Santa Fe Institute Events Wiki - User contributions [en]

CSSS 2008 Beijing-Faculty

2008-07-08T07:18:30Z

Hanjing: /* Partial List of Confirmed Faculty */

{{CSSS 2008 Beijing}}



== Partial List of Confirmed Faculty ==

[[Lee Altenberg]] University of Hawaii at Manoa

[[Aaron Clauset]] Santa Fe Institute

[[CHEN Xiaosong]] Institute of Theoretical Physics, CAS

[[Dave Feldman|David Feldman]] College of the Atlantic

[[Marc Feldman]] Stanford University

[[(Samuel) Qing-Shan JIA]] Tsinghua University

[[HAO Bai-Lin]] Fudan University

[[Daniel Hruschka]] Santa Fe Institute

[[LI Shuzhuo ]] Xian Jiaotong University

[[Eric Smith]] Santa Fe Institute

[[Susanne Still]] University of Hawaii at Manoa

[[William Tracy]] Rensselaer Polytechnic Institute

[[Jon Wilkins]] Santa Fe Institute

[[Chris Wiggins]] Columbia University

[[Henry Wright]] University of Michigan

[[ZHAO Li-Ping]] Shanghai Jiaotong University

[[HAN Jing]] Academcy of Mathematics and Systems Science

CSSS 2008 Beijing-Readings-Week-Two

2008-07-08T04:14:09Z

Hanjing: /* HAN Jing */

{{CSSS 2008 Beijing}}



==Aaron Clauset==

* Power Laws
* Introduction to Networks I
* Introduction to Networks II

===Background Reading===

The following references cover background material for the three lectures.

* [http://siamdl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=SIREAD000045000002000167000001 "The Structure and function of complex networks." M. E. J. Newman, ''SIAM Review'' '''45''', 167-256 (2003)]
* [[Media:CSN_07_PowerlawDistributionsInEmpiricalData_arxiv.pdf|"Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).]]

==DI Zengru==

Introduction to Weighted Networks

===Background Reading===
* Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. [[Media:WeightCommunityMethod.pdf | Accuracy and precision of methods for community identification in weighted networks]]. Physica A 377 (2007) 363372.
* S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. [[Media:06-Complex_networks-_Structure_and_dynamics.pdf | Complex networks: Structure and dynamics]]. Physics Reports 424 (2006) 175 308.
* Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. [[Media:PLAWeightedNetwork.pdf | Small-world effect induced by weight randomization on regular networks]]. Physics Letters A 364 (2007) 488493.
* Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. [[Media:Njp6_5_072.pdf| Modelling weighted networks using connection count]]. New Journal of Physics 8 (2006) 72.

==HAN Jing==

Collective Behavior of Multi-agent systems.

Lecture 1: Graph Coloring Problems – Analysis and Design.

Lecture 2: Synchronization and “Soft Control”.

===Background Reading===
[http://complex.amss.ac.cn/hanjing/softcontrol/JSSC-19(1)-054-062.pdf Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62]

[http://complex.amss.ac.cn/hanjing/dl/258735_2ndproof.pdf Local Evaluation Functions and Global Evaluation Functions for Computational Evolution. Jing Han. Complex Systems, 15, Issue 4 (c) 2005, pages 307 – 347.]

==HAN Zhangang==
* [[Media: Han_Zhangang.08.ppt |Division of Labor in an Agent System with a Market Mechanism]]
===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First part of the
lecture) and [[Media:asd.pdf | Applied symbolic dynamics from 1D to 2D to ODE ]] (Second part of the lecture)

* Lecture 2: [[Media:csss08b.ppt | Visualization of DNA data and a few nice math therefrom ]] (A PPT that contains more than used in class)

===Background Reading===
Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,
a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
Hao's apology: Since not all figures in this book were Postscript files and
I have not made them into .eps yet, I have put an image of my personal copy
in my website. It is a file of more than 20MB. That is why I did not put it
in the SFI Wiki. I hope I will be able to do it in not-distant future. The
symbolic dynamics chapters of this book are somehow outdated. For those who
want to learn more about symbolic dynamics I suggest the following book.
2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ppt | Visualization of real DNA data and a few nice math therefrom]]

