Fall 2024
Aaronson, S., Carroll, S., Ouellette, L. Quantifying the rise and fall of complexity in closed systems: the coffee automaton. 2014.
Abrahão, F.S., Hernández-Orozco, S., Kiani, N.A., Tegnér, J., Zenil, H. Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution. PLOS Complex Syst 1.1 (2024).
Adami, C., Ofria, C. Collier, T.C. Evolution of biological complexity. PNAS 97.9 (2000).
Anagnostopoulos, A., Kumar, R., Mahdian, M., Upfal, E. Vandin, F. Algorithms on evolving graphs. ITCS 2012.
Alur, R., Courcoubetis, C., Halbwachs, N., Henzinger, T.A., Ho, P.-H., Nicollin, X., Olivero, A., Sifakis, J., Yovine, S. The Algorithmic Analysis of Hybrid Systems. Theoretical Computer Science 138 (1995).
Avin, C., Koucky, M., Lotker, Z. How to explore a fast changing world. ICALP 2008.
Bak, P., Tang, C., Wiesenfeld, K. Self-organized criticality, Phys. Rev. A 38.1 (1988).
Ball, P. A New Idea for How to Assemble Life.
Bedau, M. Artificial life: organization, adaptation and complexity from the bottom up. Trends in cognitive sciences 7.11 (2003).
Bialek, W. Statistical mechanics for natural flocks of birds. PNAS 109.13 (2012).
Cardelli, L. Abstract machines of systems biology. Transactions on computational systems biology III (2005).
Chandrasekhar, A., Gordon, D.M., Navlakha, S. A distributed algorithm to maintain and repair the trail networks of arboreal ants. Scientific Reports 8.1 (2018).
Chen, H., Zhu, Y., Hu, K. Self-Adaptation in Bacterial Foraging Optimization Algorithm. ISKE 2008.
Condon, A., Lipton, R.J. On the Complexity of Space Bounded Interactive Proofs. FOCS 1989.
Conradt, L, Roper, T.J. Group decision-making in animals. Nature 421 (2003).
Couzin, I.D. Collective minds. Nature 445 (2007).
Couzin, I.D., Krause, J. Self-organization and collective behavior of vertebrates. Advances in the Study of Behavior 32 (2003).
Couzin, I.D., Krause, J., Franks, N.R., Levin, S.A. Effective leadership and decision-making in animal groups on the move. Nature 433 (2005).
Couzin, I.D., Krause, J., James, R., Ruxton, G.D., Franks, N.R. Collective memory and spatial sorting in animal groups. Journal of Theoretical Biology 218 (2002).
Crutchfield, J.P. Between order and chaos. Nature Physics 8.1 (2012).
Cucker, F., Smale, S. Emergent behavior in flocks. IEEE Trans. Automatic Control 52 (2007).
Cucker, F., Smale, S. The mathematics of emergence. Japanese Journal of Mathematics 2 (2007).
Cuevas, E., Fausto, F., Gonzalez, A. New Advancements in Swarm Algorithms: Operators and Applications. 2020.
DasGupta, B., Enciso, G.A., Sontag, E.D., Zhang, Y. Algorithmic and complexity aspects of decompositions of biological networks into monotone subsystems. BioSystems 89 (2007).
Dechert, W.D., Sprott, J.C., Albers, D.A. On the probability of chaos in large dynamical systems: a Monte Carlo study. Journal of Economic Dynamics and Control 23.8 (1999).
Denysyuk, O., Rodrigues, L. Random walks on directed dynamic graphs. DYNAS 2010.
Diaz, J., Serna, M., Spirakis, P. Linear and non-linear systems: a survey. 1997.
Dodds, P.S., Watts, D.J. A generalized model of social and biological contagion. Journal of Theoretical Biology 232.4 (2005).
Dorigo, M., Birattari, M., Stuetzle, T. Ant colony optimization. IEEE Comp. Intelligence Magazine 1.4 (2006).
Doty, D. Theory of Algorithmic Self-Assembly. CACM 55.12 (2012).
England, J.L. Dissipative adaptation in driven self-assembly. Nature Nanotechnology 10.11 (2015).
England, J.L. Self-organized computation in the far-from-equilibrium cell. Biophysics Rev. 3 (2022).
England, J.L. Statistical physics of self-replication. The Journal of Chemical Physics 139.12 (2013).
Fax, J.A., Murray, R.M. Information flow and cooperative control of vehicle formations. IEEE Trans. Automatic Control 49 (2004).
Flierl, G., Grunbaum, D., Levin, S., Olson, D. From Individuals to Aggregations: the Interplay between Behavior and Physics, Journal of Theoretical Biology 196.4 (1999).
Friston, K. Life as we know it. Journal of the Royal Society Interface 10.86 (2013).
Gartner, F.M., Graf, I.R., Frey, E. The time complexity of self-assembly. PNAS 119.4 (2022).
Gazi, V., Passino, K.M. Stability analysis of swarms. IEEE Trans. Automatic Control 48 (2003).
Goldenfeld, N. Woese, C. Life is physics. Annu. Rev. Condens. Matter Phys. 2.1 (2011).
Gros, C. Complex and Adaptive Dynamical Systems. 2010.
Henzinger, T.A., Ho, P.-H., Wong-Toi, H. Algorithmic analysis of nonlinear hybrid systems. IEEE Trans. Automatic Control 43 (1998).
