· **Instructor:** Dr. Ivan Garibay, UT-556, 2-1163, igaribay@ucf.edu

· **Class Time and Location:** T/R 3:00 PM – 4:15 PM, ENGR 383

· **Class website: **http://ivan.research.ucf.edu/classes/CAP6675_Fall2012/

Skip to Lecture Notes (topics covered, distributed material, homeworks, deadlines, etc.)

Skip to Important Dates

Skip to Assigned Papers

Skip to Student Papers Presentations Schedule

Skip to Recommended Reading

Skip to Project Progress Presentation Schedule

Skip to Final Project Presentation Schedule

**Papers 1 (Complexity)**

**Murray Gell-Mann**(1995).**What is Complexity**?*Complexity*, 1:1.**Yaneer Bar-Yam**(2003).**Chapter 0: Overview: The Dynamics of Complex Systems -- Examples, Questions, Methods, and Concepts**.*Dynamics of Complex Systems*. Westview Press.**Herbert A. Simon**(1962),**The Architecture of Complexity**,*Proceedings of the American Philosophical Society,***106**(6) 467-482

**Papers 2 (Cellular Automata)**

**Stephen Wolfram**(1983).**Statistical mechanics of cellular automata**.*Reviews of Modern Physics*, 55, 601-644.**Martin Gardner**(1970).**Mathematical games: The fantastic combinations of John Conway's new solitaire game "Life"**.*Scientific American*, 223: 120-123.

**Papers 3 (Cellular Automata)**

**Melanie Mitchell**,**Peter T. Hraber**, and**James P. Crutchfield**(1993).**Revisiting the edge of chaos: Evolving cellular automata to perform computations**.*Complex Systems*, 7, 89-130.**Robert Axelrod**(1980).**More effective choice in the Prisoner's Dilemma.***Journal of Conflict Resolution*, 24:3, 379-403.

**Papers 4 (Agent-Based Social Sciences)**

**Joshua M. Epstein**(2002).**Modeling civil violence: An agent-based computational approach**,*Proceedings of the National Academy of Sciences of the United States of America,*vol. 99, May 14, p. 7243-7250.**Jae-Woo Kim and Robert A. Hanneman**(2011),**A Computational Model of Worker Protest**,*Journal of Artificial Societies and Social Simulation***14**(3) 1**Joshua M. Epstein Longini I, Halloran M, Nizam, A, Yang Y, Xu S, Burke D, Cummings D**(2007). Containing a Large Bioterrorist Smallpox Attack: A Computer Simulation,*Int. Journal of Infectious Diseases*.;**11**(2): 98-108.

**Papers 5 (Agent-Based Social Sciences)**

**Joshua M. Epstein**(2006),**Generative Social Science: Studies in Agent-Based Computational Modeling**, Chapter 1, pp. 4-46**Joshua M. Epstein**(2006), Remarks on The Foundation of Agent-Based Generative Social Science,*Handbook of Computational Economics: Agent-Based Computational Economics*, Volume 2, Eds. L Tesfatsion and K. Judd, 1585-1602**Robert Axelrod**(2006),**Agent-Based Modeling as a Bridge Between Disciplines**,*Handbook of Computational Economics: Agent-Based Computational Economics*, Volume 2, Eds. L Tesfatsion and K. Judd, 1565-1584**Robert Axtell**,**Robert Axelrod**,**Joshua M. Epstein**and**Michael D. Cohen**(1996)**Aligning simulation models: A case study and results**,*Computational & Mathematical Organization Theory***1**:2 123-141,

**Papers 6 (Evolution of Cooperation)**

**Robert L. Axtell**(2002),**Non-Cooperative Dynamics of Multi-Agent Teams**,*In Proc. of the International Conference on Autonomous Agents and Multi-Agent Systems*.**Robert Axelrod**and WD Hamilton (1981),**The evolution of cooperation**, Science**211**(4489), 1390-1396**Marco Dorigo**,**V. Maniezzo**, and**A. Colorni**(1996).**The ant system: Optimization by a colony of cooperating agents.**, 26:1, 29-41.*Transactions on Systems, Man, and Cybernetics, Part B***D. Challet**and**Y. C. Zhang**(1997).**Emergence of cooperation and organization in an evolutionary game**.*Physica A*, 246, 407-418.