1. Shen Junjie at al., [[Media: SeeDNA_GPB.pdf | SeeDNA: a visualization tool for long DNA sequences and complete genomes]] It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website:
http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, [[Media:HaoXie_SFI.pdf | Factorizable Language: From Dyanmics to Biology]]

3. Xiaoli Shi et al., [[Media:jkps07.pdf | Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

4. Bailin Hao and Lei Gao, [[Media:ProkBranch_jse08.pdf | Prokaryotic branch of tree of life: a composition vector approach]]

==Dan Hruschka==

* [[Media:Hruschka_Lecture1.pdf | Models of Cultural Diversity ]]
* [[Media:Hruschka Lecture2.pdf | Simple Models of Social Learning ]]
* [[Media:Hruschka_Lecture3_final.pdf | Neutral Models of Language Change ]]

===Background Reading===

* Joseph Henrich and Richard McElreath, [[Media: HenrichandMcElreath.pdf | The Evolution of Cultural Evolution ]], Evolutionary Anthropology 12:123135 (2003).

==LI Ming==

===Background Reading===

==ZHAO Liping==

* [[Media:Zhao.CSSS.08.2x2.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] Four slides on each page.
* [[Media:Zhao.CSSS.08.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] One slide on each page.

===Background Reading===
# Pang et al., [[Media:Pang_2007_ISME-J.pdf | Inter-species transplantation of gut microbiota from human to pigs]], The ISME J. 1(2007): 156-162)
# Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, [[Media:JIA_2008_NRDD.pdf | Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery]], 7 (Feb 2008): 123-129.
# Min Li et al., [[Media:Limin_2008_PNAS.pdf | Symbiotic gut microbes modulate human metabolic phenotypes]], Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.

==ZHOU Haijin==

===Background Reading===

CSSS 2008 Beijing-Readings-Week-Two

2008-07-08T04:13:30Z

Hanjing: /* HAN Jing */

{{CSSS 2008 Beijing}}



==Aaron Clauset==

* Power Laws
* Introduction to Networks I
* Introduction to Networks II

===Background Reading===

The following references cover background material for the three lectures.

* [http://siamdl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=SIREAD000045000002000167000001 "The Structure and function of complex networks." M. E. J. Newman, ''SIAM Review'' '''45''', 167-256 (2003)]
* [[Media:CSN_07_PowerlawDistributionsInEmpiricalData_arxiv.pdf|"Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).]]

==DI Zengru==

Introduction to Weighted Networks

===Background Reading===
* Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. [[Media:WeightCommunityMethod.pdf | Accuracy and precision of methods for community identification in weighted networks]]. Physica A 377 (2007) 363372.
* S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. [[Media:06-Complex_networks-_Structure_and_dynamics.pdf | Complex networks: Structure and dynamics]]. Physics Reports 424 (2006) 175 308.
* Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. [[Media:PLAWeightedNetwork.pdf | Small-world effect induced by weight randomization on regular networks]]. Physics Letters A 364 (2007) 488493.
* Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. [[Media:Njp6_5_072.pdf| Modelling weighted networks using connection count]]. New Journal of Physics 8 (2006) 72.

==HAN Jing==

Collective Behavior of Multi-agent systems.
Lecture 1: Graph Coloring Problems – Analysis and Design.
Lecture 2: Synchronization and “Soft Control”.

===Background Reading===
[http://complex.amss.ac.cn/hanjing/softcontrol/JSSC-19(1)-054-062.pdf Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62]

[http://complex.amss.ac.cn/hanjing/dl/258735_2ndproof.pdf Local Evaluation Functions and Global Evaluation Functions for Computational Evolution. Jing Han. Complex Systems, 15, Issue 4 (c) 2005, pages 307 – 347.]

