Difference between revisions of "CSSS 2008 Santa Fe-Readings"
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+ | ---- | ||
== Week One: Modeling/Nonlinear Dynamics == | == Week One: Modeling/Nonlinear Dynamics == | ||
− | ===Liz Bradley: | + | ===Liz Bradley: Introduction to Nonlinear Dynamics=== |
'''Nonlinear Dynamics''' | '''Nonlinear Dynamics''' | ||
+ | * [[Media:CSSS-Bradley-Syllabus.pdf|Syllabus]] | ||
* [[Media:Ode.pdf|Numerical Solution of Differential Equations: Notes for CSCI3656]] | * [[Media:Ode.pdf|Numerical Solution of Differential Equations: Notes for CSCI3656]] | ||
* [[Media:Ida.pdf|Time Series Analysis]] | * [[Media:Ida.pdf|Time Series Analysis]] | ||
+ | * [[Media:CSSS-08-L1.pdf|Slides for Lecture 1]] | ||
+ | * [[Media:CSSS-08-L2.pdf|Slides for Lecture 2]] | ||
+ | * [[Media:CSSS-08-L3.pdf|Slides for Lecture 3]] | ||
+ | * [[Media:CSSS-08-L4.pdf|Slides for Lecture 4]] | ||
===Owen Densmore & Steve Guerin: Modeling=== | ===Owen Densmore & Steve Guerin: Modeling=== | ||
Line 21: | Line 27: | ||
***To see the code, click on the Procedures tab | ***To see the code, click on the Procedures tab | ||
* Finally, under the "Help" menu, click "User Manual" and explore! | * Finally, under the "Help" menu, click "User Manual" and explore! | ||
+ | |||
+ | Note: the url discussed in class is: http://backspaces.net/csss08 which contains the models.zip file, which in turn contains the commandcenter.rtf file we used to build our model. CSSS08Day1.pdf is the slide set used for the first half of the class. | ||
+ | |||
+ | ===Josh Epstein: Modeling in the Social Sciences=== | ||
+ | |||
+ | * [[media: Civil Violence (PNAS 2002).pdf | Modeling Civil Violence: An Agent-based Computational Approach]]. Epstein. <i>PNAS</i> 99:3, 7243-7250 (2002). | ||
+ | * [[media: EpsteinGlobalFlu.pdf | Controlling Pandemic Flu: The Value of International Air Restrictions]]. Epstein, Goedecke, Yu, Wagener, and Bobashev. <i>PLOS One</i> 5, 1-11 (2007). | ||
+ | * [[media: Population growth in Anasazi (PNAS 1999).pdf | Population Growth and Collapse in a Multiagent Model of the Kayenta Anasazi in Long House Valley]]. Axtell, Epstein, Dean, Gumerman, Swedlund, Harburger, Chakravarty, Hammond, Parker, and Parker. <i>PNAS</i> 99:3, 7275-7279 (2002). | ||
+ | * [[media: 07-12-048.pdf | Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations]]. Epstein, Parker, Cummings, and Hammond. <i>SFI Working Paper</i> 07-12-048 (2007). | ||
+ | |||
+ | Slide Presentations: | ||
+ | * [[media: SFI_Civil.ppt | Social Sciences Modeling I]]. Epstein. 06-03-08. | ||
+ | * [[media: Epstein_Health.ppt | Social Sciences Modeling II]]. Epstein. 06-04-08. | ||
+ | * [[media: Epstein_Adaptive.ppt | Social Sciences Modeling III]]. Epstein. 06-05-08. | ||
+ | |||
+ | ===David Krakauer=== | ||
+ | Here is a link to the pdf of David's Lecture on Evolutionary Dynamics | ||
+ | * [http://www.cs.dartmouth.edu/~rockmore/Evol_Dynamics.pdf CSSS 2008 Evolutionary Dynamics.] | ||
+ | |||
+ | ===Mark Newman=== | ||
+ | Here is a link to the pdf of Mark's 4 lectures on Networks | ||
+ | * [http://www.umich.edu/~mejn/csss08_newman.pdf CSSS 2008 Networks.] | ||
+ | |||
+ | ===Tom Carter=== | ||
+ | Here is a link to a page with various background readings -- I'll be talking about some of this material, watch the wiki for days/times | ||
+ | * [http://astarte.csustan.edu/~tom/SFI-CSSS/index.html Summer School readings.] | ||
+ | ---- | ||
== Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems == | == Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems == | ||
Line 26: | Line 59: | ||