Holme, P. Modern temporal network theory: A colloquium. The European Physical Journal B 88 (2015).
Jonas, E, Kording, K. Could a neuroscientist understand a microprocessor? PLoS Computational Biology 13.1 (2017)
Karr, J.R., Sanghvi, J.C. A whole-cell computational model predicts phenotype from genotype. Cell 150.2 (2012).
Kennedy, J. The particle swarm: Social adaptation of knowledge. ICEC 1997.
Lazebnik, Y. Can a biologist fix a radio? Cancer Cell 2.3 (2002).
Lenski, R, Ofria, C., Pennock, R.T., Adami, C. The evolutionary origin of complex features. Nature 423 (2003).
Leonard, N., Fiorelli, E. Virtual leaders, artificial potentials and coordinated control of groups. IEEE Conference on Decision and Control 2001.
Lin, H.W., Tegmark, M., Rolnick, D. Why does deep and cheap learning work so well? Journal of Statistical Physics 168 (2017).
Linderman, S.W., Johnson, M.J., Miller, A.C., Adams, R.P., Blei, D.M., Paninski, L. Bayesian Learning and Inference in Recurrent Switching Linear Dynamical Systems. AISTATS 2017.
Lim, W.A., Lee, C.M., Tag, C. Design principles of regulatory networks. Molecular Cell 49.2 (2013).
Loscos, C., Marchal, D. Intuitive crowd behaviour in dense urban environments using local laws. Theory and Practice of Computer Graphics 2003.
Maini, P.K. The impact of Turing's work on pattern formation in biology. 2004.
Marshall, J.A. Formations of vehicles in cyclic pursuit. IEEE Trans. Automatic Control 49 (2004).
Martinez, S., Cortes, J., Bullo, F. Motion coordination with distributed information. IEEE Control Systems Magazine 27.4 (2007)
Miller, G.F., Cliff, D. Co-evolution of pursuit and evasion I: biological and game-theoretic foundations. 1994.
Mirtabatabaei A., Bullo, F. Opinion Dynamics in Heterogeneous Networks: Convergence Conjectures and Theorems. SIAM Journal on Control and Optimization 50.5 (2012).
Mora, T., Bialek, W. Are biological systems poised at criticality? 2010.
Nabet, B., Leonard, N., Couzin, I.D., Levin, S.A. Dynamics of decision making in animal group motion. Journal of Nonlinear Science 19.4 (2009).
Navlakha, S., Bar-Joseph, Z. Algorithms in nature. Mol. Bio. 2011.
Ohtsuki, H., Hauert, C., Lieberman, E., Nowak, M.A. (I) A simple rule for the evolution of cooperation on graphs and social networks. Nature 441 (2006).
Ohtsuki, H., Hauert, C., Lieberman, E., Nowak, M.A. (II) A simple rule for the evolution of cooperation on graphs and social networks. Appendix. Nature 441 (2006).
Payne, J.L.. Moore, J.H., Wagner, A. Robustness, evolvability, and the logic of genetic regulation. Artificial life 20.1 (2014).
Rao, C.V., Wolf, D.M., Arkin, A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 (2002).
Ruelle, D. Biology and nonequilibrium. The European Physical Journal Special Topics 224.5 (2015).
Schaub, M.A., Henzinger, T.A., Fisher, J. Qualitative networks: a symbolic approach to analyze biological signaling networks. BMC Systems Biology 1 (2007)
Scott-Phillips, T.C., Blythe, R.A. Why is combinatorial communication rare in the natural world, and why is language an exception to this trend? Journal of the Royal Society Interface 10.88 (2013)
Siegal, M.L., Bergman, A. Waddington's canalization revisited. PNAS 99.16 (2002).
Soen, Y., Knafo, M., Elgart, M. A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation. Biology Direct 10 (2015).
Sprott, J.C., Vano, J.A., Wildenberg, J.C., Anderson, M.B., Noel, J.K. Coexistence and chaos in complex ecologies. Phys. Lett. A 335 (2005).
Toner, J., Tu, Y. Long-Range Order in a Two-Dimensional Dynamical XY Model: How Birds Fly Together. Phys. Rev. Lett. 75.23 (1995).
Valiant, L. Evolvability. JACM 56.1 (2009).
Vasas, V., Fernando, C., Santos, M., Kauffman, S., Szathmary, E. Evolution before genes. Biology Direct 7 (2012).
Vicsek, T., Czirsk, A., Ben-Jacob, E., Cohen, I., Shochet, O. Novel type of phase transition in a system of self-driven particles. Phys. Rev. Lett. 75.6 (1995).
Wagner, A. The molecular origins of evolutionary innovations. Trends in Genetics 27.10 (2011).
Wang, Z., Qin, C., Wan, B. Song, W. W. A Comparative Study of Common Nature-Inspired Algorithms for Continuous Function Optimization. Entropy 23.7 (2021).
Whitesides, G.M., Boncheva, M. Beyond molecules: Self-assembly of mesoscopic and macroscopic components. PNAS 99.8 (2002).
Wolpert, L. The evolutionary origin of development. Development 1994.
Yang, X.-S. A new metaheuristic bat-inspired algorithm. NISCO 2010.
Zhang, X. Jarrett, D.F. Chaos in a dynamic model of traffic flows in an origin-destination network. Chaos 8.2 (1998).