CS423/523: Complex Adaptive Systems - Spring 2013
Professor: Melanie Moses
Office: Farris Engineering Center Room 327
Office Hours: Monday 12:30-2:00pm and Thursday 9:00-11:00am.
Teaching Assistant: Matthew Fricke
Office: Farris Engineering Center Room 323
Office Hours: Wednesday 12:30-2:00pm and Tuesday 8:30-10:30am.
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, 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
Course Topics and Reading list
All readings are protected. You will recieve the username and password in class.
Logistic Map Lecture Slides
Logistic Map Bifurcation Breakdown
Matlab Code for the Logistic Map
Fourier Transform Example
Natural Selection Lecture Slides
Information Lecture Slides
Read the following by Wednesday, January 16th
- Mitchell, M. Complexity: A Guided Tour, Chapter 1, 2009
- 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
Read the following by Wednesday, January 23rd
- Mitchell, M. Complexity: A Guided Tour, Chapter 5, 2009
- Mitchell, M. Complexity: A Guided Tour, Chapter 6, 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)
Read the following by Monday, January 28th
- Mitchell, M. Complexity: A Guided Tour, Chapter 3, 2009
- Mitchell, M. Complexity: A Guided Tour, Chapter 4, 2009
Read the following by Wednesday, January 30th
- Mitchell, M. Complexity: A Guided Tour, Chapter 7, 2009
- Gell-Mann, M. What is Complexity?, Complexity, Vol 1, no. 1, 1995
Presenters: Nathan Rackley, Jacob Hobbs, and Matthew Antognoli
- Evolution and Genetic Algorithms
Genetic Algorithms Lecture Slides
Review and Reproducing Programs Lecture Slides
Read the following by Monday, February 4th
- Mitchell, M. Complexity: A Guided Tour, Chapter 8, 2009
- Mitchell, M. Complexity: A Guided Tour, Chapter 9, 2009
Read the following by Wednesday, February 6th
- Forrest, S. Genetic Algorithms: Principles of Natural Selection Applied to Computation, 1993
Presenters: April Suknot, Steven Garcia, and Jeff Bowles
- Floreano, D. Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection, 2010
Presentation (18MB rar archive)
Presenters: Pravallika Devineni,Architha Marri, and Hiba Alkhafaji.
Read the following by Monday, February 11th
- Weimer, W. Automatically Finding Patches Using Genetic Programming, 2009
Presenters: Qi Lu, Shuang Yang, and David DeBonis.
- Cellular Automata
Cellular Automata Lecture Slides
Read the following by Wednesday, February 13th
- Mitchell, M. Complexity: A Guided Tour, Chapter 10, 2009
- Wolfram, S. Cellular Automata as Models of Complexity, 1984
Read the following by Monday, February 18th
- Mitchell, M. Complexity: A Guided Tour, Chapter 11, 2009
- Mitchell M. Evolving Cellular Automata to Perform Computations: Mechanisms and Impediments, 1994
Presenters: Geoff Alexander, Xu Zhang, and Lengge Se.
- Swarm Robotics
Read the following by Wednesday, February 20th
- Flanagan, T. How Ants Turn Information into Food, 2011
- Hecker, J. Formica ex Machina: Ant Swarm Foraging From Physical to Virtual and Back Again, 2012
- Brooks, R. New Approaches to Robotics, 2010
Presenters: Oscar Mondragon and Abhishek Reddy Yeruva.
Read the following by Monday, February 25th
- Triani, V. Evolving Aggregation Behaviors in a Swarm of Robots, 2003
Presenters: Tairen Chen, Mustafa Sinan Cetin, and Wuzhenni (Jane) Hu.
Read the following by Wednesday, February 27th
- Dorigo, M. Swarmanoid: a Novel Concept for the Study of Hetrogeneous Robotic Swarms, 2011
Presenters: Karl Stolleis, Amanda Minnich, and Jason Loyd.
- Ants and Ant Colony Optimization
Ant Colony Optimization Algorithm Lecture Slides
Brains and Social Insects Lecture Slides
Read the following by Monday, March 4th
- Dorigo, M. Ant Colony Optimization: Artificial Ants as a Computational Intelligence Technique, 2006
Presenters: Munand Kotha, Vineeth reddy Yeruva, and Faiza Ayoub.
Read the following by Monday, March 18th
- Marshall, J. On Optimal Decision-Making in Brains and Social Insect Colonies, 2009
Presentation (24 MB)
Presenters: Antonio Espinoza, Wayne Just, and Sylvain Bernard.
- Midterm Exam
Miterm Review Lecture Notes
Miterm from 2012
- Midterm Review, Read Chapter 12 in Mitchell for Wednesday, March 20th
- Midterm on Monday, March 25th
- Brains, Neural Nets, and Analogies
Read the following by Wednesday, March 27th
- Ackley, D., Interactions between learning and evolution, 1991.
- Caudell, T., An Autonomous Distal Reward Learning Architecture for Embodied Agents, 1991.
Presenters: John Ericksen, Paul Groves, and Kevin Williamson.
