Biologically Inspired Computing

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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.
 
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.  
 
[[H. Lipson and J. B. Pollack (2000), "Automatic design and Manufacture of Robotic Lifeforms"]], Nature 406: 974-978.  
  
Line 9: Line 10:
 
[[Sims,K. 1994). “Evolving Virtual Creatures”]]. Proceedings of the 21st annual conference on Computer graphics and interactive techniques, pp. 15 -22   
 
[[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.  
+
[[Crutchfield, J.P. and M. Mitchell (1995)."The evolution of emergent computation."]] Proc. National Academy of Sciences, USA, 92: 10742-10746.
−
 
+
−
[[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
+
  
 
[[Kauffman, S. (1984). “Emergent Properties In Random Complex Automata”]]. Physica D. 10:145-156.  
 
[[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.  
 
[[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.  
Line 27: Line 28:
  
 
[[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.  
 
[[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.  
−
 
−
[[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
 
  
 
[[M. Dorigo, M. Birattari, T. Stützle, Ant Colony Optimization--Artificial Ants as a Computational Intelligence Technique]], IEEE Computational Intelligence Magazine, 2006  
 
[[M. Dorigo, M. Birattari, T. Stützle, Ant Colony Optimization--Artificial Ants as a Computational Intelligence Technique]], IEEE Computational Intelligence Magazine, 2006  
Line 43: Line 40:
  
 
[[Jensen, R. (2006). “Ant Colony Clustering and Feature Extraction for Anomaly Intrusion Detection”]]. In: Swarm Intelligence in Data Mining, pp. 101-123Springer.  
 
[[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.  
 
[[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.  
Line 58: Line 53:
 
[[Mattick, J.S. and M.F. Mehler(2008) "RNA editing, DNA recoding and the evolution of human cognition"]], Trends Neurosci. 31(5). 227-233  
 
[[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. Gommanset al. (2009). “RNA Editing: A Driving Force for Adaptive Evolution?”]] Submitted  
+
[[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.  
 
[[C. Huang, J. Kaur, A. Maguitman, L.M. Rocha(2007)."Agent-Based Model of Genotype Editing"]]. Evolutionary Computation, 15(3): 253-89.  
Line 64: Line 59:
 
[[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  
 
[[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  
  
−
[[H.H. Pattee (2008). “Physical and Functional Conditions for Symbols, Codes, and Languages”]]. Biosemiotics. 1:147–168
+
[[W. Riof(2008). “Understanding the Emergence of Cellular Organization”]]. Biosemiotics 1:361–377
  
−
[[K. Kull,C. Emmeche& D. Favareau(2008). “Biosemiotic Questions.”]] Biosemiotics.1:41– 55
+
[[Varela, Francisco J.; Maturana, Humberto R.; & Uribe, R. (1974). “Autopoiesis: the organization of living systems, its characterization and a model”]]. Biosystems.5 187–196.
  
−
[[W. Riof(2008). “Understanding the Emergence of Cellular Organization”]]. Biosemiotics 1:361–377
+
[[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,
+
[[faure2006dag | review]] <bibtex>@article{faure2006dag,
 
   title={{Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle}},
 
   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.},
 
   author={Faure, A. and Naldi, A. and Chaouiya, C. and Thieffry, D.},
Line 78: Line 77:
 
   year={2006},
 
   year={2006},
 
   publisher={Oxford Univ Press}
 
   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>
 
</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

Latest revision as of 17:18, 18 May 2009

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, 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

review <bibtex>@article{faure2006dag, 

 title=Template: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> review <bibtex> @article{kashtan2005sem, 

 title=Template: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> review <bibtex> @article{ramos2004ess, 

 title=Template:Evolving a stigmergic self-organized data-mining,
 author={Ramos, V. and Abraham, A.},
 journal={Arxiv preprint cs/0403001},
 year={2004}

} </bibtex> review <bibtex> @conference{dellaert1994tem, 

 title=Template: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> review <bibtex> @conference{yaeger1994cgp, 

 title=Template: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

review <bibtex> @article{ray1992eea, 

 title=Template: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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