Santa Fe Institute Events Wiki - User contributions [en]

CSSS 2010 Santa Fe-Readings

2010-06-16T19:37:56Z

Cshalizi: /* Cosma Shalizi */

{{CSSS 2010 Santa Fe}}

Please review readings before lectures. Supplemental material may be posted as well.

===Background Readings===

Please see the [[Background Readings CSSS10|Background Readings]] page for assignments.

===Dan Rockmore===
[[media:IntroCSSS2010.ppt‎ | Dan's Intro Lecture]] 
[[media:LPRS-SL-intro.pdf‎ | Draft intro to stat learning primer ]]
----

===Tanmoy Bhattacharya===

[[Media:Tanmoy_CSSS2010.pdf‎ | Inference in Historical Processes]]
----
===Liz Bradley===

*[http://www.cs.colorado.edu/~lizb/na/ode-notes.pdf Numerical Solution of Differential Equations] 
*[http://www.cs.colorado.edu/~lizb/papers/ida-chapter.pdf Time Series Analysis]
*[[Image:BradleySlides2010.pdf]]
*[[Image:BradleySyllabus2010.pdf]]
----

===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://csustan.csustan.edu/~tom/SFI-CSSS/index.html Summer School readings.]
--------

===Iain Couzin===

*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin10.pdf Complexity. An Informative Itinerary]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin09.pdf Collective Cognition in Animal Groups]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/bazazi08.pdf Collective Motion and Cannibalism in Locust Migratory Bands]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/plugins/bib2html/data/papers/couzin07.pdf Collective Minds]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin05.pdf Effective Leadership and Decision-Making in Animal Groups on the Move]
-------

===Simon DeDeo===

For the two lectures on "Physics of Reasoning" --
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1957PhRv..106..620J&link_type=EJOURNAL E.T. Jaynes, ''Information Theory and Statistical Mechanics I.'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2006q.bio....11072T&link_type=ABSTRACT Gasper, Schneidman, Berry & Bialek, ''Ising models for networks of real neurons'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1986JSP....42..647R&link_type=ABSTRACT Reiss, Hammerich & Montroll, ''Thermodynamic treatment of nonphysical systems''] -- the [http://santafe.edu/~simon/Reiss_1986_SFI.pdf off-site fulltext] is available.
more advanced --
*[http://library.unm.edu/search~S4/?searchtype=t&searcharg=spin+glasses+and+biology&searchscope=4&SORT=D&extended=1&SUBMIT=Search&searchlimits=&searchorigarg=tspin+glasses+biology ''Spin Glasses and Biology'' (ed. Daniel Stein)] (available at SFI library)
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2004PhRvE..70f6117P&link_type=ABSTRACT Park & Newman, ''Statistical Mechanics of Networks'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2004MNRAS.351L..49L&link_type=ABSTRACT A.R. Liddle, ''How many cosmological parameters?'']

If you only have time to read one, read Jaynes! If you are unable to access any of these articles, feel free to e-mail me at simon@santafe.edu
------

===Owen Densmore===
Steve Guerin and I will present modeling with NetLogo. It will have two parts, one a self-paced wiki tutorial, the second a set of real world examples of modeling we've used professionally.

Read the first page of the tutorial. Then (attempt!) to download, install, and look at the Model Library.
* [http://backspaces.net/wiki/NetLogo_Tutorial NetLogo CSSS Self-Paced Tutorial]

--------

===Peter Dodds===
* [http://www.uvm.edu/~pdodds/teaching/courses/2010-06SFI-networks/index.html Lectures on complex networks + links to further reading.]
--------

===Nathan Eagle===
* [[media:CSSS_Diversity_sm.pptx| Lecture 1]]
* [[media:CSSS_ESS_sm.pptx | Lecture 2]]

===Doug Erwin===
* [[Media:Davidson_Erwin_113_S74_lsh.pdf|Evolution]]
* [[Media:Erwin_2008_TREE.pdf|Niche Construction & Diversity]]
* [[Media:Erwin_2009_Nature_.pdf|Modeling Biodiversity]]
----

===Duncan Foley===
* [[Media:Lec1.pdf| Labor, Capital and Land in the New Economy]]
* [[Media:Albin-FoleyIntro.pdf‎|Economic Complexity and Dynamics in Interactive Systems]]
* [[Media:Minsky.pdf|Hyman Minsky and the Dilemmas of Contemporary Economic Method]]
----

===Laura Fortunato===
* [[Media:Lansing2003.pdf| Complex Systems in Anthropology]]
----