==HAN Zhangang==
* [[Media: Han_Zhangang.08.ppt |Division of Labor in an Agent System with a Market Mechanism]]
===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First part of the
lecture) and [[Media:asd.pdf | Applied symbolic dynamics from 1D to 2D to ODE ]] (Second part of the lecture)

* Lecture 2: [[Media:csss08b.ppt | Visualization of DNA data and a few nice math therefrom ]] (A PPT that contains more than used in class)

===Background Reading===
Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,
a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
Hao's apology: Since not all figures in this book were Postscript files and
I have not made them into .eps yet, I have put an image of my personal copy
in my website. It is a file of more than 20MB. That is why I did not put it
in the SFI Wiki. I hope I will be able to do it in not-distant future. The
symbolic dynamics chapters of this book are somehow outdated. For those who
want to learn more about symbolic dynamics I suggest the following book.
2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ppt | Visualization of real DNA data and a few nice math therefrom]]

1. Shen Junjie at al., [[Media: SeeDNA_GPB.pdf | SeeDNA: a visualization tool for long DNA sequences and complete genomes]] It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website:
http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, [[Media:HaoXie_SFI.pdf | Factorizable Language: From Dyanmics to Biology]]

3. Xiaoli Shi et al., [[Media:jkps07.pdf | Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

4. Bailin Hao and Lei Gao, [[Media:ProkBranch_jse08.pdf | Prokaryotic branch of tree of life: a composition vector approach]]

==Dan Hruschka==

* [[Media:Hruschka_Lecture1.pdf | Models of Cultural Diversity ]]
* [[Media:Hruschka Lecture2.pdf | Simple Models of Social Learning ]]
* [[Media:Hruschka_Lecture3_final.pdf | Neutral Models of Language Change ]]

===Background Reading===

* Joseph Henrich and Richard McElreath, [[Media: HenrichandMcElreath.pdf | The Evolution of Cultural Evolution ]], Evolutionary Anthropology 12:123135 (2003).

==LI Ming==

===Background Reading===

==ZHAO Liping==

* [[Media:Zhao.CSSS.08.2x2.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] Four slides on each page.
* [[Media:Zhao.CSSS.08.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] One slide on each page.

===Background Reading===
# Pang et al., [[Media:Pang_2007_ISME-J.pdf | Inter-species transplantation of gut microbiota from human to pigs]], The ISME J. 1(2007): 156-162)
# Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, [[Media:JIA_2008_NRDD.pdf | Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery]], 7 (Feb 2008): 123-129.
# Min Li et al., [[Media:Limin_2008_PNAS.pdf | Symbiotic gut microbes modulate human metabolic phenotypes]], Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.

==ZHOU Haijin==

===Background Reading===

CSSS 2008 Beijing-Readings-Week-Two

2008-07-08T04:12:58Z

Hanjing: /* Background Reading */

{{CSSS 2008 Beijing}}



==Aaron Clauset==

* Power Laws
* Introduction to Networks I
* Introduction to Networks II

===Background Reading===

The following references cover background material for the three lectures.

* [http://siamdl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=SIREAD000045000002000167000001 "The Structure and function of complex networks." M. E. J. Newman, ''SIAM Review'' '''45''', 167-256 (2003)]
* [[Media:CSN_07_PowerlawDistributionsInEmpiricalData_arxiv.pdf|"Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).]]

==DI Zengru==

Introduction to Weighted Networks

===Background Reading===
* Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. [[Media:WeightCommunityMethod.pdf | Accuracy and precision of methods for community identification in weighted networks]]. Physica A 377 (2007) 363372.
* S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. [[Media:06-Complex_networks-_Structure_and_dynamics.pdf | Complex networks: Structure and dynamics]]. Physics Reports 424 (2006) 175 308.
* Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. [[Media:PLAWeightedNetwork.pdf | Small-world effect induced by weight randomization on regular networks]]. Physics Letters A 364 (2007) 488493.
* Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. [[Media:Njp6_5_072.pdf| Modelling weighted networks using connection count]]. New Journal of Physics 8 (2006) 72.

