Adjunct Assistant Professor: 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 Mitchell 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) Read the following by Jan 23rd.
- The Complex World
- Dynamical Systems and Chaos (Jan 23rd - Feb 5th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 2, 2009 (Read by Jan 27th) - Flake, G.
*The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation*, Chapter 10, 2000 (Read by Jan 30th) - May, R. Simple Mathematical Models with Very Complicated Dynamics, 1976 (Read by Jan, 27th)
- Krivine, H., Discrete-time and continuous-time modelling: Some bridges and gaps, 2007 (Optional)
- Turing A., Chemical Basis of Morphogenesis (Optional)
- Lorenz, E., Computational Chaos(Advanced)(Mixon-Baca and Arefi, Feb 1st), Student Presentation
- Lectures
- 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 (Read by Feb 12th) - Crutchfield, J. Between Order and Chaos,
*Nature Physics*, 2012(Read by Feb 12th) - Evolution and Genetic Algorithms (Feb 13th - Feb 26th)
- 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
- Lecture 9: Genetic Algorithms
- Lecture 10: Genetic Algorithms
- Notes on creating figures for Project2: Genetic Algorithms
- Cellular Automata (Feb 27th - March 6th)
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 10, 2009 - Neumann, J., Theory of Self Reproducing Automata, 1966(Ridens & Shubsda, March 1st) Student Presentation
- Wolfram, S. Cellular Automata as Models of Complexity, 1984(Collishaw & Kumar, March 3rd) Student Presentation
- Mitchell, M.
*Complexity: A Guided Tour*, Chapter 11, 2009 - Mitchell M. Evolving Cellular Automata to Perform Computations: Mechanisms and Impediments, 1994
- Modelling and Game Theory (March 20th - April 2nd)
- 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(Terrell, March 22th)Student Presentation
- Ehlen, M., "The Effects of Bank Size on Equilibrium Price Dispersion", 2002(Kay, March 24th)Student Presentation
- Axelrod, R., Timing of Cyber Conflict(Cashin, March 29th)Student Presentation
- Networks and Scaling (April 3rd - April 16th)
- 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 (Optional)
- Tero A. Rules for Biologically Inspired Adaptive Network Design, 2010(Knez, April 10th)Presentation
- Meyers, C., Software systems as complex networks: Structure, function, and evolvability of software collaboration graphs, 2003(McIver & Liu, April 10th)Student Presentation
- West, G., Life's Universal Scaling Laws, 2004
- Seoane, L., Phase transitions in Pareto optimal complex networks, 2015 (Optional)
- Canonical Complex Systems (April 17th - May 14th)
- Forrest, S. Computer immunology, 2007(Smith & Macias, April 19th)Student Presentation
- Smith, D. Mapping the Antigenic and Genetic Evolution of Influenza Virus, 2004(Surjadidjaja & Cai, April 19th)Student Presentation
- Triani, V. Evolving Aggregation Behaviors in a Swarm of Robots, 2003(Tasnim & Siddiquee, April 26th)Student Presentation
- Dorigo, M. Swarmanoid: a Novel Concept for the Study of Hetrogeneous Robotic Swarms, 2011(Salmonson & Tashakkori, April 28th)
- Brooks, R. New Approaches to Robotics, 1991(Bojja, May 3rd)Student Presentation
- 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 (Optional)
- Marshall, J. On Optimal Decision-Making in Brains and Social Insect Colonies, 2009 (Optional)
- Doyle, J., Robustness and the Internet(Byrd, May 3rd)
- The Internet
- Immunology
- Social Systems and Economics
- Swarm Robotics
- Ant Colonies
- Cognition and Neural Networks
- Autocatalysis and Chemical Reaction Networks
- Software
- Projects: 4x15%=60%
- Exams: 2x15%=30%
- Class participation: 10%
- 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

Speaker: Josh Hecker, Ph.D., UNM-NASA Swarmathon Technical Lead, March 31st. "Modeling Swarm Robotics as a Complex System".

Presentation

Presentation

Speaker: Lance Williams, Ph.D., Associate Professor, UNM CS, April 21st.

Presentation

Note: Instructor will be at Kennedy Space Center from April 15th to April 22nd. Guest lecturers will cover classes.

You will be assigned to work groups.

Assigned Jan 23th.

Papers due on February 10th. Reviews due on February 17th.

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

Portable Memory Array Redcode Simulator: pmars

and with support for graphics: pmarsx.

Manual

Don't forget to change permissions on pmars to make it executable: chmod +x pmars

Assigned Feb 20th.

Papers due on March 10th. Reviews due on March 20th. In class competition on March 20th.

Assigned March 21st.

Papers due on April 14th. Reviews due April 21st.

Assigned April 21st.

Papers due on May 5th. There will be no reviews for this project.

April 14th is the last day to drop without dean's permission.

Content: there will be two versions of the exams. For *undergraduate* students the exams will cover material from the assigned readings in Complexity a Guided Tour. For *graduate* students the exams will also cover the papers listed on the course website. The questions will be designed to test whether students have read and understand the main ideas of the readings. All students will also be expected to be able discuss the ideas and tools they used in writing their projects.

Format: short answer and multiple choice.

Undergraduate Midterm Solutions

Date: March 10th

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