===Greg Leibon===

* [[Media:CSSS10Pickle.pdf | Lecture one notes]]
* [[Media:CSSS10Pickle(Slides).pdf| Lecture one slides]]
* [[Media:shoe.pdf | Markov Chains In A Shoebox]]
* [[Media:pickle.pdf | Conformal Geometry of Markov Chains]]
------

===John Harte===
* [[Media:MaxEntEcology.pdf|Maximum Entropy and the State-Variable Approach to Macroecology]]
* [[Media:Univ_SAR_Ecol_Lett.pdf|Biodiversity Scaling]]
----

===Jure Leskovec===
1) -- models and link prediction in large social networks:

* [http://cs.stanford.edu/people/jure/pubs/kronecker-jmlr10.pdf Kronecker Graphs]
* [http://cs.stanford.edu/people/jure/pubs/microEvol-kdd08.pdf Microscopic Evolution of Social Networks ]
* [http://arxiv.org/abs/0810.1355 Community Structure in Large Networks]

2) -- tracking information diffusion, finding influencers and
detecting disease outbreaks in networks
* [http://cs.stanford.edu/people/jure/pubs/quotes-kdd09.pdf Meme Tracking & News Cycle Dynamics]
* [http://www.cs.cornell.edu/home/kleinber/kdd03-inf.pdf Maximizing the Spread of Influence through a Social Network]
* [http://cs.stanford.edu/people/jure/pubs/detect-kdd07.pdf Outbreak Detection in Social Networks]
* [http://www.blogpulse.com/papers/2005/AdamicGlanceBlogWWW.pdf 2004 Election Political Blogger Networks ]

3) -- models of networks with positive and negative ties
* [http://www.iw3c2.org/WWW2004/docs/1p403.pdf Trust & Distrust]
* [http://cs.stanford.edu/people/jure/pubs/triads-chi10.pdf Signed Networks & Social Media:]
* [http://cs.stanford.edu/people/jure/pubs/signs-www10.pdf Predicting Postive & Negative Links in Online Social Networks]
* [http://cs.stanford.edu/people/jure/pubs/voting-icwsm10.pdf Governance in Social Media]
--------

===Cosma Shalizi===
* [http://arxiv.org/abs/nlin.AO/0409024 Quantifying Self-Organization with Optimal Predictors] 
* [http://arxiv.org/abs/nlin.AO/0307015 Methods and Techniques of Complex Systems Science: An Overview] 
* [http://arxiv.org/abs/cs.LG/0406011 Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences] 
* [http://arxiv.org/abs/nlin.CG/0508001 Automatic Filters for the Detection of Coherent Structure in Spatiotemporal Systems] 
* [http://arxiv.org/abs/cond-mat/9907176 Computational Mechanics: Pattern and Prediction, Structure and Simplicity] 
* [http://arxiv.org/abs/1001.0036 The Computational Structure of Spike Trains] 
* [http://arxiv.org/abs/q-bio.NC/0609008 Discovering Functional Communities in Dynamical Networks] 
* [http://arxiv.org/abs/q-bio.NC/0506009 Measuring Shared Information and Coordinated Activity in Neuronal Networks] 
* [http://arxiv.org/abs/math.PR/0305160 Optimal Nonlinear Prediction of Random Fields on Networks]
--------
[http://www.stat.cmu.edu/~cshalizi/350/ Data mining and statistical learning lecture notes] 
[http://www.stat.cmu.edu/~cshalizi/462/ Chaos, complexity and inference lecture notes]
--------
CSSS lecture slides:
* [[Media:2010-06-15-info-theory.pdf|Information theory]] 
* [[Media:2010-06-15-optimal-prediction.pdf|Optimal prediction]] 
* [[Media:2010-06-16-complexity.pdf|Quantitative complex measures]]

=== Bill Croft, Ian Maddieson, Eric Smith===
* [[Media:Croft2008ARA.pdf‎|Evolutionary Linguistics, I]]

* [[Media:CCroft_comp_lang.pd‎|Evolutionary Linguistics, II]]

* [[Media:Smith_comp_lang.pdf‎|Opportunities in quantitative historical linguistics]]

* [[Media:Maddieson_comp_lang.pdf‎|Typological patterns in language and their relation to linguistic history]]

----

===Alfred Hübler===
* [http://www.how-why.com/cgi-bin/cyberprof/os.exe?document=http://www.how-why.com/phys194/Notes/index.html Physics 194 notes]
* [http://www.how-why.com/cgi-bin/cyberprof/os.exe?home=&document=http://www.how-why.com/ph510/Notes/index.html PHYCS510 UIUC notes]
----
===Scott Pauls===

* [[Media:CSSS10-PDM.pptx | Lecture]] on using the PDM on voting data.
* [http://www.math.dartmouth.edu/~pauls/PDM_Toolkit.zip Code package].