==HAN Jing==

Collective Behavior of Multi-agent systems
Lecture 1: Graph Coloring Problems – �Analysis and Design
Lecture 2: Synchronization and “Soft Control”

Collective Behavior of Multi-agent systems.
Lecture 1: Graph Coloring Problems – Analysis and Design.
Lecture 2: Synchronization and “Soft Control”.

===Background Reading===
[http://complex.amss.ac.cn/hanjing/softcontrol/JSSC-19(1)-054-062.pdf Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62]

[http://complex.amss.ac.cn/hanjing/dl/258735_2ndproof.pdf Local Evaluation Functions and Global Evaluation Functions for Computational Evolution. Jing Han. Complex Systems, 15, Issue 4 (c) 2005, pages 307 – 347.]

==HAN Zhangang==
* [[Media: Han_Zhangang.08.ppt |Division of Labor in an Agent System with a Market Mechanism]]
===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First part of the
lecture) and [[Media:asd.pdf | Applied symbolic dynamics from 1D to 2D to ODE ]] (Second part of the lecture)

* Lecture 2: [[Media:csss08b.ppt | Visualization of DNA data and a few nice math therefrom ]] (A PPT that contains more than used in class)

===Background Reading===
Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,
a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
Hao's apology: Since not all figures in this book were Postscript files and
I have not made them into .eps yet, I have put an image of my personal copy
in my website. It is a file of more than 20MB. That is why I did not put it
in the SFI Wiki. I hope I will be able to do it in not-distant future. The
symbolic dynamics chapters of this book are somehow outdated. For those who
want to learn more about symbolic dynamics I suggest the following book.
2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ppt | Visualization of real DNA data and a few nice math therefrom]]

1. Shen Junjie at al., [[Media: SeeDNA_GPB.pdf | SeeDNA: a visualization tool for long DNA sequences and complete genomes]] It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website:
http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, [[Media:HaoXie_SFI.pdf | Factorizable Language: From Dyanmics to Biology]]

3. Xiaoli Shi et al., [[Media:jkps07.pdf | Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

4. Bailin Hao and Lei Gao, [[Media:ProkBranch_jse08.pdf | Prokaryotic branch of tree of life: a composition vector approach]]

==Dan Hruschka==

* [[Media:Hruschka_Lecture1.pdf | Models of Cultural Diversity ]]
* [[Media:Hruschka Lecture2.pdf | Simple Models of Social Learning ]]
* [[Media:Hruschka_Lecture3_final.pdf | Neutral Models of Language Change ]]

===Background Reading===

* Joseph Henrich and Richard McElreath, [[Media: HenrichandMcElreath.pdf | The Evolution of Cultural Evolution ]], Evolutionary Anthropology 12:123135 (2003).

==LI Ming==

===Background Reading===

==ZHAO Liping==

* [[Media:Zhao.CSSS.08.2x2.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] Four slides on each page.
* [[Media:Zhao.CSSS.08.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] One slide on each page.

===Background Reading===
# Pang et al., [[Media:Pang_2007_ISME-J.pdf | Inter-species transplantation of gut microbiota from human to pigs]], The ISME J. 1(2007): 156-162)
# Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, [[Media:JIA_2008_NRDD.pdf | Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery]], 7 (Feb 2008): 123-129.
# Min Li et al., [[Media:Limin_2008_PNAS.pdf | Symbiotic gut microbes modulate human metabolic phenotypes]], Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.

==ZHOU Haijin==

===Background Reading===

CSSS 2008 Beijing-Readings-Week-Two

2008-07-08T04:09:56Z

Hanjing: /* Background Reading */

{{CSSS 2008 Beijing}}



==Aaron Clauset==

* Power Laws
* Introduction to Networks I
* Introduction to Networks II

===Background Reading===

The following references cover background material for the three lectures.

* [http://siamdl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=SIREAD000045000002000167000001 "The Structure and function of complex networks." M. E. J. Newman, ''SIAM Review'' '''45''', 167-256 (2003)]
* [[Media:CSN_07_PowerlawDistributionsInEmpiricalData_arxiv.pdf|"Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).]]

