Complex Systems Summer SChool 2012-Lecture Readings

Complex Systems Summer School 2012

Liz Bradley

NetLogo Lorenz attractor (Right click - save - open with Netlogo 3D)

Lorenz Water Wheel (Right click - save - open in Netlogo)

TISEAN

TISEAN 3.0.1: Nonlinear Time Series Analysis Software

Jim Crutchfield

Lecture 1.1
Lecture 1.2
Lecture 2.1
Lecture 2.2

Ryan

Information Theory for Tralfamadorians

Simon DeDeo

Computation in Natural Systems

Cris Moore's Lecture notes on automata, languages, and grammars covers, elegantly, all of the basic automata concepts in the lecture, and much more besides. A supplement to The Nature of Computation.

Jim Crutchfield & Karl Young's paper, Computation at the Onset of Chaos provides a detailed and compelling account of (among other things) how a naturalistic process (in this case, the logistic map) violates the bounds of both the regular and context-free grammars.

For an introduction to the connection between (semi)groups and the regular grammars, as well as a preview of the Emergence module, see Effective Theories for Circuits and Automata.

Data on the edit histories of the George Bush wikipedia article, along with ruby code to read in and otherwise play, can be downloaded here.

Statistics and Stochastic Processes

Overall book: David J.C. MacKay, Information Theory, Inference, and Learning Algorithms.

Lecture 1 (Thursday)

E.T. Jaynes' Information Theory and Statistical Mechanics (free copy).

Elliott W. Montroll On the entropy function in sociotechnical systems. Focus on the Sears-Roebuck Catalog; we will read this critically in class. Optional: Thermodynamic Treatment of Nonphysical Systems: Formalism and an Example (Single-Lane Traffic) (with Reiss & Hammerich; see touching "Note in Closing").

Tkacik, Schneidman, Berry, and Bialek. Ising Models for Networks of Real Neurons. Optional (but compelling; see back to Montroll's PNAS paper, top left of pg. 7841): Mora and Bialek, Are biological systems poised at criticality?

Lectures 2 & 3 (Friday)

Null models & significance testing. DeDeo, Krakauer & Flack. Evidence of strategic periodicities in collective conflict dynamics (free copy). Optional: Weidmann & Toft. Promises and Pitfalls in the Spatial Prediction of Ethnic Violence (a critical examination of the claims in this Science article.)

Parameter Estimation and Bayesian Reasoning. Clauset, Shalizi & Newman Power-law distributions in empirical data.

Model selection. Cosma Shalizi on Methods for Selection. David Deutsch on Scientific Argument. Optional: Multi-Model Inference (AIC).

Data and analysis code for the seating of students in the June 14th lecture, including basic code to implement null models for gender and field distribution, is available here.

Additional material on the thermodynamics of computation. Bennett, the Thermodynamics of Computation—a Review (free copy). Landauer, Computation: a Fundamental Physical View (free copy). Anthology of articles: Maxwell's Demon 2