Foundational Papers in Complexity Science pp. 2143–2209
DOI: 10.37911/9781947864559.69
Connecting Connectionist Models
Author: Stephanie Forrest, University of Arizona; Santa Fe Institute
Excerpt
How do systems like the brain, the immune system, ecosystems, or financial markets learn and adapt over time? From the early days of computing, scientists and engineers alike have sought to abstract the key mechanisms of adaptation, learning, and intelligence and encode them in a computer. Norbert Weiner, an early cyberneticist, hypothesized that feedback mechanisms were the key ingredient of intelligence (Wiener 1948), Ross Ashby’s general theory of adaptive systems emphasized system states and the role of modeling in intelligence (Ashby 1956), and Donald O. Hebb’s influential book Organization of Behavior emphasized synaptic learning and cell assemblies (Hebb 1949). Meanwhile, engineers developed computational realizations of different aspects of adaptive systems: neural networks (McCulloch and Pitts 1943), genetic algorithms and classifier systems (Holland 1962, 1975; Holland et al. 1989), reinforcement learning and minimax algorithms (Samuel 1959; Kaelbling, Littman, and Moore 1996; Russell and Norvig 2003), and symbolic artificial intelligence models (Newell and Simon 1956). For understandable reasons, these efforts focused primarily on intelligence in the brain and on human thought processes, and over time each developed its own formalisms, terminology, and research communities specific to the type of system being studied. As computing matured, other researchers developed computational models in fields far afield from the brain, including chemical reaction networks and immunology.
Bibliography
Ashby, W. R. 1956. An Introduction to Cybernetics. London, UK: Chapman and Hall Ltd.
Ashkenasy, G., R. Jagasia, M. Yadav, and M. R. Ghadiri. 2004. “Design of a Directed Molecular Network.” Proceedings of the National Academy of Sciences 101 (30): 10872–7. https://doi.org/10.1073/pnas. 0402674101.
Bertsekas, D. P. 2019. Reinforcement Learning and Optimal Control. Belmont, MA: Athena Scientific.
— . 2022. Lessons from AlphaZero for Optimal, Model Predictive, and Adaptive Control. Belmont, MA: Athena Scientific.
Dam, H. H., H. A. Abbass, C. Lokan, and X. Yao. 2008. “Neural-Based Learning Classifier Systems.” IEEE Transactions on Knowledge and Data Engineering 20 (1): 26–39. https://doi.org/10.1109/TKDE. 2007.190671.
Dick, J. M., and E. L. Shock. 2021. “The Release of Energy During Protein Synthesis at Ultramafic‐Hosted Submarine Hydrothermal Ecosystems.” Journal of Geophysical Research: Biogeosciences 126 (11): e2021JG006436. https://doi.org/10.1029/2021JG006436.
Farmer, J. D., N. H. Packard, and A. S. Perelson. 1986. “The Immune System, Adaptation, and Machine Learning.” Physica D: Nonlinear Phenomena 22 (1–3): 187–204. https://doi.org/10.1016/0167-2789(86)90240-X.
Haralampos, N. M., C. Mathis, W. Xuan, D.-L. Long, R. Pow, and L. Cronin. 2020. “Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters.” Proceedings of the National Academy of Sciences 117 (20): 10699–705. https://doi.org/10.1073/pnas.1921536117.
Hebb, D. O. 1949. “The Organization of Behaviour.” (New York, NY).
Hochreiter, S., and J. Schmidhuber. 1997. “Long Short-Term Memory.” Neural Computation 9 (8): 1735– 1780. https://doi.org/10.1162/neco.1997.9.8.173.
Holland, J. H. 1962. “Outline for a Logical Theory of Adaptive Systems.” Journal of the ACM 9 (3): 297–314. https://doi.org/10.1145/321127.321128.
— . 1975. “Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artiificial Intelligence.” (Ann Arbor, MI).
Holland, J. H., K. J. Holyoak, R. E. Nisbett, and P. R. Thagard. 1989. Induction: Processes of Inference, Learning, and Discovery. Cambridge, MA: MIT Press.
Hordijk, W., L. Hasenclever, J. Gao, D. Mincheva, and J. Hein. 2014. “An Investigation into Irreducible Autocatalytic Sets and Power Law Distributed Catalysis.” Natural Computing 13:287–296. https://doi.org/10.1007/s11047-014-9429-6.
Jernbom, A. F., L. Skoglund, E. Pin, R. Sjöberg, H. Tegel, S. Hober, E. Rostami, et al. 2024. “Prevalent and Persistent New-Onset Autoantibodies in Mild to Severe COVID-19.” Nature Communications 15:8941. https://doi.org/10.1038/s41467-024-53356-5.
Jerne, N. K. 1973. “The Immune System.” Scientific American 229 (1): 52–63. https://doi.org/10.1038/scientificamerican0773-52.
— . 1974. “Towards a Network Theory of the Immune System.” Annales D’Immunologie 125:373–389.
Kaelbling, L. P., M. L. Littman, and A. W. Moore. 1996. “Reinforcement Learning: A Survey.” Journal of Artificial Intelligence Research 4 (1): 237–285. https://doi.org/10.5555/1622737.1622748.
Kim, D.-E., and G. F. Joyce. 2004. “Cross-Catalytic Replication of an RNA Ligase Ribozyme.” Chemistry & Biology 11 (11): 1505–12. https://doi.org/10.1016/j.chembiol.2004.08.021.