==DI Zengru==

Introduction to Weighted Networks

===Background Reading===
* Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. [[Media:WeightCommunityMethod.pdf | Accuracy and precision of methods for community identification in weighted networks]]. Physica A 377 (2007) 363372.
* S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. [[Media:06-Complex_networks-_Structure_and_dynamics.pdf | Complex networks: Structure and dynamics]]. Physics Reports 424 (2006) 175 308.
* Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. [[Media:PLAWeightedNetwork.pdf | Small-world effect induced by weight randomization on regular networks]]. Physics Letters A 364 (2007) 488493.
* Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. [[Media:Njp6_5_072.pdf| Modelling weighted networks using connection count]]. New Journal of Physics 8 (2006) 72.

==HAN Jing==

Collective Behavior of Multi-agent systems
Lecture 1: Graph Coloring Problems – �Analysis and Design
Lecture 2: Synchronization and “Soft Control”

===Background Reading===
[http://complex.amss.ac.cn/hanjing/softcontrol/JSSC-19(1)-054-062.pdf Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62]

[http://complex.amss.ac.cn/hanjing/dl/258735_2ndproof.pdf Local Evaluation Functions and Global Evaluation Functions for Computational Evolution. Jing Han. Complex Systems, 15, Issue 4 (c) 2005, pages 307 – 347.]

==HAN Zhangang==
* [[Media: Han_Zhangang.08.ppt |Division of Labor in an Agent System with a Market Mechanism]]
===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First part of the
lecture) and [[Media:asd.pdf | Applied symbolic dynamics from 1D to 2D to ODE ]] (Second part of the lecture)

* Lecture 2: [[Media:csss08b.ppt | Visualization of DNA data and a few nice math therefrom ]] (A PPT that contains more than used in class)

===Background Reading===
Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,
a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
Hao's apology: Since not all figures in this book were Postscript files and
I have not made them into .eps yet, I have put an image of my personal copy
in my website. It is a file of more than 20MB. That is why I did not put it
in the SFI Wiki. I hope I will be able to do it in not-distant future. The
symbolic dynamics chapters of this book are somehow outdated. For those who
want to learn more about symbolic dynamics I suggest the following book.
2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ppt | Visualization of real DNA data and a few nice math therefrom]]

1. Shen Junjie at al., [[Media: SeeDNA_GPB.pdf | SeeDNA: a visualization tool for long DNA sequences and complete genomes]] It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website:
http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, [[Media:HaoXie_SFI.pdf | Factorizable Language: From Dyanmics to Biology]]

3. Xiaoli Shi et al., [[Media:jkps07.pdf | Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

4. Bailin Hao and Lei Gao, [[Media:ProkBranch_jse08.pdf | Prokaryotic branch of tree of life: a composition vector approach]]

==Dan Hruschka==

* [[Media:Hruschka_Lecture1.pdf | Models of Cultural Diversity ]]
* [[Media:Hruschka Lecture2.pdf | Simple Models of Social Learning ]]
* [[Media:Hruschka_Lecture3_final.pdf | Neutral Models of Language Change ]]

===Background Reading===

* Joseph Henrich and Richard McElreath, [[Media: HenrichandMcElreath.pdf | The Evolution of Cultural Evolution ]], Evolutionary Anthropology 12:123135 (2003).

==LI Ming==

===Background Reading===

==ZHAO Liping==

* [[Media:Zhao.CSSS.08.2x2.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] Four slides on each page.
* [[Media:Zhao.CSSS.08.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] One slide on each page.

===Background Reading===
# Pang et al., [[Media:Pang_2007_ISME-J.pdf | Inter-species transplantation of gut microbiota from human to pigs]], The ISME J. 1(2007): 156-162)
# Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, [[Media:JIA_2008_NRDD.pdf | Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery]], 7 (Feb 2008): 123-129.
# Min Li et al., [[Media:Limin_2008_PNAS.pdf | Symbiotic gut microbes modulate human metabolic phenotypes]], Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.

