Beal, “Functional blueprints: an approach to modularity in grown systems,” in Proceedings of the ANTS 2010: 7th International Conference on Swarm Intelligence, pp. 179–190, Springer, 2010.
- J. Werfel, “Biologically realistic primitives for engineered morphogenesis,” in Proceedings of the ANTS 2010: 7th International Conference on Swarm Intelligence, pp. 131–141, Springer, 2010.
- I. Salazar-Ciudad and J. Jernvall, “A computational model of teeth and the developmental origins of morphological variation,” Nature, vol. 464, no. 7288, pp. 583–586, 2010.
- S. von Mammen, D. Phillips, T. Davison, H. Jamniczky, B. Hallgrmsson, and C. Jacob, “Swarm-based computational development,” in Morphogenetic Engineering, Springer.
- J. Klein, “Breve: a 3D environment for the simulation of decentralized systems and artificial life,” in Proceedings of the 8th International Conference on Artificial life, pp. 329–334, MIT Press, 2002.
- C. Huepe and M. Aldana, “New tools for characterizing swarming systems: a comparison of minimal models,” Physica A, vol. 387, no. 12, pp. 2809–2822, 2008.
- C. W. Reynolds, “Flocks, herds, and schools: a distributed behavioral model,” in Proceedings of the SIGGRAPH '87 Conference, vol. 4, pp. 25–34, Anaheim, Calif, USA, 1987.
- I. Derényi and T. Vicsek, “Cooperative transport of brownian particles,” Physical Review Letters, vol. 75, no. 3, pp. 374–377, 1995.
- A. Czirók and T. Vicsek, “Collective behavior of interacting self-propelled particles,” Physica A, vol. 281, no. 1, pp. 17–29, 2000.
- T. Vicsek and A. Zafiris, “Collective motion,” Reviews of Modern Physics. In press.
- E. Bonabeau, M. Dorigo, and G. Theraulaz, Swarm Intelligence: From Natural to Artificial Systems, Santa Fe Institute Studies in the Sciences of Complexity Oxford University Press, New York, NY, USA, 1999.
- S. Camazine, J.-L. Deneubourg, N. R. Franks, J. Sneyd, G. Theraulaz, and E. Bonabeau, Self-Organization in Biological Systems, Princeton Studies in Complexity, Princeton University Press, Princeton, NJ, USA, 2003.
- J. Kennedy, R. C. Eberhart, and Y. Shi, Swarm Intelligence, The Morgan Kaufmann Series in Evolutionary Computation, Morgan Kaufmann, San Francisco, Calif, USA, 2001.
- M. Dorigo, V. Maniezzo, and A. Colorni, “Ant system: optimization by a colony of cooperating agents,” IEEE Transactions on Systems, Man, and Cybernetics B, vol. 26, no. 1, pp. 29–41, 1996.
- M. Pilat, “Wasp-inspired construction algortihms,” Tech. Rep., University of Calgary, 2004.
- P. Prusinkiewicz and A. Lindenmayer, The Algorithmic Beauty of Plants, Springer, 1996.
- C. J. Jacob, G. Hushlak, J. E. Boyd, P. Nuytten, M. Sayles, and M. Pilat, “SwarmArt: interactive art from swarm intelligence,” Leonardo, vol. 40, no. 3, pp. 248–254, 2007.
- H. Kwong and C. Jacob, “Evolutionary exploration of dynamic swarm behaviour,” in Proceedings of the Evolutionary Computation, IEEE Press, Canberra, Australia, 2003.
- S. Von Mammen and C. Jacob, “Genetic swarm grammar programming: ecological breeding like a gardener,” in Proceedings of the IEEE Congress on Evolutionary Computation (CEC '07), pp. 851–858, Singapore, September 2007.
- S. Von Mammen and C. Jacob, “The evolution of swarm grammars- growing trees, crafting art, and bottom-up design,” IEEE Computational Intelligence Magazine, vol. 4, no. 3, pp. 10–19, 2009.
- A. Esmaeili and C. Jacob, “A multi-objective differential evolutionary approach toward more stable gene regulatory networks,” BioSystems, vol. 98, no. 3, pp. 127–136, 2009.
- D. Andre, F. H. Bennett III, and J. R. Koza, “Discovery by genetic programming of a cellular automata rule that is better than any known rule for the majority classification problem,” in Proceedings of the 1st Annual Conference on Genetic Programming, pp. 3–11, MIT Press, Stanford University, Palo Alto, Calif, USA, 1996.
- C. Jacob, Illustrating Evolutionary Computation with Mathematica, Morgan Kaufmann, San Francisco, Calif, USA, 2001.
- V. Sarpe, A. Esmaeili, I. Yazdanbod, T. Kubik, M. Richter, and C. Jacob, “Parametric evolution of a bacterial signalling system formalized by membrane computing,” in Proceedings of the IEEE Congress on Evolutionary Computation (CEC '10), IEEE Press, Barcelona, Spain, July 2010.
- N. Minar, R. Burkhart, C. Langton, and M. Askenazi, “The swarm simulation system: a toolkit for building multi-agent simulations,” Tech. Rep., Santa Fe Institute, Santa Fe, NM, USA, 1996.
- S. Rasmussen, N. A. Baas, B. Mayer, M. Nilsson, and M. W. Olesen, “Ansatz for dynamical hierarchies,” Artificial Life, vol. 7, no. 4, pp. 329–353, 2001.