CSSS 2010 Santa Fe-Readings

2010-06-16T19:34:59Z

Cshalizi: /* Cosma Shalizi */

{{CSSS 2010 Santa Fe}}

Please review readings before lectures. Supplemental material may be posted as well.

===Background Readings===

Please see the [[Background Readings CSSS10|Background Readings]] page for assignments.

===Dan Rockmore===
[[media:IntroCSSS2010.ppt‎ | Dan's Intro Lecture]] 
[[media:LPRS-SL-intro.pdf‎ | Draft intro to stat learning primer ]]
----

===Tanmoy Bhattacharya===

[[Media:Tanmoy_CSSS2010.pdf‎ | Inference in Historical Processes]]
----
===Liz Bradley===

*[http://www.cs.colorado.edu/~lizb/na/ode-notes.pdf Numerical Solution of Differential Equations] 
*[http://www.cs.colorado.edu/~lizb/papers/ida-chapter.pdf Time Series Analysis]
*[[Image:BradleySlides2010.pdf]]
*[[Image:BradleySyllabus2010.pdf]]
----

===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://csustan.csustan.edu/~tom/SFI-CSSS/index.html Summer School readings.]
--------

===Iain Couzin===

*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin10.pdf Complexity. An Informative Itinerary]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin09.pdf Collective Cognition in Animal Groups]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/bazazi08.pdf Collective Motion and Cannibalism in Locust Migratory Bands]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/plugins/bib2html/data/papers/couzin07.pdf Collective Minds]
*[http://webscript.princeton.edu/%7Eicouzin/website/wp-content/uploads/2010/05/couzin05.pdf Effective Leadership and Decision-Making in Animal Groups on the Move]
-------

===Simon DeDeo===

For the two lectures on "Physics of Reasoning" --
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1957PhRv..106..620J&link_type=EJOURNAL E.T. Jaynes, ''Information Theory and Statistical Mechanics I.'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2006q.bio....11072T&link_type=ABSTRACT Gasper, Schneidman, Berry & Bialek, ''Ising models for networks of real neurons'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1986JSP....42..647R&link_type=ABSTRACT Reiss, Hammerich & Montroll, ''Thermodynamic treatment of nonphysical systems''] -- the [http://santafe.edu/~simon/Reiss_1986_SFI.pdf off-site fulltext] is available.
more advanced --
*[http://library.unm.edu/search~S4/?searchtype=t&searcharg=spin+glasses+and+biology&searchscope=4&SORT=D&extended=1&SUBMIT=Search&searchlimits=&searchorigarg=tspin+glasses+biology ''Spin Glasses and Biology'' (ed. Daniel Stein)] (available at SFI library)
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2004PhRvE..70f6117P&link_type=ABSTRACT Park & Newman, ''Statistical Mechanics of Networks'']
*[http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2004MNRAS.351L..49L&link_type=ABSTRACT A.R. Liddle, ''How many cosmological parameters?'']

If you only have time to read one, read Jaynes! If you are unable to access any of these articles, feel free to e-mail me at simon@santafe.edu
------

===Owen Densmore===
Steve Guerin and I will present modeling with NetLogo. It will have two parts, one a self-paced wiki tutorial, the second a set of real world examples of modeling we've used professionally.

Read the first page of the tutorial. Then (attempt!) to download, install, and look at the Model Library.
* [http://backspaces.net/wiki/NetLogo_Tutorial NetLogo CSSS Self-Paced Tutorial]

--------

===Peter Dodds===
* [http://www.uvm.edu/~pdodds/teaching/courses/2010-06SFI-networks/index.html Lectures on complex networks + links to further reading.]
--------

===Nathan Eagle===
* [[media:CSSS_Diversity_sm.pptx| Lecture 1]]
* [[media:CSSS_ESS_sm.pptx | Lecture 2]]

===Doug Erwin===
* [[Media:Davidson_Erwin_113_S74_lsh.pdf|Evolution]]
* [[Media:Erwin_2008_TREE.pdf|Niche Construction & Diversity]]
* [[Media:Erwin_2009_Nature_.pdf|Modeling Biodiversity]]
----