==ZHOU Haijin==

===Background Reading===

CSSS 2008 Beijing-Readings-Week-Two

2008-07-08T04:08:39Z

Hanjing: /* Background Reading */

{{CSSS 2008 Beijing}}



==Aaron Clauset==

* Power Laws
* Introduction to Networks I
* Introduction to Networks II

===Background Reading===

The following references cover background material for the three lectures.

* [http://siamdl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=SIREAD000045000002000167000001 "The Structure and function of complex networks." M. E. J. Newman, ''SIAM Review'' '''45''', 167-256 (2003)]
* [[Media:CSN_07_PowerlawDistributionsInEmpiricalData_arxiv.pdf|"Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).]]

==DI Zengru==

Introduction to Weighted Networks

===Background Reading===
* Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. [[Media:WeightCommunityMethod.pdf | Accuracy and precision of methods for community identification in weighted networks]]. Physica A 377 (2007) 363372.
* S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. [[Media:06-Complex_networks-_Structure_and_dynamics.pdf | Complex networks: Structure and dynamics]]. Physics Reports 424 (2006) 175 308.
* Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. [[Media:PLAWeightedNetwork.pdf | Small-world effect induced by weight randomization on regular networks]]. Physics Letters A 364 (2007) 488493.
* Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. [[Media:Njp6_5_072.pdf| Modelling weighted networks using connection count]]. New Journal of Physics 8 (2006) 72.

==HAN Jing==

Collective Behavior of Multi-agent systems
Lecture 1: Graph Coloring Problems – �Analysis and Design
Lecture 2: Synchronization and “Soft Control”

===Background Reading===
[http://complex.amss.ac.cn/hanjing/softcontrol/JSSC-19(1)-054-062.pdf Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62]

==HAN Zhangang==
* [[Media: Han_Zhangang.08.ppt |Division of Labor in an Agent System with a Market Mechanism]]
===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First part of the
lecture) and [[Media:asd.pdf | Applied symbolic dynamics from 1D to 2D to ODE ]] (Second part of the lecture)

* Lecture 2: [[Media:csss08b.ppt | Visualization of DNA data and a few nice math therefrom ]] (A PPT that contains more than used in class)

===Background Reading===
Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,
a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
Hao's apology: Since not all figures in this book were Postscript files and
I have not made them into .eps yet, I have put an image of my personal copy
in my website. It is a file of more than 20MB. That is why I did not put it
in the SFI Wiki. I hope I will be able to do it in not-distant future. The
symbolic dynamics chapters of this book are somehow outdated. For those who
want to learn more about symbolic dynamics I suggest the following book.
2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ppt | Visualization of real DNA data and a few nice math therefrom]]

1. Shen Junjie at al., [[Media: SeeDNA_GPB.pdf | SeeDNA: a visualization tool for long DNA sequences and complete genomes]] It runs on RedHat Linux with GTK support. Its C source may be downloaded from Hao's website:
http://www.itp.ac.cn/~hao/SeeDNA.tar.gz.

2. Bailin Hao and Huimin Xie, [[Media:HaoXie_SFI.pdf | Factorizable Language: From Dyanmics to Biology]]

3. Xiaoli Shi et al., [[Media:jkps07.pdf | Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

4. Bailin Hao and Lei Gao, [[Media:ProkBranch_jse08.pdf | Prokaryotic branch of tree of life: a composition vector approach]]

==Dan Hruschka==

* [[Media:Hruschka_Lecture1.pdf | Models of Cultural Diversity ]]
* [[Media:Hruschka Lecture2.pdf | Simple Models of Social Learning ]]
* [[Media:Hruschka_Lecture3_final.pdf | Neutral Models of Language Change ]]

===Background Reading===

* Joseph Henrich and Richard McElreath, [[Media: HenrichandMcElreath.pdf | The Evolution of Cultural Evolution ]], Evolutionary Anthropology 12:123135 (2003).

==LI Ming==

===Background Reading===

==ZHAO Liping==

* [[Media:Zhao.CSSS.08.2x2.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] Four slides on each page.
* [[Media:Zhao.CSSS.08.pdf | Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology ]] One slide on each page.

