Complex Systems Summer SChool 2012-Lecture Readings

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Liz Bradley

Slides

Syllabus

Slides

Readings

Numerical Solution of Differential Equations
Time Series Analysis ODE notes IDA chapter

| Chaos weblinks

Lorenz Attractor

Lorenz Attractor explorer

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

Lorenz Water Wheel (Right clock - 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

Background/follow-up Reading for 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.

Background/follow-up Reading for Statistics and Stochastic Processes

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

Josh Garland

Lab 1

Lab 2

Here is a zip archive of data files for your use in this lab:

http://tuvalu.santafe.edu/files/DAT_files.zip

Compiled TISEAN code for Mac OS-X 10.6 can be found here: I had to posted it on my website because the wiki does not accept .zip files.

John Harte

John Harte Lecture Slides

Alfred Hubler

Alfred Hubler Lecture Slides for Talk 1

Alfred Hubler Lecture Slides for Talk 2

Anne Kandler

Anne Kandler Lecture Slides

Mark Newman

Mark Newman Lecture Slides

| Clauset / Newman Paper