- A. Dorin and J. McCormack, “Self-assembling dynamical hierarchies,” in Proceedings of the 8th International Conference on Artificial Life, p. 423, 2003.
- J. L. Dessalles and D. Phan, “Emergence in multi-agent systems: cognitive hierarchy, detection, and complexity reduction part I: methodological issues,” Artificial Economics, vol. 564, pp. 147–160, 2006.
- J. Denzinger and J. Hamdan, “Improving observation-based modeling of other agents using tentative stereotyping and compactification through kd-tree structuring,” Web Intelligence and Agent Systems, vol. 4, no. 3, pp. 255–270, 2006.
- C. Lavelle, H. Berry, G. Beslon et al., “From Molecules to organisms: towards multiscale integrated models of biological systems,” Theoretical Biology Insights, vol. 1, pp. 13–22, 2008.
- S. von Mammen and C. Jacob, “Swarming for games: immersion in complex systems,” in Proceedings of the Applications of Evolutionary Computing Part II, Lecture Notes in Computer Science, pp. 293–302, Springer, Tübingen, Germany, 2009.
- C. W. Reynolds, “Flocks, herds, and schools: a distributed behavioral model,” Computer Graphics, vol. 21, no. 4, pp. 25–34, 1987.
- S. Von Mammen, C. Jacob, and G. Kókai, “Evolving swarms that build 3D structures,” in Proceedings of the IEEE Congress on Evolutionary Computation (CEC '05), pp. 1434–1441, IEEE Press, Edinburgh, UK, September 2005.
- S. von Mammen, Evolving Artificial Constructive Swarms—Experimental Models and Methodologies, VDM, Saarbrucken, Germany, 2008.
- I. Burleigh, “Vigo::3d: a framework for simulating and visualizing of threedimensional scenes,” October 2008, http://vigo.sourceforge.net/docs/.
- S. von Mammen and C. Jacob, “The spatiality of swarms—quantitative analysis of dynamic interaction networks,” in Proceedings of the Artificial Life XI, pp. 662–669, MIT Press, Winchester, UK, 2008.
- A. J. Lotka, “Contribution to the theory of periodic reactions,” Journal of Physical Chemistry, vol. 14, no. 3, pp. 271–274, 1910.
- V. Volterra, “Variazioni e fluttuazioni del numero d'individui in specie animali conviventi,” Atti della R. Accademia Nazionale dei Lincei. Memorie della Classe di Scienze Fisiche, vol. 2, pp. 31–113, 1926.
- E. Keogh, S. Chu, D. Hart, and M. Pazzani, “An online algorithm for segmenting time series,” in Proceedings of the 1st IEEE International Conference on Data Mining (ICDM '01), pp. 289–296, IEEE Computer Society, Washington, DC, USA, December 2001.
- H. Sakoe and S. Chiba, “Dynamic programming algorithm optimization for spoken word recognition,” IEEE Transactions on Acoustics, Speech, and Signal Processing, vol. 26, no. 1, pp. 43–49, 1978.
- D. J. Berndt and J. Clifford, “Using dynamic time warping to find patterns in time series,” in Proceedings of the AAAI-94 Worshop on Knowledge Discovery in Databases (KDD '94), pp. 359–370, 1994.
- J. Kennedy and R. Eberhart, “Particle swarm optimization,” in Proceedings of the IEEE International Conference on Neural Networks, vol. 4, pp. 1942–1948, December 1995.
- F. Azuajeu, “Computational discrete models of tissue growth and regeneration,” Briefings in Bioinformatics, vol. 12, no. 1, Article ID bbq017, pp. 64–77, 2011.
- S. von Mammen, J.-P. Steghöfer, J. Denzinger, and C. Jacob, “Self-organized middle-out abstraction,” in Self-Organizing Systems, C. Bettstetter and C. Gershenson, Eds., Lecture Notes in Computer Science, pp. 26–31, Springer, Karslruhe, Germany, 6557 edition, 2011.
- A. S. Shirazi, S. von Mammen, and C. Jacob, “Adaptive modularization of the MAPK signaling pathway using the multiagent paradigm,” in Proceedings of the 11th International Conference on Parallel Problem Solving from Nature: Part II (PPSN '10), vol. 6239, pp. 401–410, IEEE Press, Department of Computer Science, Faculty of Science, University of Calgary, Canada, September 2010.
- C. Y. F. Huang and J. E. Ferrell, “Ultrasensitivity in the mitogen-activated protein kinase cascade,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 19, pp. 10078–10083, 1996.
- B. N. Kholodenko, “Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades,” European Journal of Biochemistry, vol. 267, no. 6, pp. 1583–1588, 2000.
- A. S. Shirazi, S. von Mammen, and C. Jacob, “Hierarchical self-organized learning in agent-based modeling of the MAPK signaling pathway,” in Proceedings of the IEEE Congress on Evolutionary Computation (CEC '11), pp. 2245–2251, June 2011.
- J. B. MacQueen, “Some methods for classification and analysis of MultiVariate observations,” in Proceedings of the 5th Berkeley Symposium on Mathematical Statistics and Probability, L. M. Le Cam and J. Neyman, Eds., vol. 1, pp. 281–297, University of California Press, 1967.