===Duncan Foley===
* [[Media:Lec1.pdf| Labor, Capital and Land in the New Economy]]
* [[Media:Albin-FoleyIntro.pdf‎|Economic Complexity and Dynamics in Interactive Systems]]
* [[Media:Minsky.pdf|Hyman Minsky and the Dilemmas of Contemporary Economic Method]]
----

===Laura Fortunato===
* [[Media:Lansing2003.pdf| Complex Systems in Anthropology]]
----

===Greg Leibon===

* [[Media:CSSS10Pickle.pdf | Lecture one notes]]
* [[Media:CSSS10Pickle(Slides).pdf| Lecture one slides]]
* [[Media:shoe.pdf | Markov Chains In A Shoebox]]
* [[Media:pickle.pdf | Conformal Geometry of Markov Chains]]
------

===John Harte===
* [[Media:MaxEntEcology.pdf|Maximum Entropy and the State-Variable Approach to Macroecology]]
* [[Media:Univ_SAR_Ecol_Lett.pdf|Biodiversity Scaling]]
----

===Jure Leskovec===
1) -- models and link prediction in large social networks:

* [http://cs.stanford.edu/people/jure/pubs/kronecker-jmlr10.pdf Kronecker Graphs]
* [http://cs.stanford.edu/people/jure/pubs/microEvol-kdd08.pdf Microscopic Evolution of Social Networks ]
* [http://arxiv.org/abs/0810.1355 Community Structure in Large Networks]

2) -- tracking information diffusion, finding influencers and
detecting disease outbreaks in networks
* [http://cs.stanford.edu/people/jure/pubs/quotes-kdd09.pdf Meme Tracking & News Cycle Dynamics]
* [http://www.cs.cornell.edu/home/kleinber/kdd03-inf.pdf Maximizing the Spread of Influence through a Social Network]
* [http://cs.stanford.edu/people/jure/pubs/detect-kdd07.pdf Outbreak Detection in Social Networks]
* [http://www.blogpulse.com/papers/2005/AdamicGlanceBlogWWW.pdf 2004 Election Political Blogger Networks ]

3) -- models of networks with positive and negative ties
* [http://www.iw3c2.org/WWW2004/docs/1p403.pdf Trust & Distrust]
* [http://cs.stanford.edu/people/jure/pubs/triads-chi10.pdf Signed Networks & Social Media:]
* [http://cs.stanford.edu/people/jure/pubs/signs-www10.pdf Predicting Postive & Negative Links in Online Social Networks]
* [http://cs.stanford.edu/people/jure/pubs/voting-icwsm10.pdf Governance in Social Media]
--------

===Cosma Shalizi===
* [http://arxiv.org/abs/nlin.AO/0409024 Quantifying Self-Organization with Optimal Predictors] 
* [http://arxiv.org/abs/nlin.AO/0307015 Methods and Techniques of Complex Systems Science: An Overview] 
* [http://arxiv.org/abs/cs.LG/0406011 Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences] 
* [http://arxiv.org/abs/nlin.CG/0508001 Automatic Filters for the Detection of Coherent Structure in Spatiotemporal Systems] 
* [http://arxiv.org/abs/cond-mat/9907176 Computational Mechanics: Pattern and Prediction, Structure and Simplicity] 
* [http://arxiv.org/abs/1001.0036 The Computational Structure of Spike Trains] 
* [http://arxiv.org/abs/q-bio.NC/0609008 Discovering Functional Communities in Dynamical Networks] 
* [http://arxiv.org/abs/q-bio.NC/0506009 Measuring Shared Information and Coordinated Activity in Neuronal Networks] 
* [http://arxiv.org/abs/math.PR/0305160 Optimal Nonlinear Prediction of Random Fields on Networks]
--------

[[Media:2010-06-15-info-theory.pdf|Information theory lecture slides]]

[[Media:2010-06-15-optimal-prediction.pdf|Optimal prediction lecture slides]]

[[Media:2010-06-16-complexity.pdf|Quantitative complex measures lecture slides]]

=== Bill Croft, Ian Maddieson, Eric Smith===
* [[Media:Croft2008ARA.pdf‎|Evolutionary Linguistics, I]]

* [[Media:CCroft_comp_lang.pd‎|Evolutionary Linguistics, II]]

* [[Media:Smith_comp_lang.pdf‎|Opportunities in quantitative historical linguistics]]

