Robustness and Adaptation in Morphogenetic Collective Systems
Project Website
This project was supported by the NSF Robust Intelligence Program (Award #: NSF IIS-1319152).
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
About the Project
The objective of this project was to understand the roles of general morphogenetic principles such as heterogeneity of components, differentiation/re-differentiation of components, and local information exchange among components in the self-organization of biological collectives, and to utilize them to improve the performance of collective artificial systems. The research was conducted on the following four subtasks: (1) Study the effects of morphogenetic principles on self-organizing patterns of heterogeneous collectives using mathematical/computational models. (2) Apply the results of theoretical investigation to construct models of actual self-organizing patterns found in real-world heterogeneous biological collectives. (3) Introduce the morphogenetic principles to existing collective artificial systems and develop mechanisms for programming their structures and behaviors. (4) Measure the overall performance of the proposed morphogenetic collective systems in decentralized optimization and exploration tasks. This research contributes to biology and ecology by providing new theoretical insight into how heterogeneous collectives may self-organize without centralized control, and also to computational science and engineering by bringing an unexplored combination of morphogenetic principles into bio-inspired computational systems. This project has produced societal impacts by providing a novel framework for the design of growing, self-organizing, self-repairing, and evolving artifacts. This project involved the following educational activities: (1) Integration of project outcomes into courses offered through the interdisciplinary graduate certificate program in complex systems science at Binghamton University. (2) Regional high school research program. (3) Public exhibition of morphogenetic collective systems through online videos and simulation software.
Research Team
Principal investigator
- Hiroki Sayama, D.Sc. (PI; Professor, Department of Systems Science and Industrial Engineering)
Graduate Students
- Xinpei Ma (PhD in Systems Science, graduated)
- Hyobin Kim (PhD candidate in Systems Science)
- Farnaz Zamani Esfahlani (PhD candidate in Systems Science)
- Jeffrey Schmidt (PhD candidate in Systems Science)
- Ali Jazayeri (graduate student, Drexel University)
Collaborators
- René Doursat, Ph.D. (Research Scientist, CNRS/Ecole Polytechnique, France)
- J. Scott Turner, Ph.D. (Professor of Biology, SUNY-ESF, NY)
Publications
Journal Articles
- Hyobin Kim and Hiroki Sayama, How criticality of gene regulatory networks affects the resulting morphogenesis under genetic perturbations, Artificial Life, 24(2), 85-105, 2018. Abstract/PDF Preprint
- Hyobin Kim and Hiroki Sayama, The role of criticality of gene regulatory networks in morphogenesis, IEEE Transactions on Cognitive and Developmental Systems, accepted pending revisions. Preprint
- Xinpei Ma and Hiroki Sayama, Hierarchical heterogeneous particle swarm optimization: Algorithms and evaluations, International Journal of Parallel, Emergent and Distributed Systems, 31, 504-516, 2016. Abstract/PDF
- Xinpei Ma, Chun-An Chou, Hiroki Sayama, and Wanpracha Art Chaovalitwongse, Brain response pattern identification of fMRI data using a particle swarm optimization-based approach, Brain Informatics 3: 181-192, 2016. Abstract/PDF.
- Rene Doursat, Hiroki Sayama and Olivier Michel, A review of morphogenetic engineering, Natural Computing, 12, 517-535, 2013.
