Biologically Inspired Computing

2009-05-18T17:18:24Z

74.233.57.111:

Much of this is from Luis's course (http://informatics.indiana.edu/rocha/i-bic/) (http://life-inspired.blogspot.com/), or led from it. A good amount of ALife.

==Read==
[[H. Lipson and J. B. Pollack (2000), "Automatic design and Manufacture of Robotic Lifeforms"]], Nature 406: 974-978.

[[Lipson H. (2005) "Evolutionary Design and Evolutionary Robotics"]], Biomimetics, CRC Press (Bar Cohen, Ed.) pp. 129-155

[[Bongard J., ZykovV., Lipson H. (2006), “Resilient Machines Through Continuous Self-Modeling"]], Science. 314. (5802): 1118 -1121

[[Sims,K. 1994). “Evolving Virtual Creatures”]]. Proceedings of the 21st annual conference on Computer graphics and interactive techniques, pp. 15 -22

[[Crutchfield, J.P. and M. Mitchell (1995)."The evolution of emergent computation."]] Proc. National Academy of Sciences, USA, 92: 10742-10746.

[[Kauffman, S. (1984). “Emergent Properties In Random Complex Automata”]]. Physica D. 10:145-156.

[[Kauffman, S. (1986). "Adaptive Automata Based on Darwinian Selection"]]

[[Gershenson, C. (2004). “Introduction to Random Boolean Networks”]]. In Bedau, M., P. Husbands, T. Hutton, S. Kumar, and H. Suzuki (eds.) Workshop and Tutorial Proceedings, Ninth International Conference on the Simulation and Synthesis of Living Systems (ALifeIX). pp. 160-173.

[[Willadsen, K. and Wiles, J. 2007 Robustness and state-space structure of Boolean gene regulatory models]]. Journal of Theoretical Biology, 249(4):749-65

[[C. Christensen, J. Thakar, and R. Albert (2007) "Systems-level insights into cellular regulation: Inferring, Analyzing And Modeling Intercellular Networks"]], IET Systems Biology. 1, 61-77

[[T. Helikar, J. Konvalina, J. Heidel, and J.A. Rogers (2008) "Emergent decision-making in biological signal transduction networks."]], PNAS. 105(6): 1913-1918

[[J. Timmis, P. Andrews, N. Owens and E. Clark (2008) "An interdisciplinary perspective on artificial immune systems"]], Evolutionary Intelligence 1(1), 5-26

[[De Sousa, et. al. 2004. An Immune-Evolutionary Algorithm for Multiple Rearrangements of Gene Expression Data|De Sousa, J. S., De C. T. Gomes, L., Bezerra, G. B., De Castro, L. N., and Von Zuben, F. J. 2004. An Immune-Evolutionary Algorithm for Multiple Rearrangements of Gene Expression Data ]]. Genetic Programming and Evolvable Machines 5, 2 (Jun. 2004), 157-179.

[[M. Dorigo, M. Birattari, T. Stützle, Ant Colony Optimization--Artificial Ants as a Computational Intelligence Technique]], IEEE Computational Intelligence Magazine, 2006

[[Dussutour A, Fourcassie V, Helbing D, Deneubourg JL. (2004). “Optimal traffic organization in ants under crowded conditions”]]. Nature. 428(6978):70-3

[[Grosan, C., A. Abraham, and M. Chis(2006). “Swarm Intelligence in Data Mining”]]. In: Swarm Intelligence in Data Mining, pp. 1-20. Springer.

[[Ramos V., C. Fernandes, A.C. Rosa(2006). “On Self-Regulated Swarms, Societal Memory, Speed and Dynamics”]], in Artificial Life X -Proc. of the Tenth Int. Conf. on the Simulation and Synthesis of Living Systems, L.M. Rocha, L.S. Yaeger, M.A. Bedau, D. Floreano, R.L. Goldstone and A. Vespignani (Eds.), MIT Press, pp. 393-399.

[[Jensen, R. (2006). Performing Feature Selection with ACO]]. In: Swarm Intelligence in Data Mining, pp. 45-73. Springer.

[[Jensen, R. (2006). “Ant Colony Clustering and Feature Extraction for Anomaly Intrusion Detection”]]. In: Swarm Intelligence in Data Mining, pp. 101-123Springer.

[[Hauert, Ch., Traulsen, A., Brandt, H., Nowak, M. A. & Sigmund, K. (2007) "Via freedom to coercion: the emergence of costly punishment"]], Science 316, 1905-1907.

[[Langer, P., Nowak, M. A. & Hauert, Ch. (2008) "Spatial Invasion of Cooperation"]], J. theor. Biol. 250, 634-641.