===Background Reading===
# Pang et al., [[Media:Pang_2007_ISME-J.pdf | Inter-species transplantation of gut microbiota from human to pigs]], The ISME J. 1(2007): 156-162)
# Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, [[Media:JIA_2008_NRDD.pdf | Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery]], 7 (Feb 2008): 123-129.
# Min Li et al., [[Media:Limin_2008_PNAS.pdf | Symbiotic gut microbes modulate human metabolic phenotypes]], Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122.

==ZHOU Haijin==

===Background Reading===

CSSS 2007 Beijing-Readings-Week-Three

2007-07-30T14:31:42Z

Hanjing: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Jia Qing-Shan (Samuel)==

===Lecture Notes===

*Ordinal Optimization: Soft Optimization for Hard Problems. [[Media:AddOn.ppt|Introduction]] [[Media:IntroOOv4.ppt|Main Presentation]]

===Additional Reading===
*[http://cfins.au.tsinghua.edu.cn/cn/resource/index.php Some references] (in Chinese)
* Ho, Y.-C., Zhao, Q.-C., and Jia, Q.-S., Ordinal Optimization: Soft Optimization for Hard
Problems, Springer, 2007.

==Han Jing==

===Lecture Notes===
*[[Media:lecture1.pdf|The Collective Behavior of Multi-Agent Systems 1]]
*[http://complex.amss.ac.cn/hanjing/dl/hanjing-CSSS07-lec2-sch.pdf The Collective Behavior of Multi-Agent Systems 2-1], [http://complex.amss.ac.cn/hanjing/dl/hanjing-CSSS07-lec2-NE.pdf The Collective Behavior of Multi-Agent Systems 2-2]

===Additional Reading===

==Jim Glazier==

===Lecture Notes===
*[[Media:Compucell3d_quickstartguide_0.5.pdf|CompuCell 3D Quickstart Guide]]
*[[Media:CompuCellManual.doc|CompuCell3D Manual]]
*[[Media:CompuCellPlayerManual.doc|CompuCell Player]]
*[[Media:Installing_CompuCell_linux.doc |Installing CompuCell on Linux systems]]
*[[Media:Running_CompuCell3D.doc|CompuCell3D Running Modes]]
*[[Media:SummerSchoolExercises.doc|CompuCell3D Introduction - tutorials]]

===Additional Reading===

<ul>
<li> Balter, et al., [[Media:Balter_proofs.pdf| The Glazier-Graner-Hogeweg Model: Extension, future directions, and opportunities for further study.]] in Single-Cell-Based Models in Biology and Medicine, Anderson, et al.
(eds), Mathematics and Biosciences in Interation 151-167. 2007.

<li> Glazier, et al., [[Media:Glazier_proofsv2.pdf|Magnetization to Morphogenesis: A brief history of the Blazier-Graner-Hogeweg model]]. in Single-Cell-Based Models in Biology and Medicine, Anderson, et al.
(eds), Mathematics and Biosciences in Interation 79-106. 2007.

</ul>

==Raissa D'Souza==

===Lecture Notes===
*[[Media:DSlecture1.pdf|Understanding networks: Topology, Activity, Phase transitions]]

===Additional Reading===

==David Feldman==

===Lecture Notes===

*[[Media:Presentation.slides.4.pdf|Advice on Giving Research Presentations]]

Jing Han

2007-07-16T04:48:18Z

Hanjing:

Hello, everyone!
[http://complex.amss.ac.cn/hanjing/index.html Han Jing's Homepage]

HAN Jing

2007-07-16T04:42:21Z

Hanjing:

[http://complex.amss.ac.cn/hanjing/index.html Han Jing's Homepage]