Kim, J.-Y., and S.-B. Cho. 2019. “Exploiting Deep Convolutional Neural Networks for a Neural-Based Learning Classifier System.” Neurocomputing 354:61–70. https://doi.org/10.1016/j.neucom.2018.05.137.
Kitchin, J. R. 2018. “Machine Learning in Catalysis.” Nature Catalysis 1 (4): 230–232. https://doi.org/10.1038/s41929-018-0056-y.
Matziner, P. 1994. “Tolerance, Danger, and the Extended Family.” Annual Review of Immunology 12:991–1045. https://doi.org/10.1146/annurev.iy.12.040194.005015.
McCulloch, W. S., and W. Pitts. 1943. “A Logical Calculus of the Ideas Immanent in Nervous Activity.” The Bulletin of Mathematical Biophysics 5 (4): 115–33. https://doi.org/10.1007/BF02478259.
Miikkulainen, R., J. Liang, E. Meyerson, A. Rawal, D. Fink, O. Francon, B. Raju, et al. 2019. “Evolving Deep Neural Networks.” In Artificial Intelligence in the Age of Neural Networks and Brain Computing, edited by R. Kozma, C. Alippi, Y. Choe, and F. C. Morabito, 267–287. Amsterdam, Netherlands: Elsevier. https://doi.org/10.1016/B978-0-323-96104-2.00002-6.
Newell, A., and H. Simon. 1956. “The Logic Theory Machine: A Complex Information Processing System.”IRE Transactions on Information Theory 2 (3): 61–79. https://doi.org/10.1109/TIT.1956.1056797.
Piovesan, A., F. Antonaros, L. Vitale, P. Strippoli, M. C. Pelleri, and M. Caracausi. 2019. “Human Protein-Coding Genes and Gene Feature Statistics in 2019.” BMC Research Notes 12 (1): 315. https://doi.org/10.1186/s13104-019-4343-8.
Richert, C. 2018. “Prebiotic Chemistry and Human Intervention.” Nature Communications 9 (5177). https://doi.org/10.1038/s41467-018-07219-5.
Russell, S., and P. Norvig. 2003. Artificial Intelligence: A Modern Approach. https://aima.cs.berkeley.edu/. Samuel, A. L. 1959. “Some Studies in Machine Learning Using the Game of Checkers.” IBM Journal of Research and Development 3 (3): 210–29. https://doi.org/10.1147/rd.33.0210.
Segel, L. A., and R. L. Bar-Or. 1999. “On the Role of Feedback in Promoting Conflicting Goals of the Adaptive Immune System.” Journal of Immunology 163 (3): 1342–1349. https://doi.org/10.4049/jimmunol.163.3.1342.
Segel, L. A., and I. R. Cohen. 2001. Design Principles for the Immune System and Other Distributed Autonomous System. New York, NY: Oxford University Press.
Sievers, D., and G. Von Kiedrowski. 1994. “Self-replication of Complementary Nucleotide-based Oligomers.” Nature 369 (6477): 221–4. https://doi.org/10.1038/369221a0.
Smith, D. J. 1999. Immunological Memory is Associative, edited by D. Dasgupta, 105–14. Berlin, Germany: Springer. https://doi.org/10.1007/978-3-642-59901-9_6.
Smith, D. J., S. Forrest, D. H. Ackley, and A. S. Perelson. 1999. Variable Efficacy of Repeated Annual in Infuenza Vaccination. 96:14001–6. 24. https://doi.org/10.1073/pnas.96.24.14001.
Solé, R., M. Moses, and S. Forrest. 2019. “Liquid Brains, Solid Brains.” Philosophical Transactions of the Royal Society B 374:20190040. https://doi.org/10.1098/rstb.2019.0040.
Sompayrac, L. M. 2022. How the Immune System Works. Hoboken, NJ: John Wiley & Sons.
Stanley, K., and R. Miikkulainen. 2002. “Evolution of Neural Networks through Augmenting Topologies.”
Evolutionary Computation 10 (2): 99–127. https://doi.org/10.1162/106365602320169811.
Sutton, A.G., and R.S. Barto. 1990. “Time-Derivative Models of Pavlovian Reinforcement.” In Learning and Computational Neuroscience: Foundations of Adaptive Networks, edited by M. Gabriel and J. Moore, 497–537. Cambridge, MA: MIT Press.
Vaidya, N., M. L. Manapat, I. A. Chen, R. Xulvi-Brunet, E. J. Hayden, and N. Lehman. 2012. Spontaneous Network Formation Among Cooperative RNA Replicators. 491:72–77. https://doi.org/10.1038/nature11549.
Vasas, V., C. Fernando, M. Santos, S. Kauffman, and E. Szathmáry. 2012. “Evolution before Genes.” Biology Direct 7:1–14. https://doi.org/10.1186/1745-6150-7-1.
Wiedemann, G. M., E. K. Santosa, S. Grassmann, S. Sheppard, J.-B. Le Luduec, N. M. Adams, C. Dang,
K. C. Hsu, J. C. Sun, and C. M. Lau. 2021. “Deconvoluting Global Cytokine Signaling Networks in Natural Killer Cells.” Nature Immunology 22:627–638. https://doi.org/10.1038/s41590-021-00909-1.
Wiener, N. 1948. Cybernetics: or Control and Communication in the Animal and the Machine. New York, NY: John Wiley & Sons.
Xavier, J. C., W. Hordijk, S. Kauffman, M. Steel, and W. F. Martin. 2020. “Autocatalytic Chemical Networks at the Origin of Metabolism.” Proceedings of the Royal Society B 287 (1922): 20192377. https://doi.org/10.1098/rspb.2019.2377.