**Papers 7 (Agent-Based Computational Economics)**

**Farmer, J. Doyne**and Geanakoplos, John (2009).**The virtues and vices of equilibrium and the future of financial economics**,*Complexity*, 14 (3) 11-38**W. Brian Arthur**(2006), Out-of-Equilibrium Economics and Agent-Based Modeling, In*Handbook of Computational Economics: Agent-Based Computational Economics*, Volume 2, Eds. L Tesfatsion and K. Judd, 1551-1563**W. Brian Arthur**(1995),**Complexity in Economic and Financial Markets**, Complexity, 1 (1)

**Papers 8 (Agent-Based Computational Economics)**

**Gianfranco Giulioni**(2011).**The product innovation process and GDP dynamics**,*Journal of Evolutionary Economics*(2011) 21:595–618**Zahra Kodia**,**Lamjed Ben Said**, and**Khaled Ghedira**(2010).**Stylized Facts Study through a Multi-Agent Based Simulation of an Artificial Stock Market**,*In M. LiCalzi et al. (eds.), Progress in Artificial Economics***Blake LeBaron**(2006),**Agent-Based Computational Finance**, In*Handbook of Computational Economics: Agent-Based Computational Economics*, Volume 2, Eds. L Tesfatsion and K. Judd, 1187-1227**Harbert Dawid**(2006), Agent-Based Models of Innovation and Technological Change,*Handbook of Computational Economics: Agent-Based Computational Economics*, Volume 2, Eds. L Tesfatsion and K. Judd, 1235-1267

**Papers 9 (Networks)**

**Albert-Laszlo Barabasi**and**Reka Albert**(1999).**Emergence of scaling in random networks**.*Science*, 286, 509-512.**Duncan J. Watts**and**Steven H. Strogatz**(1998).**Collective dynamics of 'small-world' networks**.*Nature*, 393, 440-442.**Robert Axtell**(2001).**Zipf Distribution of U.S. Firm Sizes**, Science, 293 1818-1819

**Papers 10 (Evolution of Complexity)**

**A. M. Turing**(1952)**The Chemical Basis of Morphogenesis**,*Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences*, Vol. 237, No. 641, pp. 37-72.**Stuart A. Kauffman**(1994),**Whispers From Carnot: The Origins of Order and Principles of Adaptation in Complex Nonequilibrium Systems**, In*Complexity: Methaphors, Models, and Reality*, Edited by G. Cowan, D. Pines and D. Meltzer, pp. 83-136 Addison-Wesley.

Complex adaptive systems (CAS) are a broad class of systems consisting of multiple interacting adaptive agents. These systems, which span a wide range of disciplines, have a number of characteristics in common. They are large distributed systems consisting of many self-similar components that interact and adapt. These interactions among the distributed components are self-organizing and produce emergent collective behavior in the system as a whole. CAS tend to be difficult to analyze using traditional analytical models. Agent-based models have been shown to be effective methods for studying CAS. This course will introduce the basic definitions of CAS, discuss example cases of CAS and their features, and implement and analyze computational simulations of CAS.

__Topics:__

- Cellular automata

- Social systems

- Evolution of cooperation

- Self-organization

- Social networks

- Agent-Based Computational Economics

This course will be structured as follows:

- Two papers will be assigned each week. You will be asked to read the papers and write a one-page summary/critique/comparison of the papers each week. These summaries will make up 15% of your final grade. Late summaries will not be accepted. You may drop two summaries.

- Each week two students will be asked to present the papers for that week to the class in an oral presentation. This presentation will include summarizing the paper and leading a discussion on the paper topic. These presentations will make up 20% of your final grade.

- You will have two homework projects during the first half of the course. All programming can be done in any programming language. These homeworks will be worth 25% of your final grade.

- Throughout the class you will work on a final research project. Before the middle of the course each student proposes an individual project. The proposed ideas are discussed in one or more individual meetings and one particular project is agreed upon between the instructor and the student. During the second half of the course, the student carries out the agreed project. The student writes up his/her work in a 8 to 10 pages paper (in the style of a conference paper). Towards the end of the semester all students will be ask to present their project to the class. The project due date, students must bring three extra copies of their project to be distributed to other three students to be anonymously peer reviewed. The last day of classes all students must bring their written reviews. Your final project grade will be partially based on the peer reviews of your work and the reviews that you write about other student’s projects. All projects will be compiled into a class book and published as an EECS Technical Report and also in the class website. Copies of this book will be distributed to all students. This final research project is worth 40% of your final grade.

**August 28, 2012**

**Homework -1 Assignment**

**September 18, 2012**

- Homework Assignment #1 Due
**Final Project Assignment**

**October 9, 2012**

- Progress Report Due (2 page write-up, 5 minute presentation)

**November 15, 2012**

- Final Project Due (8-10 page write-up, 15 minute presentation)

**Complex Adaptive Systems**

- Complexity a Guided Tour by Melanie Mitchell. An excellent book to understand the big picture of the science of complexity. The key developments and the key people involved. Lacks, by design, mathematical treatment of subjects.
- Complex and Adaptive Dynamical Systems: A Primer, by Claudius Gros. A concise and to-the-point treatment of most important subjects in complexity theory. Well explained and with an adequate mathematical treatment. It is a great complement for Mitchell’s book.
- The Computational Beauty of Nature: computer explorations of fractals, chaos, complex systems, and adaptation by Gary William Flake. This wonderful book with many great descriptions of computational examples, clearly explained for their relevance. Covers: fractals, chaos, complex systems and adaptation.

