Instructor: Matthew Fricke |
Teaching Assistant: Bianca Cesina Bologa |

**Mailing List:**

A graduate level introduction to selected topics in complex adaptive systems focusing on computational tools to simulate and measure complexity, and analysis of biological and social complex adaptive systems. Topics include definitions of complexity, cellular automata, networks, evolution and genetic algorithms, dynamical systems, scaling and fractals, ant colony algorithms and swarm intelligence.

We don't have a textbook for this course, but we'll use as a guide *Complexity, A Guided Tour*. Each week we'll read journal articles to explore concepts from the book in more technical and intellectual depth.

Title: Complexity: A Guided Tour Author: Melanie Mitchel Publisher: Oxford University Press Paperback (2011): ISBN-10: 0199798109 ISBN-13: 978-0199798100 or, Hardcover (2009): ISBN-10: 0195124413 ISBN-13: 978-0195124415 |

- Background (January 16, 2017 - January 22, 2017)
- The Complex World
- Historical Context
- Dynamical Systems and Chaos (Jan 23rd - Feb 5th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 2, 2009 - Flake, G.
*The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation*, Chapter 10, 2000 - Turing A., Chemical Basis of Morphogenesis
- Lorenz, E., Computational Chaos
- Basic Concepts
- Systems of Coupled Differential Equations
- Dynamical Systems
- Deterministic Chaos
- Computational Chaos
- Measures of Complexity (Feb 6th - Feb 12th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 3, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 4, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 7, 2009 - Gell-Mann, M. What is Complexity?,
*Complexity, Vol 1, no. 1*, 1995

- Information Theory
- Algorithmic Complexity
- Generative Complexity
- Evolution and Genetic Algorithms (Feb 13th - Feb 19th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 5, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 6, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 8, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 9, 2009 - Hughes, A. The Central Dogma and Basic Transcription, 2003
- Losos, J. Evolutionary Biology for the 21st Century, 2013
- Wilson, E. Evolution and Our Inner Conflict, 2012(optional)
- Forrest, S. Genetic Algorithms: Principles of Natural Selection Applied to Computation, 1993
- Floreano, D. Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection, 2010
- Weimer, W. Automatically Finding Patches Using Genetic Programming, 2009
- Cellular Automata (Feb 20th - Feb 26th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 10, 2009 - Neumann, J., Theory of Self Reproducing Automata, 1966
- Wolfram, S. Cellular Automata as Models of Complexity, 1984
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 11, 2009 - Mitchell M. Evolving Cellular Automata to Perform Computations: Mechanisms and Impediments, 1994
- Modeling and Game Theory (Feb 27th - Marth 5th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 13, 2009

- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 14, 2009 - Axelrod, R.
*The Evolution of Cooperation*Chapters 1, 2, and 9, 1981 - Press, W. Iterated Prisoner's Dilemma Contains Strategies that Dominate any Evolutionary Opponent, 2012
- Axelrod, R., Timing of Cyber Conflict
- Midterm Review, Read Chapter 12 in Mitchell for Wednesday, March 8th
- Midterm on Friday, March 10th

- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 15, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 16, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 17, 2009 - Clauset, A. Power-law Distributions in Empirical Data, 2009
- Barabasi, A. Emergence of Scaling in Random Networks, 1999
- Tero A. Rules for Biologically Inspired Adaptive Network Design, 2010
- Meyers, C. Software systems as complex networks: Structure, function, and evolvability of software collaboration graphs, 2003
- West, G. Life's Universal Scaling Laws, 2004
- Seoane, L., Phase transitions in Pareto optimal complex networks, 2015

- Forrest, S. Computer immunology, 2007
- Smith, D. Mapping the Antigenic and Genetic Evolution of Influenza Virus, 2004
- Triani, V. Evolving Aggregation Behaviors in a Swarm of Robots, 2003
- Dorigo, M. Swarmanoid: a Novel Concept for the Study of Hetrogeneous Robotic Swarms, 2011
- Brooks, R. New Approaches to Robotics, 2010
- Williams, L. Evolution of Tail-Call Optimization in a Population of Self-Hosting Compilers, 2013
- Dorigo, M. Ant Colony Optimization: Artificial Ants as a Computational Intelligence Technique, 2006
- Marshall, J. On Optimal Decision-Making in Brains and Social Insect Colonies, 2009
- Doyle, J., Robustness and the Internet

- Ant Colonies
- The Internet
- Immunolgy
- Social Systems and Economics
- Swarm Robotics
- Cognition and Neural Networks
- Autocatalisis and Chemical Reaction Networks
- Software

- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 18, 2009 - Mitchell, M.
*Complexity: A Guided Tour*, Chapter 19, 2009

- Projects: 4x15%=60%
- Exams: 2x15%=30%
- (Graduate Students) Class Presentation: 10%

You will be assigned to work groups.

- github.com
*commits*: 35%
You will be graded on:
*Commit*message quality.- Code organisation and readability.
- Code progression.
- A least 10
*commits*across at least 5 different days. - Github readme describing how to compile the code under Ubuntu 14.04 or 16.04, including required packages.
- 5 page paper: 35%
- Paper peer review: 30%
- You will be graded on how accurately you review the two papers you are assigned.
- Project Review Guidelinestex

Assigned Jan 18th.

Papers due on February 3rd. Reviews due on February 10th.

February 3rd is also the drop without a 'W' grade and full refund deadline.

Assigned Feb 13th.

Papers due on Feb 14th. Reviews due on March 6th.

Assigned March 8th.

Papers due on Mar 29th. Reviews due April 5th.

February 27th is the last day to drop without dean's permission.

Assigned April 7th.

Papers due on April 28th. Reviews due on May 5th.

Date: March 10th

O'Conner, K., "Should I Give the Exam Before or After the Break?",May 12th, 7:30-9:30am.