- Natural and Computational Immunology
Read the following by Monday, April 1st
- Forrest, S. Computer immunology, 2007
- Smith, D. Mapping the Antigenic and Genetic Evolution of Influenza Virus, 2004
Presenters: Matt Chase, Jianyu Yang, and Feng Huo.
- Modeling and the Prisoner's Dilemma
Read the following by Wednesday, April 3rd
- Mitchell, M. Complexity: A Guided Tour, Chapter 13, 2009
Presenters: Xinhua Zhang, Lidong Wang, and Jiani Chen.
Read the following by Monday, April 8th
- 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
Presenters: Cianan Sims, Mahnush Movahedi, and Srinivasa Somepalli.
- Networks, Scaling and Fractals
Read the following by Wednesday, April 10th
- Mitchell, M. Complexity: A Guided Tour, Chapter 15, 2009
- Mitchell, M. Complexity: A Guided Tour, Chapter 16, 2009
- Barabasi, A. Emergence of Scaling in Random Networks, 1999
Presenters: Qian Yu, Zhenjie Chen, and Torin Adamson.
Read the following by Monday, April 15th
- Mitchell, M. Complexity: A Guided Tour, Chapter 17, 2009
- West, G. Life's Universal Scaling Laws, 2004
Presenters: Parvathi Somasundara velayudham, Taylor Groves, and Dewan Shafi.
Read the following by Wednesday, April 17th
- An Introduction to Fractal Image Compression, Texas Instruments, 1997
Presenters: Amir Arbabshirani, Mohammad Faraz Alam and Thomas Jones
- Complexity Revisited
Read the following by Monday, April 22nd
- Mitchell, M. Complexity: A Guided Tour, Chapter 18, 2009
- Tero A. Rules for Biologically Inspired Adaptive Network Design, 2010
Presenter: Carlos Alvarez
Read the following by Wednesday, April 24th
- Mitchell, M. Complexity: A Guided Tour, Chapter 19, 2009
- Williams, L. Evolution of Tail-Call Optimization in a Population of Self-Hosting Compilers, 2013
Presenter: Lance Williams
For each project in this class you will submit an electronic version and a printed version. The electronic copy will consist of the following files: a pdf document containing your report, any data files you used, source code for your project, and a README.txt file (example). The readme file will contain a description of the files you are submitting, instructions on how to compile and run your project code, and a list of group members (Full Name and UNM CS Login ID) submitting the project.
We must be able to compile and run your programs on the CS linux computers. If we cannot run your code using the instructions in your readme file on the CS machines you will receive zero points for the project.
- The code should have a clear comment block at the top of each file with team members names
- All modifications to code should be clearly delineated by a comment block explaining if it was a modification or addition to original code
- A core dump or seg fault will get a zero
The printed copy will be a printout of your report (no source code, no data files, etc). Make sure the names of all group members and their CS Login IDs are printed at the top of the report. You may divide up work on the assignments between group members but all group members will recieve the same grade. Therefore it is in your interest to make sure you have reviewed and agree with the solutions your groupmates produce.
How to Submit your Projects
Turn in one copy of the printed report per group during class on the day the assignment is due.
To submit the digital copy of your project login to your CS account and use the turnin script to send us your files. Only one person per group should turn in a digital copy.
Files to be turned in must be world readable for the script to work. Run the command chmod a+r myfile(s) before running the turnin script.
Usage: turnin [Assignment Name] [Your File Name]
Example: turnin Project1 ~/cs523/Project1/Report.pdf # Submits Report.pdf for grading as part of Project1
Usage: turnin -rm [Assignment Name]
Example: turnin -rm Project1 # Removes all the files you submitted for Project1
Usage: turnin -ls [Assignment Name]
Example: turnin -ls Project1 # List all the files you have submitted for Project1
You should run chmod a-r myfile(s) on your files after turning them in so that your homework remains private.
Project 1: Population Dynamics
Due on February 4th.
Turnin Name: Project1
Example Report 1, Example Report 2.
Time series: X, Y, and Z.
Example Solution 1, Example Solution 2.
Project 2: Genetic Algorithms
Friday, March 8th by 4:00pm, + 10 points (350 possible)
Monday, March 11th by 4:00pm, - 10 points (330 possible)
Tuesday, March 12th by 4:00pm, - 10% (-34 points)
Wednesday, March 13th by 4:00pm, -10% (-72 points)
No submissions will be accepted after March 13th.
Turn the hard copy of your report in to the CS office on the first floor of the Farris Engineering Center.
Turn in the electronic version using the turnin script. Turnin Name: Project2
Assignment - Parts 1 & 2.
Ant Project Class Slides.
See the README files for version changes.
AntBots Release 1.2. Feb 20th 2013.
AntBots Release 1.3. Feb 22nd 2013.
AntBots Release 1.4. Feb 25th 2013.
AntBots Release 1.5. Feb 26th 2013.
VisRun Release 1.1. Feb 26th 2013.
Recruitment and Site Fidelity (Background reading for Part 2)
Part 2 Parameter Table
Project 3: Complex Adaptive Systems
Turnin Name: Project3
AntBot Code (Version from Josh's Lab)
Quiz 1 Solution: b, b, c, c.Quiz 2 Solution: True, abc, a or b, a, b, True.