**Complex Adaptive Systems in Social Sciences & Economics**

- Growing Artificial Societies: Social Science from the Bottom Up by Joshua M. Epstein and Robert Axtell
- Complex Adaptive Systems: An introduction to computational models of social life by John H. Miller and Scott E. Page. Great treatment of models of complex adaptive social systems.
- Generative Social Science: Studies in Agent-Based Computational Modeling by Joshua M. Epstein. This book starts with the “generativist manifesto” and continues with a collection of good papers on agent-based modeling applied to social phenomena.
- Handbook of Computational Economics: Agent-based Computational Economics, Volume 2, Eds. Leigh Tesfatsion and Kenneth L. Judd

**Mathematical Treatment of Complex Systems**

- Complex Systems by Terri R. J. Bossomaier and David G. Green: Good compendium of theoretical essays of different aspects of complex systems.
- Dynamical Systems: Stability, Symbolic Dynamics and Chaos by Clark Robinson
- Nonlinear Dynamics and Chaos by Steven H. Strogatz

**Agent-Based Modeling and Simulation**

- Agent-Based Models by Nigel Gilbert
- Simulation for the social scientist by Nigel Gilbert and Klaus G. Troitzsch
- Turtles, Termites, and Traffic Jams: Explorations in Massively Parallel Microworlds by Mitchel Resnick.

**Complex Systems (Some Related Accounts and Seminal Works):**

- Hidden Order by John Holland. Holland’s seminal work on CAS and ECHO.
- A New Kind of Science by Stephen Wolfram. This is a great treatment of cellular automata with a massive graphical compilation of many CAs.
- Networks: An Introduction by Mark E. J. Newman
- The Selfish Gene by Richard Dawkins
- Self-made Tapestry: Pattern Formation in Nature by Philip Ball
- Complexity by M. Mitchell Waldrop. An engaging account of how the Santa Fe Institute came to be focusing on the emergence of the science of complexity.
- Exploring Complexity: An Introduction by Gregoire Nicolis and Ilya Prigogine
- Complexity: Metaphors, Models, and Reality, Edited by George A. Cowan, David Pines and David Meltzer.
- The Origins of Order by Stuart A. Kauffman
- The Quark and the Jaguar: Adventures in the Simple and the Complex by Murray Gell-Mann

**August 21, 2012 - Introduction**

- Course introduction and administrative stuff
- Materials:
**CAP 6675 Syllabus**- Presentations Schedule
- Papers 1Assigned

**August 23, 2012 - Complexity**

- Topics Covered:
**Complex Adaptive Systems (CAS): What are they?**- Reductionism and the scientific method
- New approach to science: Complexity Sciences
- Examples of CAS
- Ant Colonies
- Brain
- Economies
- Properties of CAS (M. Mitchell)
- Complex Collective Behavior
- Signaling and Information Processing
- Adaptation: Learning and/or Evolutionary
**Complexity a guided tour by Melanie Mitchell**, Chapter 1

**August 28, 2012 - Complexity**

- Topics Covered:
- Self-organization, Emergence
- What is Complexity?
- How Can Complexity Be Measured
- Complexity as Size
- Complexity as Entropy
- Deadlines: Papers-1 Summaries Due
- Materials:
**CAP6675 Homework Assignment 1**- Due September 18, 2012
**Nigel Gilbert. Agent-Based Models**: 4.3 Building the Collectivities Model Step by Step- Papers 2 assigned
- Readings:
**Complexity a guided tour by Melanie Mitchell**, Chapter 7**Complex Adaptive Systems by Claudius Gros**, Chapter 3

**August 30, 2012- Complexity **

- Topics Covered:
- Complexity as Algorithmic Information Content (Kolmogorov)
- Effective Complexity (Murray Gell-Mann)
- Complexity as Degrees of Hiearchy (Herbert Simon)
- Readings:
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 8- The Computational Beauty of Nature by Flake, Chapter 15