===Aaron Clauset: MCMC for Simulation and Inference === | ===Aaron Clauset: MCMC for Simulation and Inference === | ||
− | + | Here is a pdf copy of Aaron's lecture notes | |
+ | |||
+ | * [[Media:Clauset_2008_MCMC_Week2.pdf|Introduction to Markov chain Monte Carlo]] | ||
+ | |||
+ | These three references cover a wide variety of details related to Markov chain Monte Carlo (MCMC) 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 first shows an application of MCMC methods in the context of learning the large-scale structure of networks. | ||
+ | |||
+ | * [[Media:CMN_08_Hierarchy_Preprint.pdf|"Hierarchical structure and the prediction of missing links in networks."]] Clauset, Moore and Newman. <i>Nature</i> <b>453</b>, 98-101 (2008). | ||
+ | * [http://www-personal.umich.edu/~mejn/nbook/ <i>Monte Carlo Methods in Statistical Physics.</i>] Newman and Barkema. Oxford University Press (1999). | ||
+ | * [http://citeseer.ist.psu.edu/andrieu03introduction.html "An Introduction to MCMC for Machine Learning."] Andrieu, de Freitas, Doucet and Jordan. <i>Machine Learning</i> <b>50</b>, 5-43 (2003). | ||
+ | |||
+ | ===Jennifer Dunne: Foodwebs === | ||
+ | |||
+ | Jennifer Dunne is a Research Fellow at the Santa Fe Institute, and is Co-Director of the Pacific Ecoinformatics and Computational Ecology Lab in Berkeley, CA. Dr. Dunne will lecture on ecological network structure and recommends the following article (Williams and Martinez, 2000) as a starting point for learning about such research. Her lectures will use this Nature paper as a jumping off point for discussing recent advances in research on food-web topology and robustness. | ||
+ | |||
+ | Williams and Martinez, 2000 Nature [http://www.cs.dartmouth.edu/~rockmore/Williams2000Nature.pdf] | ||
+ | |||
+ | For more info about ecological networks, go to http://www.foodwebs.org | ||
+ | |||
+ | [http://www.santafe.edu/profiles/?pid=67ml/ <i> Dr. Dunne’s SFI web page </i>] | ||
+ | |||
+ | [http://santafe.edu/education/csss/files01/dunne.ppt 08-SFI CSSS Dunne 1 & 2] <br /> | ||
+ | [[Media:08-SFICSSSMartinez1.ppt|08-SFI CSSS Martinez 1 PowerPoint]]<br /> | ||
+ | [[Media:08-SFICSSSMartinez2.ppt|08-SFI CSSS Martinez 2 PowerPoint]]<br /> | ||
+ | [http://santafe.edu/education/csss/files01/dunnemovie.mov FoodWeb3D Movie]<br /> | ||
+ | |||
+ | === D. Eric Smith: Chemical Carnot Cycles, Landauer's Principle, and the Thermodynamics of Natural Selection === | ||
+ | |||
+ | |||
+ | Here is a pdf copy of Eric's lecture notes: [http://www.cs.dartmouth.edu/~rockmore/LandauerCSSS.pdf | ||
+ | |||
+ | ===Dan Stein: Quenched Disorder, Spin Glasses, and Complexity === | ||
+ | |||
+ | This course is designed to introduce the participant to the study of systems with quenched disorder, which are fascinating systems in their own right but which also helped introduce many of the ideas and concepts that have become central to complexity studies. These ideas have found applications to problems from fields as diverse as biology, computer science, and economics, and we will explore some of these as well. | ||
+ | |||
+ | The course presupposes no prior knowledge of physics or statistical mechanics, and math will be kept to a minimum. If you'd like a flavor of some of the things we'll be discussing, you can take a look at D.L. Stein, ``Spin Glasses'', Scientific American v. 261, pp. 52--59 (1989). Despite the passage of time, many of the issues and questions discussed in that article remain open! | ||
+ | |||
+ | For those who would like to access the subject on a more technical level (which is unnecessary for this course), here are some references: | ||
+ | |||