* [[Media:Maddieson_comp_lang.pdf‎|Typological patterns in language and their relation to linguistic history]]

----

===Alfred Hübler===
* [http://www.how-why.com/cgi-bin/cyberprof/os.exe?document=http://www.how-why.com/phys194/Notes/index.html Physics 194 notes]
* [http://www.how-why.com/cgi-bin/cyberprof/os.exe?home=&document=http://www.how-why.com/ph510/Notes/index.html PHYCS510 UIUC notes]
----
===Scott Pauls===

* Lecture on using the PDM on voting data.
* Code package
* Sample voting data

File:2010-06-16-complexity.pdf

2010-06-16T19:28:11Z

Cshalizi: Cosma Shalizi's complexity measures slides

Cosma Shalizi's complexity measures slides

File:2010-06-15-optimal-prediction.pdf

2010-06-16T18:34:25Z

Cshalizi: Cosma Shalizi's optimal prediction slides

Cosma Shalizi's optimal prediction slides

File:2010-06-15-info-theory.pdf

2010-06-16T18:33:32Z

Cshalizi: Cosma Shalizi's information theory slides

Cosma Shalizi's information theory slides

CSSS 2006 Beijing-Readings

2006-07-14T02:15:22Z

Cshalizi:

{{CSSS 2006 Beijing}}

__FORCETOC__

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further.

== Readings Associated with Particular Lecturers ==

=== Week One ===

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 1 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:

'''Part One-''' Foragers and the Emergence of Agriculture
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:CSSS_Wright1_Foragers.ppt|PowerPoint presentation of Part 1]]
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed.
*[[Media:ch3-1.pdf|Guila Naquitz in Spacial, Temporal, and Cultural Context]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:ch4.pdf|The Physical Environment of the Guila Naquitz Cave Group]], Kirkby, M. J., A. V. Whyte, and K. V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Reynolds_introduction_to_model.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Robert Reynolds. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:Diamond_Nature_02.pdf| Jared Diamond's Overview of the Emergence of Food Production]]

'''Part Two-''' Villages and the Emergernce of Tribal Alliance Systems
*[[Media:Modeling_Villages.doc|Brief Syllabus of Sources on the “Village” Project]]
*[[Media:CSSS_Villager2_2006.ppt|Revised PowerPoint presentation of Part 2]]
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds
*[[Media:Gumerman_eta_.pdf|Long House Valley Simulation]]
*[[Media:Kohler_etal_Agent_Based_Mdling_SFI96.doc|Agent-Based Modeling of Prehistoric Settlement Systems in the Northern American Southwest]] Kohler, T. A., C. R. Van West, E. P. Carr and C. G. Langton
*[[Media:Reynolds_Algorithms_2002.ppt|Cultural Algorithms: A Tutorial]] Robert G. Reynolds
*[[Media:Kobti_Reynolds_Kohler_Resilience_IEEE03.pdf|A Multi-Agent Simulation Using Cultural Algorithms: The Effect of Culture on the Resilience of Social Systems]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Reynolds_Kohler_Kobti_Resilience_CMOT04.pdf|The Effects of Generalized Reciprocal Exchange on the Resilience of Social Networks: An Example from the Prehispanic Mesa Verde Region]] Reynolds, R. G., T. A. Kohler and Z. Kobti
*[[Media:Kobti_Reynlds_Kohler_Kinship_IEEE04.pdf|The Effect ofKinship Cooperation Learning Stategy and culture on the Resilience of Social Systems in the Village Mulit-Agent Simulation]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Kobti_etal_SwarmFest_Cultural_Algorithms_04.pdf|Agent-Based Modeling of Cultural Change in Swarm Using Cultural Algorithms]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Reynolds_etal_Gaming_IEEE05.pdf|Unraveling Ancient Mysteries: Reimagining the Past Using Evolutionary Computation in a Complex Gaming Environment]] Reynolds, R. G., Z. Kobti, T. A. Kohler, and L. Y. L. Yap
*[[Media:VILLAGE_and_BALI_URLs.doc|Web Access to Kohler's VILLAGE and Lansing''s BALI]]

