CSSS 2008 Beijing-Readings-Week-One

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CSSS 2008 Beijing

Dave Feldman

Lecture Notes

Additional Reading

  • James Crutchfield, What Lies between Order and Chaos?, in Art and Complexity, J. Casti, editor, Oxford University Press (2002). An interesting, non-technical essay discussing how new patterns are discovered, and how complexity arises from the interplay between order and chaos. This is an excellent introduction to the notions of complexity and emergence, and history of one strand of the study of complex systems.
  • Cosma Shalizi, Methods and Techniques of Complex Systems Science: An Overview. Chapter 1 (pp. 33--114) in Thomas S. Deisboeck and J. Yasha Kresh (eds.), Complex Systems Science in Biomedicine (New York: Springer, 2006.) This is an excellent, thorough review of the "field" -- to the extent that there is such a thing -- of complex systems. Covers many tools: statistical learning and model selection; time series analysis; cellular automata; agent-based models; the evaluation of complex-systems models; information theory; and ways of measuring complexity. Contains over 250 references. Also available here.
  • J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. cond-mat:0102181. This is a long paper discussing the entropy rate and excess entropy and including many different examples.
  • C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences", Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference (UAI 2004), pp. 504--511. Best description of the CSSR algorithm. cs.LG/0406011
  • K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", Advances in Neural Information Processing Systems 18 (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). q-bio.NC/0506009

Miguel Fuentes

Laplace's Deterministic Paradise Lost

Hao Bailin

Lecture Notes

A Brief Introduction to Written Chinese

Will Tracy

Lecture Notes

Additional Reading

Jon Wilkins

Lecture Notes

Lecture 1: Monday, June 30

Lecture 2: Wednesday, July 2

Additional Reading

Coalescent Theory:

Here are two different introductions to coalescent theory. One is a review article written by Magnus Nordborg:

The other is a chapter from John Wakeley's book called Coalescent Theory

If you are interesed in learning a lot more about the subject, I recommend the rest of the book as well

Genomic Imprinting:

Here are a couple of review articles that talk about the evolution of genomic imprinting

Here are some modeling papers on imprinting. The first two are the models that I used as an example in Wednesday's lecture

These are some papers that look at what happens when there are more than two "players" or "genetic factions" that are co-evolving

Also, here is a paper that talks about how the level of analysis in evolutionary problems affects how you perceive the role of natural selection in evolution It is now out it the Blackwell Companion to the Philosophy of Biology. It is the article entry on "Adaptationism" I don't have the final PDF with me, though, so I have attached the final draft that we sent to the publishers. I suspect that it is similar, though.

  • Adaptationism Godfrey Smith and Wilkins, Blackwell Companion to the Philosophy of Biology, 1997

Approximate Bayesian Computation

Here are a few papers that describe the basic ideas of Approximate Bayesian Computation. In these papers, the applications are specifically population genetic. One warning: the techniques used in these papers to deal with the issues of correlations among statistics, etc. are completely ad hoc. The procedure that I outlined on Friday is somewhat less ad hoc. Soon, I hope to post something that provides a written description of what I talked about. Conceivably, even some code to implement these steps.

Henry Wright

Lecture Notes

Additional Reading

Foragers and the Emergence of Agriculture

Villages and the Emergernce of Tribal Alliance Systems

Raising Civilizations

Richard Callahan

Download SIENA

  • Go to to download StOCHNET, the Graphical User Interface that houses SIENA. StOCHNET comes built in with last year's version of SIENA. Download the .zip file for version 1.8 and run the executable.
  • There's also a brand-new version of SIENA that came out on Monday that you can download from You should just have to switch the executables for SIENA that unpack with StOCHNET with these newer ones. Apologies but I haven't yet done this myself, so I can't verify that the process works as it should.


Lecture Notes

Additional Reading

  • Link to and click on 'Literature'. Also useful (but copyrighted, so you have to get it from your library unfortunately): Robins, Snijders, Wang, Handcock and Pattison, "Recent Developments in Exponential Random Graph Models for Social Networks", Social Networks 29(2007): 192-215.