CSSS 2008 Santa Fe-Readings

Week One: Modeling/Nonlinear Dynamics

Liz Bradley: Non-Linear Dynamics I-IV

Nonlinear Dynamics

• Numerical Solution of Differential Equations: Notes for CSCI3656
• Time Series Analysis

Owen Densmore & Steve Guerin: Modeling

Before the modeling class (afternoon the first day!) you should:

• Download the most recent versions of both NetLogo and NetLogo 3D from http://ccl.northwestern.edu/netlogo/
• Run some of the Model Library examples for both NetLogo and NetLogo 3D:
  • Start the application
    • Click Model Library in the File menu, try these:
    • NetLogo: Art > Diffusion Graphics
    • NetLogo 3D: 3D > Sample Models > Raindrops 3D
      Note: move the 3D raindrop world by click & drag
    • To run most of the models, click "Setup" then "Go"
    • To see the code, click on the Procedures tab
• Finally, under the "Help" menu, click "User Manual" and explore!

Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems

Aaron Clauset: Markov chain Monte Carlo for Simulation and Inference

The following three references cover a wide variety of details related to Markov chain Monte Carlo methods. The second and third are general references, written for physics and machine learning audiences. (The Newman and Barkema book should be available through the SFI Library.) The second shows an application of MCMC methods in the context of learning the large-scale structure of networks.

• "Hierarchical structure and the prediction of missing links in networks." Clauset, Moore and Newman. Nature 453, 98-101 (2008).
• Monte Carlo Methods in Statistical Physics. Newman and Barkema. Oxford University Press (1999).
• "An Introduction to MCMC for Machine Learning." Andrieu, de Freitas, Doucet and Jordan. Machine Learning 50, 5-43 (2003).