Complex Systems, Neutral Evolution, etc

Adami, C., (1995) Learning and Complexity in Genetic Auto-Adaptive Systems Physica D, vol. 80, p l54, 1995
Adami, C., Self-organized Criticality in Living Systems
Adami, C., On Modelling Life Artificial Life IV: Fourth International Workshop on the Synthesis and Simulation of Living Systems,p 269.
Adami, C., Brown, C. T., Evolutionary Learning in the 2D Artificial Life System "Avida" Artificial Life IV: Fourth International Workshop on the Synthesis and Simulation of Living Systems,p 377.
Adami, C., Brown, C. T., Haggerty, M. R., (1995) Abundance-Distributions in Artificial Life and Stochastic Models: "Age and Area" revisitedThird European Conference on Artificial Life.
Ancel, L.W., Fontana, W. (1999) Plasticity, Evolvability and Modularity in RNA SFI Working Paper 99-12-077
Balbi de Oliveira, P.P.,An empirical exploration of computations with a cellular-automata-based artificial life world Cognitive Science Research Paper 373 School of Cognitive and Computing Sciences, University of Sussex.
Balkenius, C., (1994) Neural Mechanisms for Self-organization of Emergent Schemata, Dynamical Schema Processing, and Semantic Constraint Satisfaction Cognitive Science Department, Lund University
Barnett, L., (1997) Tangled Webs: Evolutionary Dynamics on Fitness Landscapes with Neutrality, MSc dissertation, MSc in Evolutionary and Adaptive Systems, University of Sussex. September 1997.
Barnett, L. (1998) Collapsing the state space - Applying Markov analysis to evolutionary systems. Workshop presentation at the Sixth International Conference on Artificial Life, UCLA, 27-29 June, 1998.
Barnett, L. (1998) Recombination and bistability in finite populations. Presented to the Evolutionary Dynamics Workshop, at the Santa Fe Institute, 5-9 October 1998.
Barnett, L. (1998) Ruggedness and neutrality: The NKP family of fitness landscapes. Sixth International Conference on Artificial Life, C Adami, R Belew, H Kitano and C Taylor (eds), MIT Press pp 17-27.
Barnett, L. (submitted) The effects of recombination on a haploid quasispecies evolving on a single-peak fitness landscape. Journal of theoretical biology
Bedau, M.A., Snyder, E., Brown, C.T., Packard. N. H., (1997) A Comparison of Evolutionary Activity in Artificial Evolving Systems and the Biosphere Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press.
Bedau, M. A., Bahm, A., (1994) Bifurcation Structure and Diversity Dynamics. Alife IV 6-8 July 1994.
Coveney, P.V., Emerton, A.N. Boghosian, B.M. (1996) Simulation of Self-Reproducing Micelles using a Lattice-Gas Automaton J. Amer. Chem. Soc. 118 (1996) 10719-10724.
Crutchfield, J. P.,(1994) The Calculi of Emergence: Computation, Dynamics, and Induction, Physica D 75 (1994) 11-54. Abstract
Crutchfield, J. P.,(1994) Is Anything Ever New? Considering Emergence, in Complexity: Metaphors, Models, and Reality, G. Cowan, D. Pines, and D. Melzner, editors, SFI Series in the Sciences of Complexity XIX, Addison-Wesley, Redwood City (1994) 479-497. Abstract
Crutchfield, J. P., Mitchell, M., (1994) The Evolution of Emergent Computation Proceedings of the National Academy of Sciences, USA , 92 (1995) 10742-10746. SFI Working Paper 94-03-012.
Crutchfield, J.P., Mitchell, M. , Das, R. (1998) The Evolutionary Design of Collective Computation in Cellular Automata (adap-org/9809001).
Crutchfield, J.P., van Nimwegen, E. (1999) The Evolutionary Unfolding of Complexity (adap-org/9903001).
Darley, V., (1994) Emergent Phenomena and Complexity. ALife IV.
Das, R., Mitchell, M., Crutchfield, J. P.,(1994) A Genetic Algorithm Discovers Particle-Based Computation in Cellular AutomataThird Parallel Problem-Solving From Nature Conference March, 1994.
Das, R., Crutchfield, J. P., Mitchell, M., Hanson, J. E. (1995) Evolving Globally Synchronous Cellular Automata Sixth International Conference on Genetic Algorithms.
de Dinechin, F., (1997) Self-replication in a 2D von Neumann architecture Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press.
Di Paolo, E. A. (2000) Searching for rhythms in asynchronous Boolean Networks. Artificial Life VII: The 7th International Conference on the Simulation and Synthesis of Living Systems, Reed College, Portland, Oregon, USA, 1-6 August, 2000.