[[M. Mitchell. (2006) "Complex systems: Network thinking."]], Artificial Intelligence. 170,(18):1194 1212

[[C. Barrett, S. Eubank and M. Marathe(2006) "Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction Based Approach ."]], Interactive Computation: The New Paradigm . D. Goldin, S.A. Smolkaand P. Wegner (Eds.), pp. 353-392

[[Bettencourt, L.M.A., J.Lobo, D. Helbing, C. Kühnert, and G.B. West (2007) Growth, innovation, scaling, and the pace of life in cities."]], PNAS104(17), 7301-7306

[[Mattick, J.S. and M.F. Mehler(2008) "RNA editing, DNA recoding and the evolution of human cognition"]], Trends Neurosci. 31(5). 227-233

[[W. Gommans et al. (2009). “RNA Editing: A Driving Force for Adaptive Evolution?”]] Submitted

[[C. Huang, J. Kaur, A. Maguitman, L.M. Rocha(2007)."Agent-Based Model of Genotype Editing"]]. Evolutionary Computation, 15(3): 253-89.

[[L.M. Rocha and J. Kaur (2007)."Genotype Editing and the Evolution of Regulation and Memory"]]. Proceedings of the 9th European Conference on Artificial Life. Lecture Notes in Artificial Intelligence (LNAI), 4648: 63-73

[[W. Riof(2008). “Understanding the Emergence of Cellular Organization”]]. Biosemiotics 1:361–377

[[Varela, Francisco J.; Maturana, Humberto R.; & Uribe, R. (1974). “Autopoiesis: the organization of living systems, its characterization and a model”]]. Biosystems.5 187–196.

[[Varela, F.J. (1996). "The early days of autopoiesis"]]. Systems Research, 13(3):407-416.

[[Varela, F.J. (1997). "Patterns of Life: Intertwining Identity and Cognition"]]. Brain and Cognition, 34(1):72-87.

[[Evolutionary Phenomena in Simple Dynamics Lindgren 1991]]

[[faure2006dag | review]] <bibtex>@article{faure2006dag,
title={{Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle}},
author={Faure, A. and Naldi, A. and Chaouiya, C. and Thieffry, D.},
journal={Bioinformatics},
volume={22},
number={14},
year={2006},
publisher={Oxford Univ Press}
}
</bibtex>
[[kashtan2005sem|review]] <bibtex>
@article{kashtan2005sem,
title={{Spontaneous evolution of modularity and network motifs}},
author={Kashtan, N. and Alon, U.},
journal={Proceedings of the National Academy of Sciences},
volume={102},
number={39},
pages={13773--13778},
year={2005},
publisher={National Acad Sciences}
}
</bibtex>
[[ramos2004ess|review]] <bibtex>
@article{ramos2004ess,
title={{Evolving a stigmergic self-organized data-mining}},
author={Ramos, V. and Abraham, A.},
journal={Arxiv preprint cs/0403001},
year={2004}
}
</bibtex>
[[dellaert1994tem|review]] <bibtex>
@conference{dellaert1994tem,
title={{Toward an evolvable model of development for autonomous agent synthesis}},
author={Dellaert, F. and Beer, R.D.},
booktitle={Artificial Life IV, Proceedings of the Fourth International Workshop on the Synthesis and Simulation of Living Systems},
year={1994}
}
</bibtex>
[[yaeger 1994 cgp|review]] <bibtex>
@conference{yaeger1994cgp,
title={{Computational genetics, physiology, metabolism, neural systems, learning, vision, and behavior or Poly World: Life in a new context}},
author={Yaeger, L.},
booktitle={SANTA FE INSTITUTE STUDIES IN THE SCIENCES OF COMPLEXITY-PROCEEDINGS VOLUME-},
volume={17},
pages={263--263},
year={1994},
organization={ADDISON-WESLEY PUBLISHING CO}
}
</bibtex>

[[Synthetic neuroethology Pete Mandik 2002]]

[[ray 1992 eea|review]] <bibtex>
@article{ray1992eea,
title={{Evolution, ecology and optimization of digital organisms}},
author={Ray, T.S.},
journal={Santa Fe},
year={1992}
}
</bibtex>

==To Read==
[[D. Peak, J.D. West, S.M. Messinger, and K.A. Mott. (2004) "Evidence for complex, collective dynamics and distributed emergent computation in plants."]], PNAS. 101(4): 918–922

[[Helbing, D., I. Farkas, T. Vicsek(2000). “Simulating dynamical features of escape panic”]]. Nature 407, 487-490

[[Helbing, D., A. Johansson, and H.Z. Al-Abideen(2007). “The Dynamics of Crowd Disasters: An Empirical Study”]]. arXiv.org:physics/0701203

[[H.H. Pattee (2008). “Physical and Functional Conditions for Symbols, Codes, and Languages”]]. Biosemiotics. 1:147–168

[[K. Kull,C. Emmeche& D. Favareau(2008). “Biosemiotic Questions.”]] Biosemiotics.1:41– 55

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Biologically Inspired Computing