'''Part Three-''' Raising Civilizations
*[[Media:Modeling_States.doc|Brief Syllabus of Sources on the “States” Project]]
*[[Media:CSSS_Wright3_States.ppt|PowerPoint presentation of Part 3]]
*[[Media:Carneiro 1970.pdf|A Theory of the Origin of the State]] Robert L. Carneiro
*[[Media:Wright 1977.pdf|Recent Research on the Origin of the State]] Henry T. Wright
*[[Media:Johnson_Uruk_Administration copy.pdf|The Changing Organization of Uruk Administration on the Susiana Plain]] Gregory A. Johnson. In ''The Archaeology of Western Iran'', Frank Hole, ed.
*[[Media:Wright_UrukStates.pdf|Uruk States in Southwestern Iran]] Henry T. Wright. In ''Archaic States'', Gary M. Feinman and Joyce Marcus, eds.
*[[Media:Wright_UrukWorld.pdf|Cultural Action in the Uruk World]] Henry T. Wright. In ''Uruk Mesopotamia & Its Neighbors'', Mitchell S. Rothman, ed.
*[[Media:Liu_LongShan_96.pdf|Settlement Patterns, Chiefdom Variability, and the Development of Early States in North China]] Li Liu
*[[Media:Underhill_etall_02.pdf|Regional survey and the development of complex societies in southeastern Shandong, China]] Underhill, A. P., G. M. Feinman, L. M. Nicholas, G. Bennett, H. Fang, F. Luan, H. Yu and F. Cai
*[[Media:Lee_Erlitou.pdf|control strategies and polity competition in the lower Yi-Luo Valley, North China]] Yun Kuen Lee
*[[Media:System-dependent Selection.pdf|System-dependent Selection, Ecological Feedback and the Emergence of Functional Struction in Ecosystems]] Lansing, S. J., J. N. Kremer, and B. B. Smuts
*[[Media:Digitizing_Devpmnt.pdf|Digitizing 'Development']] Stefan Helmreich
*[[Media:Foucault.pdf|Foucault and the Water Temples]] Steve Lansing

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]], [[Media:chaos.1.4.pdf|Part I]], [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]], [[Media:Info.2.4.slides.pdf|Part II]]
* Lecture 3: Computation Theory. [[Media:Comp.1.4.pdf|Automata and Computation Theory]], [[Media:Comp.theory.2.4.pdf|Computability and Computational Complexity]]
* Lecture 4: Measures of Complexity. [[Media:Comp.mech.4.pdf|Computational Mechanics]], [[Media:Complexity.measures.4.pdf|Measures of Complexity]], [[Media:Conclusion.slides.4.pdf|Conclusion]]

Further reading

*J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. [http://arxiv.org/abs/cond-mat/0102181 cond-mat:0102181]. This is a long paper discussing the entropy rate and excess entropy and including many different examples.
*[[Media:Comp.ent.diagrams.4.pdf|Complexity Entropy Diagrams: Exploring the Relationships between Complexity and Randomness]]. Talk given in February 2006 at the Center for Computational Science and Engineering at UC Davis. Additional info on some of the ideas from Lecture 4.

'''Cosma Shalizi'''

* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

* Lecture 2: [[Media:Shalizi-CSSS06-2-inference.pdf|Statistical Inference for Complex Systems Models]]

See also:[[Media:Shalizi.overview.pdf|Methods and Techniques of Complex Systems Science: An Overview]], [http://arxiv.org/abs/nlin.AO/0307015 nlin.AO/0307015].

* Lecture 3: [[Media:Shalizi-CSSS06-3-model-discovery.pdf|Optimal Prediction, Model Discovery and Self-Organization]]

C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]

K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]

=== Week Two ===

=== Week Three ===

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

=== Week Four ===

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

== General Background ==

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].

File:Shalizi-CSSS06-3-model-discovery.pdf

2006-07-14T02:04:44Z

Cshalizi:

CSSS 2006 Beijing-Readings

2006-07-12T02:12:58Z

Cshalizi:

{{CSSS 2006 Beijing}}

__FORCETOC__

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further.

== Readings Associated with Particular Lecturers ==

=== Week One ===

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 1 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:

'''Part One-''' Foragers and the Emergence of Agriculture
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:CSSS_Wright1_Foragers.ppt|PowerPoint presentation of Part 1]]
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed.
*[[Media:ch3-1.pdf|Guila Naquitz in Spacial, Temporal, and Cultural Context]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:ch4.pdf|The Physical Environment of the Guila Naquitz Cave Group]], Kirkby, M. J., A. V. Whyte, and K. V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Reynolds_introduction_to_model.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Robert Reynolds. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:Diamond_Nature_02.pdf| Jared Diamond's Overview of the Emergence of Food Production]]

