Difference between revisions of "CSSS 2007 Santa Fe-Readings"
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Modeling of Terrorist Activity<br/>
Modeling of Terrorist Activity<br/>
[http://.//On the frequency of severe terrorist events] (Clauset, Young, Gleditsch
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|CSSS Santa Fe 2007
Week One: Modeling/Nonlinear Dynamics
Introduction to Nonlinear Dynamics
Presentation Slides, 1 of 2
Presentation Slides, 2 of 2
Syllabus & References: CSSS 2005
Numerical Solution of Differential Equations: Notes for CSCI3656
Time Series Analysis
CSCI 4446/6446 Course materials for Spring 2006
Chapter 1 from 'The Difference'
'Interpreted and Generated Signals' by Lu Hong and Scott Page
'Consistency and Coordination' by Bednar, Bramson, Jones-Rooy, and Page
'Adjustment Dynamics and Equilibrium Selection: Why How Players Learn Matters' by Russell Golman and Scott Page
Stephen Guerin, Owen Densmore, Josh Thorp
Stephen@Redfish.com, Owen@Redfish.com, Josh@Redfish.com
First of all, download the NetLogo 4.0 application: NetLogo Home Make sure to use the Versions menu on the download page to pick 4.0beta rather than the 3.1.4 default version.
Then read the documents: NetLogo Docs which are also in the application under the Help menu.
Note that the documentation within the Netlogo application is preferred, being 4.0, but slightly "in process" due to being beta.
Homework: Run NetLogo and look at the documentation .. especially the Learning and Reference sections. Then run and look at the code for at least three of the Model Library examples which are under the File Menu -> Model Library.
Web: Several models we'll be using in the class, along with a pdf file of the slides are available on The Modeling Web Site
miscellaneous readings -- I'll add more as time goes by . . .
Jennifer Dunne & Neo Martinez
Network structure and biodiversity loss in food webs: robustness increases with connectance
Food-web structure and network theory: The role of connectance and size
Simple rules yield complex food webs
Allometric scaling enhances stability in complex food webs
Stabilization of chaotic and non-permanent food web dynamics
The Network Structure of Food Webs
Food Web Refs from CSSS 2006
'Scaling up keystone effects from simple to complex ecological networks' Eco Letters, Brose, Berlow, Martinez
Software and demos from Neo's talks:  
Allometric Scaling Enhances Stability in Complex Food Webs
Ecological Network Structure Slides Pt. 1
Ecological Network Structure Slides Pt. 2
Ecological Network Structure Slides Pt. 3
Ecological Network Structure Slides Pt. 4
Martinez Slides Pt. 1
Martinez Slides Pt. 2
Martinez Slides Pt. 3
General Networks Refs:
The Structure and Function of Complex Networks
Exploring Complex Networks
Refs for Lecture 1:
Power laws, Pareto distributions and Zipf's law (Newman)
Power-law distributions in empirical data (Clauset, Shalizi, Newman)
Software, tutorials, and references are linked to the following page: 
- with Austin Gerig
- with Eric Smith
- with Neda Zamani
- Introduction to Evolutionary Computation: GA, EP, ES, PSO
- Genetic Programming, Embedded EAs
- Research Group Projects in GA and GP
Lecture Relevant Articles (will try to upload articles here):
- An overview of evolution algorithms for parameter optimization by T. Back, HP Schwefel in Evolutionary Computation, 1993.
- Check out the Genetic Programming.org website.
- Particle swarm optimization. Kennedy, J. and Eberhart, R. C. Proc. IEEE int'l conf. on neural networks Vol. IV, pp. 1942-1948. IEEE service center, Piscataway, NJ, 1995.
- Evolvable Hardware:
- Evolvable Hardware Chips for Industrial Applications by T. Higuchi and N. Kajihara.
- On Evolvable Hardware by T. Gordon, P.J. Bentley.
Nothing here is a must to date. I will bring some CDs with me. One has a lot of tutorials on subtopics in the field. Check out the GECCO 2007 website to see the list of tutorials this year. The CD has the tutorial handouts from last year. Plus, I'll bring some GECCO proceedings along.
Two obvious classics
- The Origin of Species by Charles Darwin.
- Adaptation in Natural and Artificial Systems by John R. Holland.
Great Reference Texts
- Evolutionary Algorithms in Theory and Practice: Evolution Strategies, Evolutionary Programming, Genetic Algorithms. Author: Thomas Back. Oxford University Press, 1996.
- An Introduction to Genetic Algorithms. Author: Melanie Mitchell. MIT Press, 1996.
- Evolvable Hardware. Editors: Tetsuya Higuchi, Yong Liu, Xin Yao. Springer, 2006.
- Spatially Structured Evolutionary Algorithms. Author: Marco Tomassini. Springer 2005.
- Hierarchical Bayesian Optimization Algorithm. Author: Martin Pelikan. Springer 2005.