+ | K. Binder and A.P. Young, ``Spin Glasses'', Rev. Mod. Phys. v. 58, p. 801 (1986). | ||
+ | |||
+ | M. Mezard, G. Parisi, and M. Virasoro, ``Spin Glass Theory and Beyond'' | ||
+ | (World Scientific, 1986). | ||
+ | |||
+ | Spin Glasses and Biology, edited by D.L. Stein (World Scientific Publishing Co., Singapore, 1992) | ||
+ | |||
+ | J.A. Hertz and K.H. Fischer, ``Spin Glasses'' (Cambridge, 1989). | ||
+ | |||
+ | C.M. Newman and D.L. Stein, ``Topical Review: Ordering and Broken Symmetry in Short-Ranged Spin Glasses'', Journal of Physics: Condensed Matter 15, R1319--R1364 (2003). | ||
+ | |||
+ | The last of these can be accessed from my [http://www.physics.nyu.edu/~ds1752/techpubs18.html <i> Web page </i>] | ||
+ | |||
+ | The slides from Dan's lectures can be found here: | ||
+ | [http://www.cs.dartmouth.edu/~rockmore/sg1.ppt <i> Lecture 1 </i>] | ||
+ | [http://www.cs.dartmouth.edu/~rockmore/sg2.ppt <i> Lecture 2 </i>] | ||
+ | [http://www.cs.dartmouth.edu/~rockmore/sg3.ppt <i> Lecture 3 </i>] | ||
+ | |||
+ | ===Jon Wilkins: Adaptationism and the Adaptive Landscape === | ||
+ | |||
+ | Here is a ppt copy of Jon's lecture notes - related to genomic imprinting, notions of optimality in evolution: [http://www.cs.dartmouth.edu/~rockmore/WilkinsCSSS2008.ppt] | ||
+ | |||
+ | ---- | ||
+ | == Week Three: Econ/Finance/AI == | ||
+ | |||
+ | === Gidon Eshel: The Interactions between Diet and Climate === | ||
+ | |||
+ | Lecture 1: [http://www.cs.dartmouth.edu/~rockmore/EshelClimChange08SF.pdf Global, and Local, Climate Change] | ||
+ | |||
+ | Lecture 2: [http://www.cs.dartmouth.edu/~rockmore/EshelDietSantaFe08SF.pdf Diet, Climate, and Climate Change] | ||
+ | |||
+ | Reference: [http://www.cs.dartmouth.edu/~rockmore/AJCNpaper-1.pdf Geophysics and nutritional science: Toward a novel, unified paradigm] | ||
+ | |||
+ | === Doyne Farmer: Finance and Innovation === | ||
+ | |||
+ | Lecture 1: [http://www.cs.dartmouth.edu/~rockmore/sfiSummerSchool08.pdf Financial Markets and Complex Systems] | ||
+ | |||
+ | Lecture 2: [http://www.cs.dartmouth.edu/~rockmore/sfiSummerSchool2.pdf Patterns of Technological Evolution] | ||
+ | |||
+ | ===Dan Hruschka: Prehistoric Finance=== | ||
+ | |||
+ | Lecture slides: [http://www.cs.dartmouth.edu/~rockmore/PrehistoricFinance.pdf] | ||
+ | |||
+ | ===Willamien Kets: Group Behavior and Why Crowds May Not Be Wise=== | ||
+ | |||
+ | Lecture slides: [http://www.cs.dartmouth.edu/~rockmore/Kets_CSSS2008.pdf] | ||
+ | |||
+ | ===Greg Leibon: Statistical Learning and Complex Systems=== | ||
+ | |||
+ | Lecture slides for all three lectures: [http://www.cs.dartmouth.edu/~rockmore/GLCSSS08.zip] | ||
+ | |||
+ | ===Melanie Mitchell: Evolutionary Computing=== | ||
+ | |||
+ | Mitchell, M. (2001). Life and evolution in computers. History and | ||
+ | Philosophy of the Life Sciences, 23, 361-383. | ||
+ | [http://web.cecs.pdx.edu/~mm/life-and-evolution.pdf] | ||
+ | |||
+ | Mitchell, M (2006). Coevolutionary learning with spatially | ||
+ | distributed populations. In G. Y. Yen and D. B. Fogel (editors), | ||
+ | Computational Intelligence: Principles and Practice . New York: IEEE | ||
+ | Computational Intelligence Society. | ||
+ | [http://www.cs.pdx.edu/~mm/MitchellWCCI2006.pdf] | ||
+ | |||
+ | Lecture slides at [http://www.cs.pdx.edu/~mm/MitchellLectures1-2-EC.ppt] and | ||
+ | [http://www.cs.pdx.edu/~mm/MitchellLecture3-CAs.ppt] | ||
+ | |||
+ | ===D. Eric Smith: Classical Thermodynamics and Economic General Equilibrium Theory=== | ||
+ | |||
+ | Lecture slides: [http://www.cs.dartmouth.edu/~rockmore/Econ_Thermo_CSSS_08.pdf] | ||
+ | |||