'''Part Two-''' Villages and the Emergernce of Tribal Alliance Systems
*[[Media:Modeling_Villages.doc|Brief Syllabus of Sources on the “Village” Project]]
*[[Media:CSSS_Wright2X_Villagers.ppt|PowerPoint presentation of Part 2]]
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds
*[[Media:Kohler_etal_Agent_Based_Mdling_SFI96.doc|Agent-Based Modeling of Prehistoric Settlement Systems in the Northern American Southwest]] Kohler, T. A., C. R. Van West, E. P. Carr and C. G. Langton
*[[Media:Reynolds_Algorithms_2002.ppt|Cultural Algorithms: A Tutorial]] Robert G. Reynolds
*[[Media:Kobti_Reynolds_Kohler_Resilience_IEEE03.pdf|A Multi-Agent Simulation Using Cultural Algorithms: The Effect of Culture on the Resilience of Social Systems]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Reynolds_Kohler_Kobti_Resilience_CMOT04.pdf|The Effects of Generalized Reciprocal Exchange on the Resilience of Social Networks: An Example from the Prehispanic Mesa Verde Region]] Reynolds, R. G., T. A. Kohler and Z. Kobti
*[[Media:Kobti_Reynlds_Kohler_Kinship_IEEE04.pdf|The Effect ofKinship Cooperation Learning Stategy and culture on the Resilience of Social Systems in the Village Mulit-Agent Simulation]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Kobti_etal_SwarmFest_Cultural_Algorithms_04.pdf|Agent-Based Modeling of Cultural Change in Swarm Using Cultural Algorithms]] Kobti, Z., R. G. Reynolds, and T. A. Kohler
*[[Media:Reynolds_etal_Gaming_IEEE05.pdf|Unraveling Ancient Mysteries: Reimagining the Past Using Evolutionary Computation in a Complex Gaming Environment]] Reynolds, R. G., Z. Kobti, T. A. Kohler, and L. Y. L. Yap

'''Part Three-''' Raising Civilizations
*[[Media:Modeling_States.doc|Brief Syllabus of Sources on the “States” Project]]
*[[Media:CSSS_Wright3_States.ppt|PowerPoint presentation of Part 3]]
*[[Media:Carneiro 1970.pdf|A Theory of the Origin of the State]] Robert L. Carneiro
*[[Media:Wright 1977.pdf|Recent Research on the Origin of the State]] Henry T. Wright
*[[Media:Johnson_Uruk_Administration copy.pdf|The Changing Organization of Uruk Administration on the Susiana Plain]] Gregory A. Johnson. In ''The Archaeology of Western Iran'', Frank Hole, ed.
*[[Media:Wright_UrukStates.pdf|Uruk States in Southwestern Iran]] Henry T. Wright. In ''Archaic States'', Gary M. Feinman and Joyce Marcus, eds.
*[[Media:Wright_UrukWorld.pdf|Cultural Action in the Uruk World]] Henry T. Wright. In ''Uruk Mesopotamia & Its Neighbors'', Mitchell S. Rothman, ed.
*[[Media:Liu_LongShan_96.pdf|Settlement Patterns, Chiefdom Variability, and the Development of Early States in North China]] Li Liu
*[[Media:Underhill_etall_02.pdf|Regional survey and the development of complex societies in southeastern Shandong, China]] Underhill, A. P., G. M. Feinman, L. M. Nicholas, G. Bennett, H. Fang, F. Luan, H. Yu and F. Cai
*[[Media:Lee_Erlitou.pdf|control strategies and polity competition in the lower Yi-Luo Valley, North China]] Yun Kuen Lee
*[[Media:System-dependent Selection.pdf|System-dependent Selection, Ecological Feedback and the Emergence of Functional Struction in Ecosystems]] Lansing, S. J., J. N. Kremer, and B. B. Smuts
*[[Media:Digitizing_Devpmnt.pdf|Digitizing 'Development']] Stefan Helmreich
*[[Media:Foucault.pdf|Foucault and the Water Temples]] Steve Lansing

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]], [[Media:chaos.1.4.pdf|Part I]], [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]], [[Media:Info.2.4.slides.pdf|Part II]]
* Lecture 3: Computation Theory. [[Media:Comp.1.4.pdf|Automata and Computation Theory]], [[Media:Comp.theory.2.4.pdf|Computability and Computational Complexity]]
* Lecture 4: Measures of Complexity. [[Media:Comp.mech.4.pdf|Computational Mechanics]], [[Media:Conclusion.slides.4.pdf|Conclusion]]

Further reading

*J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. [http://arxiv.org/abs/cond-mat/0102181 cond-mat:0102181]. This is a long paper discussing the entropy rate and excess entropy and including many different examples.
*[[Media:Comp.ent.diagrams.4.pdf|Complexity Entropy Diagrams: Exploring the Relationships between Complexity and Randomness]]. Talk given in February 2006 at the Center for Computational Science and Engineering at UC Davis. Additional info on some of the ideas from Lecture 4.