- Evolutionary Algorithms for Solving Multi-Objective Problems. Editors: C. Coello Coello, D. Van Veldhuizen, G.B. Lamont. Kluwer Academic Publishers, 2002.
- Genetic programming : an introduction on the automatic evolution of computer programs and its applications. Authors: Wolfgang Banzhaf, Peter Nordin, Frank Francone. Morgan Kaufmann Publishers, 1998.
I recommend that all students look through the first couple of chapters of Reading 2. Otherwise, the students
should choose to read from among these based on what their interests and backgrounds are.
GENERAL LITERATURE ON BIOLOGICAL SCALING:
0. In the Beat of a Heart by John Whitfield
(A recent popular science book about the
history of and work on scaling relationships
1. Chapters 2 and 3 of On Growth and Form by D'arcy Thompson
(This is a seminal text for all mathematical biology.)
2. Scaling: Why is Animal Size so Important by Knut Schmidt-Nielsen
(This is an extremely clear and fairly succinct explanation of scaling in biology
up to the 1980's. This book focuses on physiology.)
3. The Ecological Implications of Body Size by R.H. Peters
(This book discusses how scaling relationships are useful
in ecology, and it has an incredibly useful set of appendices
for scaling relationships.)
4. Size, Function, and Life History by W.A. Calder
(Another good book on scaling and ecology.)
5. Scaling in Biology (SFI book), edited by J.H. Brown and G.B. West
(This book is a collection of articles by the leaders in the field,
and updates the literature in the scaling field, including numerous
theoretical advances of great importance.)
PAPERS FOR ORIGINS OF SCALING LAWS:
6. "A General Model for the Origin of Allometric
Scaling Laws in Biology", G.B. West, J.H. Brown, and B.J. Enquist
1997, Science (276) 122-126.
(This paper is a classic and puts forward the leading theory for an explanation of scaling relationships in biology.
The authors use a few simple assumptions about the structure and function of the cardiovascular system to construct the most powerfully predictive theory to date.)
7. V. M. Savage and G. B. West (2006). Biological scaling and physiological time: Biomedical applications. in Complex System Science in Biomedicine. Ed. T. S. Deisboeck and J. Y. Kresh, New York, Kluwer Academic. (The first part of this book chapter gives a more detailed account of the assumptions and derivations listed in Reading 6, and it also explains how biological rates and times depend on body temperature. This book contains several chapters by SFI faculty and alums and should provide interesting reading to those interested in the health sciences or an introduction to complex systems.)
PAPERS ON APPLYING SCALING RELATIONSHIPS TO ECOLOGY:
8. J. H. Brown, J. F. Gillooly, A. P. Allen, V. M. Savage, and G. B. West. (2004) Toward a metabolic theory of ecology (MacArthur award paper,), Ecology 85(7), 1771-1789.
(This paper lays out a modern approach to applying scaling relationships to ecological
9. V. M. Savage, J. F. Gillooly, J. H. Brown, G. B. West, and E. L. Charnov, (2004). Effects of
body size and temperature on population growth, The American Naturalist 163(3), 429-441.
(This paper gives one of the first examples of explicitly building up from scaling relationships
in individuals to those for populations.)
10. "Size and Scaling of Predator-Prey Dynamics" J Weitz and SA Levin
Ecol. Lett. 2006, (9) 548-557.
(This paper represents one of the first attempts to combine scaling relationships for body body mass with species interactions.)
11. "A Mechanistic Approach for Modeling Temperature-Dependent Consumer
Resource Dynamics", DA Vasseur and KS McCann AmNat 2005, (166) 184-198.
(This paper look at species interactions and how they are affected by temperature,
with possible implications for how global warming may affect biological systems.)
PAPERS APPLYING SCALING RELATIONSHIPS TO TISSUE- AND CELLULAR-LEVEL:
12. V. M. Savage and G. B. West, Towards a quantitative, metabolic theory of mammalian
sleep, (2007) PNAS 104(3), 1051-1056.
(This paper uses scaling relationships as a tool to better understand the function of sleep and
whether it is a process for the brain or the whole body.)
13. V. M. Savage, A.P. Allen, J. F. Gillooly, A. B. Herman, J. H. Brown, and G. B. West, (2007)
Scaling of number, size, and metabolic rate of cells with body size in mammals,
PNAS, 104(11), 4718-4713.
(This paper grapples with what the scaling relationships imply at the cellular level,
and how that might impact our understanding of cellular studies and phenomena.)
BOOKS ON POWER LAWS, FRACTALS, NON-LINEAR DYNAMICS, ETC.:
14. Fractals, Chaos, and Power Laws by Manfred Schroeder
(A good and playful introduction to these subjects.)
15. Nonlinear Dynamics and Chaos by Steven Strogatz
(An extremely well written introduction to these subjects.)