Conference Proceedings
- Hiroki Sayama, Seeking open-ended evolution in Swarm Chemistry II: Analyzing long-term dynamics via automated object harvesting, Proceedings of the 2018 Conference on Artificial Life (ALIFE 2018), Takashi Ikegami, Nathaniel Virgo, Olaf Witkowski, Mizuki Oka, Reiji Suzuki, and Hiroyuki Iizuka, eds., pp. 59-66, 2018, MIT Press. Abstract/PDF
- Hyobin Kim and Hiroki Sayama, Robustness and evolvability of multilayer gene regulatory networks, Proceedings of the 2018 Conference on Artificial Life (ALIFE 2018), Takashi Ikegami, Nathaniel Virgo, Olaf Witkowski, Mizuki Oka, Reiji Suzuki, and Hiroyuki Iizuka, eds., pp. 546-547, 2018, MIT Press. Abstract/PDF
- Hiroki Sayama, Complexity, development, and evolution in morphogenetic collective systems. To appear in Evolution, Development, and Complexity: Multiscale Models in Complex Adaptive Systems (Springer Proceedings in Complexity Series), 2018. Preprint
- Hiroki Sayama, Farnaz Zamani Esfahlani, Ali Jazayeri, and J. Scott Turner, Robust tracking and behavioral modeling of movements of biological collectives from ordinary video recordings, Proceedings of the Sixth IEEE Symposium on Artificial Life (IEEE ALIFE 2017), pp. 3167-3174, November 27-December 1, 2017, Honolulu, HI, IEEE. Preprint
- Hyobin Kim and Hiroki Sayama, Criticality of gene regulatory networks and the resulting morphogenesis, Proceedings of the Fourteenth European Conference on Artificial Life (ECAL 2017), MIT Press, pp. 245-246, 2017. Abstract/PDF
- Hyobin Kim and Hiroki Sayama, The relationship between microscopic and collective properties in gene regulatory network-based morphogenetic systems, Proceedings of the Artificial Life Conference 2016 (ALIFE XV), 2016, MIT Press, pp.370-371. Available online
- Hiroki Sayama, Behavioral diversities of morphogenetic collective systems, Proceedings of the Thirteenth European Conference on Artificial Life (ECAL 2015), 2015, MIT Press, p.41. Available online Slides
- Hiroki Sayama, Four classes of morphogenetic collective systems, Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat, and Hod Lipson, eds., 2014, MIT Press, pp. 320-327. Available online Click here for simulation galleries
- Xinpei Ma and Hiroki Sayama, Hierarchical heterogeneous particle swarm optimization, Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat, and Hod Lipson, eds., 2014, MIT Press, pp. 629-630. Available online
Conference Presentations
- Hiroki Sayama, Self-organization of morphogenetic collective systems, an invited talk at Semana de la Complejidad (Complexity Week), National Autonomous University of Mexico (UNAM), Mexico City, Mexico, January 31-February 2, 2018. Video
- Hiroki Sayama, Farnaz Zamani Esfahlani, and Ali Jazayeri, Robust tracking and behavioral modeling of pedestrian movement in ordinary video recordings, presented as a talk at the 2017 Conference on Complex Systems (CCS 2017), September 17-22, 2017, Cancun, Mexico.
- Hiroki Sayama, Evolution, development and complexity of morphogenetic collective systems, an invited talk at the Evolution, Development & Complexity Satellite Symposium at the Conference on Complex Systems 2017, September 20, 2017, Cancun, Mexico.
- Hyobin Kim and Hiroki Sayama, Criticality of gene regulatory networks and robustness of morphogenesis against perturbations, presented as a talk at the Seventh Morphogenetic Engineering Workshop, September 4, 2017, Lyon, France.
- Hiroki Sayama, Dynamics of morphogenetic collective systems, an invited talk at the 61st GRL Hamamatsu Seminar Series, Shizuoka University, Hamamatsu, Japan, July 12, 2017.
- Ewa Sulicz, Joyce Zhu, Evan George, Kashaf Nadeem, Alexis VanDonsel, Sheng-Liang Slogar, Carol Reynolds, and Hiroki Sayama, How behavioral attributes affect the cohesiveness of society: An agent-based social network simulation, presented as a poster at NetSci 2017: International School and Conference on Network Science, June 21-23, 2017, Indianapolis, IN.
- Hiroki Sayama, Analysis and design of self-organizing heterogeneous swarm systems, presented as a talk at CCS 2016 Satellite Symposium on Swarming Systems: Analysis, Modeling and Design, September 19, 2016, Amsterdam, the Netherlands.
- Hyobin Kim and Hiroki Sayama, RBN-based morphogenetic systems with spring-mass-damper kinetics, presented as a talk at the Sixth Morphogenetic Engineering Workshop, July 4, 2016, Cancun, Mexico. Abstract
- Hiroki Sayama, Ali Jazayeri, and J. Scott Turner, A finite state machine-based approach for detecting interactions among individuals with different states in a biological collective, presented as a late-breaking poster at ALIFE XV: The Fifteenth International Conference on the Synthesis and Simulation of Living Systems, Cancun, Mexico, July 4-8, 2016.
- Maitri Mangal, Haashim Shah, Graham Wilcox, Carol Reynolds, and Hiroki Sayama, How old should you be to become a father? Reconstructing the fitness function over paternal age, presented as a late-breaking poster at ALIFE XV: The Fifteenth International Conference on the Synthesis and Simulation of Living Systems, Cancun, Mexico, July 4-8, 2016.