'''Cosma Shalizi'''

* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

* Lecture 2: [[Media:Shalizi-CSSS06-2-inference.pdf|Statistical Inference for Complex Systems Models]]

* Lecture 3: Optimal Prediction, Model Discovery and Self-Organization

C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]

K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]

=== Week Two ===

=== Week Three ===

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

=== Week Four ===

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

== General Background ==

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].

File:Shalizi-CSSS06-2-inference.pdf

2006-07-12T02:10:33Z

Cshalizi:

CSSS 2006 Beijing-Readings

2006-07-10T09:37:21Z

Cshalizi: Corrected order of H. Wright files

{{CSSS 2006 Beijing}}

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. These readings are ''not'' required. I will be updating this list fairly frequently. --[[User:Dpf|Dpf]] 19:15, 26 June 2006 (MDT)

=== General Background ===

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].

----

=== Readings Associated with Particular Lecturers ===

Lecturers are listed in order of appearance.

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 1 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Reynolds_introduction_to_model.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Robert Reynolds. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]] [[Media:chaos.1.4.pdf|Part I]] [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]] [[Media:Info.2.4.slides.pdf|Part II]]
* Lecture 3: Computation Theory.

'''Cosma Shalizi'''

* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]

K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

File:Reynolds introduction to model.pdf

2006-07-10T07:33:27Z

Cshalizi:

CSSS 2006 Beijing-Readings

2006-07-10T05:42:38Z

Cshalizi:

{{CSSS 2006 Beijing}}

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. These readings are ''not'' required. I will be updating this list fairly frequently. --[[User:Dpf|Dpf]] 19:15, 26 June 2006 (MDT)

=== General Background ===

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].

----

=== Readings Associated with Particular Lecturers ===

Lecturers are listed in order of appearance.

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 2 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Guila_Naquitz_A.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]] [[Media:chaos.1.4.pdf|Part I]] [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]] [[Media:Info.2.4.slides.pdf|Part II]]
* Lecture 3: Computation Theory.

'''Cosma Shalizi'''

* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]

K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

File:Shalizi-CSSS06-1-power-laws.pdf

2006-07-10T05:39:34Z

Cshalizi: Power Laws: What They Are, What They Mean, How To Tell If You Have One (first lecture by C. R. Shalizi)

Power Laws: What They Are, What They Mean, How To Tell If You Have One (first lecture by C. R. Shalizi)

CSSS 2006 Beijing-Readings

2006-07-10T05:33:57Z

Cshalizi:

{{CSSS 2006 Beijing}}

Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. These readings are ''not'' required. I will be updating this list fairly frequently. --[[User:Dpf|Dpf]] 19:15, 26 June 2006 (MDT)

=== General Background ===

James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.

[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc On the Complexities of Complex Economic Dynamics]. ''Journal of Economic Perspectives''. '''13''':169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].

Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].

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=== Readings Associated with Particular Lecturers ===

Lecturers are listed in order of appearance.

'''Andreas Wagner'''

[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS.

'''Henry Wright'''

[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 2 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
*[[Media:Guila_Naquitz_A.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.

'''Dave Feldman'''

[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]] [[Media:chaos.1.4.pdf|Part I]] [[Media:Chaos.2.4.pdf|Part II]]
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]] [[Media:Info.2.4.slides.pdf|Part II]]
* Lecture 3: Computation Theory.

'''Cosma Shalizi'''

M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.

C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]

K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]

'''Herb Gintis'''

Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper.

'''Lee Altenberg'''

*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems.
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.

Cosma Shalizi

2006-06-23T00:38:39Z

Cshalizi:

I have a [http://www.stat.cmu.edu/~cshalizi/ professorial] and a [http://bactra.org/ personal] homepage, and between them they tell you more than you'll want to know.

Cosma Shalizi

2006-06-23T00:38:22Z

Cshalizi:

I have a [http://www.stat.cmu.edu/~cshalizi/ professorial] and a [http://bactra.org/ personal] homepage, and between them they tell you more than you'll want to know,