Ficici, S. G., Melnik, O., Pollack, J. B. (2000). A Game-Theoretic Investigation of Selection Methods Used in Evolutionary Algorithms. Proceedings of the 2000 Congress on Evolutionary Computation, A. Zalzala, et al, (eds.), IEEE Press
Forst, C.V., (1997) Molecular Evolution of Catalysis Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press.
Forst,C.V. (1996) Chaotic Interactions of Self-Replicating RNA. Computers Chem. Vol. 20, pp. 69-83, 1996.
Forst,C.V., Reidys,C. (1996) On Evolutionary Dynamics. Alife V May 1996.
Forst,C.V., Reidys, C., Weber,J. (1995) Evolutionary Dynamics and Optimization. In: F.Moran, A.Moreno, J.J.Merelo, P.Chacon (eds.): Lecture Notes in Artificial Intelligence, vol. 929: Advances in Artificial Life. Springer, Berlin, Heidelberg, New York, 1995.
Göbel,U., Forst,C.V., Schuster,P. (1997) Structural Constraints and Neutrality in RNA. In Ralf Hofestädt, editor, LNCS/LNAI Proceedings of GCB96, Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, New York, 1997.
Gruener, W., Giegerich, R., Strohmann, D., Reidys, C. Weber, J., Hofacker, I.L. Stadler, P.F., Schuster, P., (1995) Analysis of RNA Sequence-Structure Maps by Exhaustve Enumeration (part I and II), Monatshefte f. Chemie, 127:355-374(I), 127:375-389(II), 1995.
Hanson, J. E. (1993) Computational Mechanics of Cellular Automata, Ph.D. Dissertation, University of California, Berkeley (August 1993).
Hanson, J.E., Crutchfield, J. P., (1995) Computational Mechanics of Cellular Automata: An Example. Physica D (1997) also Santa Fe Institute Working Paper 95-10-095.
Harvey, I., (1997) Open the Box Workshop on Evolutionary Computation with Variable Size Representation, at ICGA97, Intl. Conf. on Genetic Algorithms, July 19--23 1997 at Michigan State University, East Lansing, Michigan.
Kauffman, S.A., Macready, W.G, Dickinson, E., Divide to Coordinate: Coevolutionary Problem Solving.
Land, M. W. S., Belew. R. K., No two-state cellular automata for density classification exists Technical Report CS93-396, Computer Science &Engr. Dept., UC San Diego, La Jolla, CA 92093-0114, 1994. Abstract
Kopp,S., Reidys, C., Schuster, P. (1996) Exploration of Artificial Landscapes based on Random Graphs. In: F. Schweitzer (ed.): Self-Organization of Complex Structures: From Individual to Collective Dynamics, vol.I, chapt. 15, London: Gordon and Breach, 1996.
Mayer, B., Rasmussen, S. (1998) Self-Reproduction of Dynamical Hierarchies in Chemical Systems Santa Fe Institute Working Paper 98-05-038, Also in ALIFE VI Abstract.
McMullin, B. (1997) Computational Autopoiesis: The Original Algorithm Santa Fe Institute Working Paper 97-01-001. HTML
McMullin, B. (1997) SCL: An Artificial Chemistry in Swarm Santa Fe Institute Working Paper 97-01-002. HTML
McMullin, B., Varela, F. (1997) Rediscovering Computational Autopoiesis Santa Fe Institute Working Paper 97-02-012. Also in ECAL'97 HTML
Menczer, F., Belew, R.K., (1995) Latent Energy Environments. Adaptive Individuals in Evolving Populations: Models and Algorithms, edited by R.K. Belew and M. Mitchell, SFI Studies in the Sciences of Complexity Vol. XXIII, Reading, MA: Addison Wesley, 1995.
Mitchell, M., Crutchfield, J. P., Das, R., (1996) Evolving Cellular Automata with Genetic Algorithms: A Review of Recent Work In Proceedings of the First International Conference on Evolutionary Computation and Its Applications (EvCA'96). Moscow, Russia: Russian Acadamy of Sciences, 1996.
Mitchell, M., Crutchfield, J. P., Hraber, P. T., (1994) Evolving Cellular Automata to Perform Computations: Mechanisms and Impediments Physica D, 75, 361-391 (1994).
Mitchell, M., Hraber, P. T., Crutchfield, J. P., (1993) Revisiting the Edge of Chaos: Evolving Cellular Automata to Perform Computations Complex Systems 7, 89--130, 1993.