- Hiroki Sayama, Swarm Chemistry: Guiding designs of self-organizing swarms, presented as an invited seminar talk at the Ikegami Laboratory, University of Tokyo, Japan, June 1, 2016.
- Hiroki Sayama, Modeling individual behavioral state transitions from experimental observations of termite collectives, presented as a talk at the 2015 Conference on Complex Systems (CCS'15), September 28-October 2, 2015, Tempe, AZ. Slides
- Hiroki Sayama, Swarm Chemistry: Guiding designs of self-organizing swarms, presented as a talk at the Engineering and Control of Self-Organization track of the CS-DC'15 World e-Conference, September 30-October 1, 2015. Recorded Talk / Slides
- Hiroki Sayama, Modeling individual behavioral state transitions from experimental observations of termite collectives, presented as a poster at the "Bring Your Poster" session at the Thirteenth European Conference on Artificial Life (ECAL 2015), July 20-24, 2015, York, UK.
- Hiroki Sayama, Collective dynamics of heterogeneous particle swarms with dynamic redifferentiation and local information sharing, presented as a talk at the 2014 European Conference on Complex Systems (ECCS'14), September 22-26, 2014, Lucca, Italy.
- Hiroki Sayama, Swarm-based morphogenetic artificial life, presented at the ECAL 2013 Workshop on Collective Behaviours and Social Dynamics, Taormina, Italy.
Book Chapters
- Hiroki Sayama, Dynamic state transitions of individuals enhance macroscopic behavioral diversity of morphogenetic collective systems, From Parallel to Emergent Computing, Andrew Adamatzky, Selim Akl, and Georgios Sirakoulis, eds., Taylor & Francis/CRC Press, Chapter 5, 2019.
- Hiroki Sayama, Guiding designs of self-organizing swarms: Interactive and automated approaches, Mikhail Prokopenko, ed., Guided Self-Organization: Inception, Springer, 2014, pp.365-387.
- René Doursat, Hiroki Sayama, and Olivier Michel, L'ingénierie morphogénétique : modèles de processus dynamiques pour la morphogenèse, in Modéliser & Simuler. Épistémologies et Pratiques de la Modélisation et de la Simulation, Tome 2, F. Varenne, M. Silberstein, S. Dutreuil and P. Huneman, eds., pp. 625-642, Éditions Matériologiques, Paris, 2014.
Dissertations
- Hyobin Kim, The Role of Criticality of Gene Regulatory Networks on Emergent Properties of Biological Systems, Ph.D. dissertation,. State University of New York at Binghamton, 2018.
- Xinpei Ma, Hierarchical Heterogeneous Particle Swarm Optimization: Algorithms, Developments and Applications. Ph.D. dissertation,. State University of New York at Binghamton, 2016.
Artwork
- Hiroki Sayama, Swarmmonster, artwork exhibited in The Art of Science at Binghamton University, Binghamton, NY, April 18, 2018. Online exhibition
- Hiroki Sayama, Corridors of light, artwork exhibited in The Art of Science at Binghamton University, Binghamton, NY, April 19, 2017. Online exhibition
Events
- MEW 2017: 7th International Morphogenetic Engineering Workshop, September 4, 2017, Lyon, France.
- MEW 2016: 6th International Morphogenetic Engineering Workshop, July 4-8, 2016, Cancun, Mexico.
- MEW 2015: 5th International Morphogenetic Engineering Workshop (held as a special session of ECAL 2015), July 21, 2015, York, UK.
- MEW 2014: 4th International Morphogenetic Engineering Workshop, July 31st, 2014, New York, NY.
Online Resources
- Swarm Chemistry website
- Simon Gladman's Swarm Chemistry iPad App "Emergent" (now available on iTunes)
- Hyobin Kim's CoCo talk "The Role of Criticality of Gene Regulatory Networks on Emergent Properties of Biological Systems"
- Hiroki Sayama's CoCo talk "Four Classes of Morphogenetic Collective Systems"
- Xinpei Ma's CoCo talk "Hierarchical Heterogeneous Particle Swarm Optimization"
- Hiroki Sayama's CoCo talk "Modeling Individual Behavioral State Transitions from Experimental Observations of Termite Collectives"
Contact Us
Please address any inquiries about this project to:
Hiroki Sayama, D.Sc.
Director, Center for Collective Dynamics of Complex Systems
Professor, Department of Systems Science and Industrial Engineering
Binghamton University, State University of New York
P.O. Box 6000, Binghamton, NY 13902-6000
Email: sayama@binghamton.edu
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