+ | ===Andreas Wagner: Robustness and Cellular Networks=== | ||
+ | |||
+ | Lecture slides: [http://www.cs.dartmouth.edu/~rockmore/AW_CSSS2008.pdf] | ||
+ | |||
+ | == Week Four: Wrapping Up == | ||
+ | |||
+ | ===Scott E. Page: Modeling in Social Sciences=== | ||
− | + | Lecture slides at [http://www.cscs.umich.edu/~spage/SFI1.pdf], [http://www.cscs.umich.edu/~spage/SFI2.ppt], [http://www.cscs.umich.edu/~spage/SFI3.ppt] | |
− | |||
− |
Latest revision as of 13:56, 2 July 2008
CSSS Santa Fe 2008 |
Contents
- 1 Week One: Modeling/Nonlinear Dynamics
- 2 Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems
- 2.1 Aaron Clauset: MCMC for Simulation and Inference
- 2.2 Jennifer Dunne: Foodwebs
- 2.3 D. Eric Smith: Chemical Carnot Cycles, Landauer's Principle, and the Thermodynamics of Natural Selection
- 2.4 Dan Stein: Quenched Disorder, Spin Glasses, and Complexity
- 2.5 Jon Wilkins: Adaptationism and the Adaptive Landscape
- 3 Week Three: Econ/Finance/AI
- 3.1 Gidon Eshel: The Interactions between Diet and Climate
- 3.2 Doyne Farmer: Finance and Innovation
- 3.3 Dan Hruschka: Prehistoric Finance
- 3.4 Willamien Kets: Group Behavior and Why Crowds May Not Be Wise
- 3.5 Greg Leibon: Statistical Learning and Complex Systems
- 3.6 Melanie Mitchell: Evolutionary Computing
- 3.7 D. Eric Smith: Classical Thermodynamics and Economic General Equilibrium Theory
- 3.8 Andreas Wagner: Robustness and Cellular Networks
- 4 Week Four: Wrapping Up
Week One: Modeling/Nonlinear Dynamics
Liz Bradley: Introduction to Nonlinear Dynamics
Nonlinear Dynamics
- Syllabus
- Numerical Solution of Differential Equations: Notes for CSCI3656
- Time Series Analysis
- Slides for Lecture 1
- Slides for Lecture 2
- Slides for Lecture 3
- Slides for Lecture 4
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
- Start the application
- Finally, under the "Help" menu, click "User Manual" and explore!
Note: the url discussed in class is: http://backspaces.net/csss08 which contains the models.zip file, which in turn contains the commandcenter.rtf file we used to build our model. CSSS08Day1.pdf is the slide set used for the first half of the class.
Josh Epstein: Modeling in the Social Sciences
- Modeling Civil Violence: An Agent-based Computational Approach. Epstein. PNAS 99:3, 7243-7250 (2002).
- Controlling Pandemic Flu: The Value of International Air Restrictions. Epstein, Goedecke, Yu, Wagener, and Bobashev. PLOS One 5, 1-11 (2007).
- Population Growth and Collapse in a Multiagent Model of the Kayenta Anasazi in Long House Valley. Axtell, Epstein, Dean, Gumerman, Swedlund, Harburger, Chakravarty, Hammond, Parker, and Parker. PNAS 99:3, 7275-7279 (2002).
- Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations. Epstein, Parker, Cummings, and Hammond. SFI Working Paper 07-12-048 (2007).
Slide Presentations:
- Social Sciences Modeling I. Epstein. 06-03-08.
- Social Sciences Modeling II. Epstein. 06-04-08.
- Social Sciences Modeling III. Epstein. 06-05-08.
David Krakauer
Here is a link to the pdf of David's Lecture on Evolutionary Dynamics
Mark Newman
Here is a link to the pdf of Mark's 4 lectures on Networks
Tom Carter
Here is a link to a page with various background readings -- I'll be talking about some of this material, watch the wiki for days/times
Week Two: Ecology/Evolution/Molecular Biology/Disordered Systems
Aaron Clauset: MCMC for Simulation and Inference
Here is a pdf copy of Aaron's lecture notes
These three references cover a wide variety of details related to Markov chain Monte Carlo (MCMC) 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 first 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).