Mitchell, M., Crutchfield, J. P., Hraber, P. T., Dynamics, Computation, and the ``Edge of Chaos'': A Re-Examination To appear in G. Cowan, D. Pines, and D. Melzner (editors), Complexity: Metaphors, Models, and Reality. Santa Fe Institute Stuides in the Sciences of Complexity, Proceedings Volume 19. Reading, MA: Addison-Wesley.
Mitchell, M. (1993) Computer Models of Adaptive Complex Systems New Scientist, February 13, 1993.
Newman, M.E.J., Eble, G. J. (1998) Decline in Extinction Rates and Self-Similarity in the Fossil Record Santa Fe Institute Working Paper 98-04-031 Abstract
Newman, M.E.J., Engelhardt, R. (1998) Effects of neutral selection on the evolution of molecular species Santa Fe Institute Working Paper 98-01-001.
Newman, M.E.J. , Watts, J.D. (1999) Renormalization Group Analysis of the Small-World Network Model Submitted to Phys. Rev. Lett.
Newman, M.E.J. , Watts, J.D. (1999) Scaling and Percolation in the Small-World Network Model Submitted to Phys. Rev. E.
Nilsson, M., Snoad, N (1999) Error Thresholds on Dynamic Fitness-Landscapes Submitted to Phys. Rev. Lett.
Ochoa, G., Harvey, I., Buxton, H. (1999) Error Thresholds and their Relation to Optimal Mutation Rates In Proceedings of the Fifth European Conference on Artificial Life (ECAL99), D. Floreano, J-D. Nicoud, F. Mondada (eds), Springer-Verlag
Ochoa, G., Harvey, I., Buxton, H. (1999) On Recombination and Optimal Mutation Rates In Gecco '99 : Proceedings of the Genetic and Evolutionary Computation Conference W. Banzhaf, J. Daida and A.E. Eiben (eds.). Morgan Kaufmann
Ochoa, G., Harvey, I. (1999) Recombination and Error Thresholds in Finite Populations In Foundations of Genetic Algorithms, W. Banzhaf (ed.). Proc. of FOGA 5 (Foundations of Genetic Algorithms Workshop, Leiden Sept 1998). Morgan Kaufmann.
Oprea, M., Forrest, S. (1999) How the Immune System Generates Diversity: Pathogen Space Coverage with Random and Evolved Antibody Libraries, 1999 Genetic and Evolutionary Computation Conference.
Peliti, L. (1997) Introduction to the statistical theory of Darwinian evolution Lectures given at an ICTP Summer College on Frustrated Systems, Trieste, August 1997.
Peliti, L. (1995) Fitness landscapes and evolution Lectures given at the NATO ASI on Physics of Biomaterials: Fluctuations, Self-Organization and Evolution, Geilo, Norway, March 27, April 6, 1995. Abstract
Reidys,C. , Forst, C. V., Schuster,P. (1998) Replication and Mutation on Neutral Networks Santa Fe Institute Working Paper 98-04-036. Abstract
Reidys,C. , Kopp,S., Schuster,P. (1996) Evolutionary Optimization of Biopolymers and Sequence Structure Maps. Alife V, May 1996.
Reidys, C., Stadler, P.F. (1996) Bio-molecular Shapes and Algebraic Structures, 1996.
Schuster, P., (1996) How Does Complexity Arise in Evolution? Santa Fe Institute Working Paper 96-05-026. To appear in Complexity.
Schuster, P., (1996) Landscapes and Molecular Evolution Santa Fe Institute Working Paper 96-07-047, Submitted to Physica D.
Seth, A.K., (1999). A cybernetic perspective on the role of noise in the Iterated Prisoner's Dilemma. Cognitive Science Research Paper 506. School of Cognitive and Computer Sciences, University of Sussex, Brighton BN1 9QH. January 1999.
Seth, A.K., (1998) The evolution of complexity and the value of variability. In: Proceedings of the Sixth International Conference on Artificial Life, C Adami, R Belew, H Kitano and C Taylor (eds), MIT Press pp 209-221.
Seth, A.K., (1997) Interaction, Uncertainty, and the Evolution of Complexity Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press.
Seth, A.K., (1998) The Evolution of Complexity and the Value of Variability In Proceedings of the 6th International Conference on Artificial Life (ALIFE VI), eds. C. Adami, R. Belew, H. Kitano, and C. Taylor, MIT Press, pp209-221.