**September 4, 2012**

- Student Paper Presentations-1
- Paper Summaries- 2 Due
- Papers- 3 assigned

**September 6, 2012**

- Student Paper Presentations-2

**September 11, 2012**

- Student Paper Presentations-3
- Paper Summaries- 3 Due
- Papers- 4 assigned

**September 13, 2012 - **

- Student Paper Presentations- 4

**September 18, 2012 - Cellular Automata**

- Topics Covered:
- Self-reproducing Computer Programs
- What is life?
- Artificial Life
- Von Neumann’s Self-reproducing Automaton
- Deadlines:
- Homework Assignment 1 is due
- Paper Summaries-4 Due
- Materials:
- Papers- 5 assigned
- Final Project
- Readings:
**The Computational Beauty of Nature**by Flake, Chapter 15**A New Kind of Science by Wolfram**, Chapters 3 and 8

**September 20, 2012 - Cellular Automata**

- Topics Covered:
- Self-Replication in DNA
- Cellular Automata
- One-Dimensional CA
- Wolfram's Classification of CAs
- Readings:
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 14

**September 25, 2012 – Cellular Automata**

- Topics Covered:
- Langton's Lambda Parameter
- Conway's Game of Life
- CA-like Phenomena in Programs and in Nature
- Universal Computation
- Principle of Computational Equivalence (NK
- Deadlines:
- Papers-5 Summaries Due
- Materials:
- Papers-6 assigned

**September 27, 2012- Competition and Cooperation**

- Topics Covered:
- Computer Models of Complex Systems
- Evolution of Cooperation
- PD, IPD
- Extensions
- Caveats of Computer Modeling
- ABM Best Practices
- Readings:
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 5, 9- Evolutionary Computation: A Unified Approach by Kenneth DeJong, CH1

**October 2, 2012 **

- Student Paper Presentations-6
- Papers-6 Summaries Due

**October 4, 2012 **

- NO CLASS

**October 9, 2012**

- Project Progress Presentation-1
- Progress Report Due (2-page write up - 5 minute presentation)

**October 11, 2012**

- Project Progress Presentation-2
- Papers-7 Assigned

**October 16, 2012- Adaptation**

- Topics Covered:
- Evolution
- Evolutionary Process
- Minimal Evolutionary Algorithm
- Readings:
- Evolutionary Computation: A Unified Approach by Kenneth DeJong, CH1
**My Rules of Thumb**By N. Gregory Mankiw

**October 18, 2012**

- Student Paper Presentations-7
- Papers-8 Assigned
- Papers-7 Summaries Due

**October 23, 2012 - Adaptation**

- Topics Covered:
- Simulating EV on a single peak landscape
- Conceptual Space, Represented Space, Reachable Space
- Simulating EV on a multiple peaks landscape
- Evolutionary Systems as Problem Solvers

**October 25, 2012**

- Topics Covered:
- Genetic Algorithms
- No Free Lunch Theorems
- Search Spaces, Fitness Landscapes
- Building Block Hypothesis
- Schema Theorem

**October 30, 2012 - Networks**

- Topics Covered:
- Small-world
- Scale-free
- Preferential Attachment
- Applications: Innovation Networks
- Readings:
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 15, 16

**November 1, 2012**

- Student Paper Presentation-9
- Papers-10 Assigned
- Papers 9 Summaries Due

**November 6, 2012 - Networks**

- Topics Covered:
- Scaling
- Power Law
- Zipf’s Law
- Readings:
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 17

**November 8, 2012**

- Student Paper Presentation- 10
- Papers- 10 Summaries Due

**November 13, 2012 - Evolution of Complexity **

- Topics Covered:
- Evo-Devo
- Kauffman’s “Origins of Order”
- Future of Sciences of Complexity
- Readings
**Complexity a Guided Tour**by Melanie Mitchell, Chapter 18, 19

**November 15, 2001**

**Final Project Presentations**:- 3:00 - 3:25 - Yazen Ghannam
- 3:25 - 3:50 -

**November 20, 2012**

**Final Project Presentations:**- 3:00 - 3:25 - Michael Gabilondo
- 3:25 - 3:50 - Fan Wu
- 3:50 - 4:15 - Jun Ding

**November 22, 2012**

- Thanksgiving Day - no class

**November 27, 2012**

- Deadlines:

**Final Project Presentations:**- 3:00 - 3:25 - David Gross

- 3:25 - 3:50 - Charles Snyder
- 3:50 - 4:15 - Zac Chenaille

**November 29, 2012**

**Final Project Presentations:**- 3:00 - 3:25 - Taranjeet Singh Bhatia
- 3:25 - 3:50 - Lisa Soros
- 3:50 - 4:15 - Syed Alam Abbas

**Final Exam Date**, December 6

**Final Project Presentations:**- 1:00 - 1:25 - Vera Kazakova
- 1:25 - 1:50 - Justin Pugh
- 1:50 - 2:15 - John Edison
- 2:15 - 2:35 - Miguel Becerra