Jennifer Dunne: Foodwebs
Jennifer Dunne is a Research Fellow at the Santa Fe Institute, and is Co-Director of the Pacific Ecoinformatics and Computational Ecology Lab in Berkeley, CA. Dr. Dunne will lecture on ecological network structure and recommends the following article (Williams and Martinez, 2000) as a starting point for learning about such research. Her lectures will use this Nature paper as a jumping off point for discussing recent advances in research on food-web topology and robustness.
Williams and Martinez, 2000 Nature [1]
For more info about ecological networks, go to http://www.foodwebs.org
08-SFI CSSS Dunne 1 & 2
08-SFI CSSS Martinez 1 PowerPoint
08-SFI CSSS Martinez 2 PowerPoint
FoodWeb3D Movie
D. Eric Smith: Chemical Carnot Cycles, Landauer's Principle, and the Thermodynamics of Natural Selection
Here is a pdf copy of Eric's lecture notes: [http://www.cs.dartmouth.edu/~rockmore/LandauerCSSS.pdf
Dan Stein: Quenched Disorder, Spin Glasses, and Complexity
This course is designed to introduce the participant to the study of systems with quenched disorder, which are fascinating systems in their own right but which also helped introduce many of the ideas and concepts that have become central to complexity studies. These ideas have found applications to problems from fields as diverse as biology, computer science, and economics, and we will explore some of these as well.
The course presupposes no prior knowledge of physics or statistical mechanics, and math will be kept to a minimum. If you'd like a flavor of some of the things we'll be discussing, you can take a look at D.L. Stein, ``Spin Glasses, Scientific American v. 261, pp. 52--59 (1989). Despite the passage of time, many of the issues and questions discussed in that article remain open!
For those who would like to access the subject on a more technical level (which is unnecessary for this course), here are some references:
K. Binder and A.P. Young, ``Spin Glasses, Rev. Mod. Phys. v. 58, p. 801 (1986).
M. Mezard, G. Parisi, and M. Virasoro, ``Spin Glass Theory and Beyond (World Scientific, 1986).
Spin Glasses and Biology, edited by D.L. Stein (World Scientific Publishing Co., Singapore, 1992)
J.A. Hertz and K.H. Fischer, ``Spin Glasses (Cambridge, 1989).
C.M. Newman and D.L. Stein, ``Topical Review: Ordering and Broken Symmetry in Short-Ranged Spin Glasses, Journal of Physics: Condensed Matter 15, R1319--R1364 (2003).
The last of these can be accessed from my Web page
The slides from Dan's lectures can be found here: Lecture 1 Lecture 2 Lecture 3
Jon Wilkins: Adaptationism and the Adaptive Landscape
Here is a ppt copy of Jon's lecture notes - related to genomic imprinting, notions of optimality in evolution: [2]
Week Three: Econ/Finance/AI
Gidon Eshel: The Interactions between Diet and Climate
Lecture 1: Global, and Local, Climate Change
Lecture 2: Diet, Climate, and Climate Change
Reference: Geophysics and nutritional science: Toward a novel, unified paradigm
Doyne Farmer: Finance and Innovation
Lecture 1: Financial Markets and Complex Systems
Lecture 2: Patterns of Technological Evolution
Dan Hruschka: Prehistoric Finance
Lecture slides: [3]
Willamien Kets: Group Behavior and Why Crowds May Not Be Wise
Lecture slides: [4]
Greg Leibon: Statistical Learning and Complex Systems
Lecture slides for all three lectures: [5]
Melanie Mitchell: Evolutionary Computing
Mitchell, M. (2001). Life and evolution in computers. History and Philosophy of the Life Sciences, 23, 361-383. [6]
Mitchell, M (2006). Coevolutionary learning with spatially distributed populations. In G. Y. Yen and D. B. Fogel (editors), Computational Intelligence: Principles and Practice . New York: IEEE Computational Intelligence Society. [7]
D. Eric Smith: Classical Thermodynamics and Economic General Equilibrium Theory
Lecture slides: [10]
Andreas Wagner: Robustness and Cellular Networks
Lecture slides: [11]