Course Readings

Introduction (2 weeks)
- Mitchell Chs. 1-3, 7
- G. Flake, Computational Beauty of Nature, Ch. 10, MIT Press (2000)
- T.D. Schneider Information theory primer (2000)
- J. Holland Hidden Order, Ch. 10, Addison-Wesley (1995)
Evolution and Genetic Algorithms (3 weeks)
- Mitchell, Chs. 5-6, 8-9
- G. Flake Computational Beauty of Nature, Ch. 20, MIT Press (2000)
- C. LeGoues et al. A systematic study of automated program repair Intl. Conf. on Software Engineering (2012)
- E. Schulte et al. Repairing COTS Router Firmware without Access to Source Code or Test Suites GECCO Genetic Improvement Workshop (2015)
- A. Wagner The role of robusteness in phenotypic adaptation and innovation Proc. R. Soc. B 279 (2012) pp. 1249–1258
- E. Schulte et al. Software Mutational Robustness GPEM 5 (2014)
- K. Stanley and R. Miikkulainen Evolving neural networks through augmenting topologies Evolutionary Computation 10:2 (2002)
- B. Woolley and K. Stanley A novel human-computer collaboration GECCO, 2014.

Cellular automata (2 weeks)
- Mitchell, Chs. 10-11
- S. Wolfram Cellular automata as models of complexity Nature 311:5985 (1984)
- M. Dorigo et al. Ant colony optimization artificial ants as a computational intelligence technique IEEE Computational Intelligence Mag. (2006)
- R. Abbott et al. Simulating the hallmarks of cancer Artificial Life 12:4 (2006)
- R. Gerety et al Modeling somatic evolution in tumorigenesis PLOS Computational Biology 2:8 (2006)
- P.Holme and F. Liljeros Mechanistic models in computational social science arXiv (2015)
- Recommended supplementary video introducing Cellular Automata and the Game of Life
- Interesting videos about modeling plant growth:
  - Part 1
  - Part 2
  - Part 3

Modeling complex adaptive systems (3 weeks)
- Mitchell, Ch. 14
- R. Axelrod The Evolution of Cooperation Chs. 1, 2, 9 (1981)
- R. Durrett and S. Levin The importance of being discrete (and spatial)
- R. Axelrod Agent-based modeling as a bridge between disciplines
- M. Nowak and R. May "The basic model of virus dynamics"
Computational Immunology
- Mitchell, Ch. 12
- Sompayrac How the Immune System Works (optional)
- A. Perelson and G. Oster Theoretical studies of clonal selection
- D. Smith et al. Variable efficacy of repeated annual influenza vaccination
- A. Read and J. Allen The economics of immunity
- Y. Moret et al. Survival for Immunity: The price of activation for bumblebee workers
- L. Martin et al. Immune activity elevates energy expenditures in house sparrows
- F. Wiegel and A. Perelson Some scaling principles for the immune system
- S. Hofmeyr and S. Forrest Architecture for an artificial immune system
- M. Groat et al. Enhancing privacy in participatory applications with multidimensional data
- Elberfeld and Textor Efficient algorithms for string-based negative selection
- E. Chastain et al. Defensive complexity and the phylogenetic conservation of immune control

Scaling, power laws, and complex networks (2 weeks)
- Mitchell Ch. 15-17
- A. Barabasi and R. Albert Emergence of scaling in random networks
- Newman Ch. 8
- A. Clauset et al. Power Law Distributions in Empirical Data (optional)
- G. West and J. Brown Life's universal scaling laws
- Moses and Forrest Beyond Biology
- S. Frank The common patterns of nature (optional)