Shalizi, C. R., Crutchfield, J. P. (2000) Pattern Discovery and Computational Mechanics SFI Working Paper 00-01-008
Shalizi, C. R., Crutchfield, J. P. (1999) Computational Mechanics: Pattern and Prediction, Structure and Simplicity SFI Working Paper 99-07-044
Shipman, R., Shackleton, M., Ebner, M., Watson, R.A. (2000). Neutral Search Spaces for Artificial Evolution: A Lesson from Life. Proceedings of Artificial Life VII, Bedau, M, McCaskill, J, Packard, N, Rasmussen, S (eds.)
Shubik, M., (1998) Game Theory, Complexity, and Simplicity Part I: A Tutorial Santa Fe Institute Working Paper 98-04-027 E.
Shubik, M., (1998) Game Theory, Complexity, and Simplicity Part II: Problems and Applications Santa Fe Institute Working Paper 98-04-028 E.
Shubik, M., (1998) Game Theory, Complexity, and Simplicity Part III: Critique and Prospective Santa Fe Institute Working Paper 98-04-029 E.
Sibani, P., Pedersen, A., (1999) Evolution dynamics in terraced NK landscapes Europhysics Lett. 48, 346-352 (1999)
Sipper, M., (1996) Co-evolving Non-uniform Cellular Automata to Perform Comuptations. Physica D, vols 90-92, 1996.
Sipper, M., (1995) Quasi-Uniform Computation-Universal Cellular Automata, ECAL'95: 3rd European conference on Artificial Life, F. Moran, A. Moreno, J.J. Merelo and P. Chacon (eds.) pp 544-554, 1995, Springer-Verlag.
Sipper, M., (1995) Studying Artificial Life Using a Simple, General Cellular Model, Artificial Life Vol 2, Num 1, p 1-35, 1995, The MIT Press.
Sipper, M., (1994) Non-Uniform Cellular Automata: Evolution in Rule Space and Formation of Complex Structures, Artificial Life IV, R.A. Brooks and P. Maes (eds.) p 394-399, The MIT Press.
Solé, R. V., Luque, B., Kauffman, S. (2000) Phase Transitions in Random Networks with Multiple States Submitted to Physical Review E
Stadler, P. Seitz, R., Wagner, G.P. (1999) Evolvability of Complex Characters: Dependent Fourier Decomposition of Fitness Landscapes Over Recombination Spaces Submitted to Bull.Math.Biol.
Taylor, T., Hallam, J., (1997) Studying Evolution with SelfReplicating Computer Programs Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press.
van Nimwegen, E., Crutchfield J.P., (1999) Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths? adap-org/9907002
van Nimwegen, E., Crutchfield, J. P., Mitchell, M., (1996) Finite populations Induce Metastability in Evolutionary Search Physics Letters A , 229 (2), 144-150. Also Santa Fe Institute Working Paper 96-08-054.
van Nimwegen, E., Crutchfield, J. P., Mitchell, M., (1997) Statistical Dynamics of the Royal Road Genetic Algorithm Special Issue on Evolutionary Computation of the journal Theoretical Computer Science, A. E. Eiben and G. Rudolph, (eds).
van Nimwegen, E., Crutchfield, J. P., (1998) Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory Submitted to the Machine Learning.
van Nimwegen, E., Crutchfield, J. P., (1998) Optimizing Epochal Evolutionary Search: Population-Size Independent Theory Special Issue on Evolutionary and Genetic Algorithms in Computational Mechanics and Engineering of the journal Computer Methods in Applied Mechanics and Engineering, D. Goldberg, editor.
van Nimwegen, E., Crutchfield, J. P., Huynen, M. (1999) Neutral Evolution of Mutational Robustness Submitted to Proceedings of the National Academy of Sciences USA.
Watson, R.A., Pollack, J.B. (2000). Recombination Without Respect: Schema Combination and Disruption in Genetic Algorithm Crossover. Proceedings of the 2000 Genetic and Evolutionary Computation Conference, Whitley, D., et al (eds.), Morgan Kaufmann.
Weinberger, E.D. (1996) NP Completeness of Kauffman's N-K Model. A tunable Fitness Landscape.. Santa Fe Institute Working Paper 96-02-003. Abstract
Werfel, J. Mitchell, M., Crutchfield, J.P. (1999) Resource Sharing and Coevolution in Evolving Cellular Automata SFI Working Paper 99-07-045
Wuensche, A., (1998) Classifying Cellular Automata Automatically SFI Working Paper 98-02-018 Abstract

Compiled by Ezequiel A. Di Paolo (c) 2000.
Suggestions, comments? Please, contact me.

ezequiel@sussex.ac.uk

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