CSSS 2006 Beijing-Readings

2006-07-26T07:20:14Z

Hanjing: /* Week Two */

{{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]]
*[http://hornacek.coa.edu/dave/Wright/csss_foragers1_rev_06.ppt PowerPoint presentation of Part 1] (Updated 21 July 2006)
*[[Media:Foragrs_talk.doc|Talk Outline]] (Updated 21 July 2006)
*[[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]]
*[http://hornacek.coa.edu/dave/Wright/csss_villages2_rev_06.ppt Revised PowerPoint presentation of Part 2] (Updated 21 July 2006)
*[[Media:Villages_talk.doc|Talk Outline]] (Updated 21 July 2006)
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds
*[[Media:Gumerman_etal_.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:States_talk_06.doc|Talk Outline]] (Updated 21 July 2006)
*[[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 ===

'''Li Shuzhuo & Marcus W.Feldman ''July 17, Morning '''''

[[Media:Population dynamics introduction.pdf|Population dynamics introduction]].

'''Marcus W.Feldman & Li Shuzhuo ''July 17, Afternoon '''''

[[Media:Rural-urban Migration in China Social Networks and Socio-demography.pdf|Rural-urban Migration in China Social Networks and Socio-demography]].

'''Marcus W.Feldman ''July 18, Morning '''''

[[Media:Niche construction A new dimension for biological and cultural evolution.pdf|Niche construction A new dimension for biological and cultural evolution]].

'''Jing Han'''
lecture notes 1, 2, 3.

About [http://complex.amss.ac.cn/hanjing/softcontrol/paper.html Soft-control].

'''Jim Crutchfield'''

Background for lecture two:
* O. Goenernup and J. P. Crutchfield, [http://cse.ucdavis.edu/~cmg/papers/hsofps.pdf Hierarchical Self-Organization in the Finitary Process Soup], Proceedings of Artificial Life X (2006) submitted.
* J. P. Crutchfield and Olof Görnerup, [http://cse.ucdavis.edu/~cmg/papers/otmo.pdf Objects That Make Objects: The Population Dynamics of Structural Complexity].

=== Week Three ===

'''Hao Bai-lin'''

*[[Media:Asd_hao.pdf|Applied Symbolic Dynamics: From 1D to 2D to ODEs]]

'''Lee Altenberg'''

'''Lecture Slides'''
*[[http://www.santafe.edu/~altenber/CSSS_BEIJING/Altenberg_Lecture_1.4up.pdf Lecture 1: Overview]][6MB]
*[[http://www.santafe.edu/~altenber/CSSS_BEIJING/Altenberg_Lecture_2.4up.pdf Lecture 2: Spectral Analysis of Evolutionary Dynamics]][1MB]

'''Background Reading'''

*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. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.
*Erik van Nimwegen, James P. Crutchfield, and Martijn Huynen [http://www.santafe.edu/~evca/Papers/nemr.pdf Neutral Evolution of Mutational Robustness.] Proceedings of the National Academy of Science U.S.A. 96:9716-9720 (1999).

'''Additional Reading'''

*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.
*Erik van Nimwegen and James P. Crutchfield. [http://www.santafe.edu/~evca/Papers/med.pdf Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?]
Bulletin of Mathematical Biology 62:5:799-848 (Sep 2000)

'''William S-Y. Wang & James W. Minett, ''July 24 & 25, 10:30-11:45 '''''

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_notes.pdf Notes to Lectures 1 and 2].

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_bibliography.pdf Bibliography to Lectures 1 and 2].

'''William S-Y. Wang & James W. Minett, ''July 26, 10:30-11:45 '''''

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_intro.pdf Introduction to Lectures 3 to 5].

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_bib.pdf Bibliography to Lectures 3 to 5].

Lecture 3: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_acquisition.pdf Modeling the ontogenetic emergence of language using recurrent neural networks].

'''William S-Y. Wang & James W. Minett, ''July 27, 10:30-11:45 '''''

Lecture 4: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_4_emergence.pdf Modeling the phylogenetic emergence of language using agent-based modeling].

'''William S-Y. Wang & James W. Minett, ''July 28, 10:30-11:45 '''''

Lecture 5: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_5_competition.pdf Modeling language competition and death using differential equations and agent-based modeling].

=== Week Four ===

'''Herbert 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. The rest will be based on various papers available from his[[http://www-unix.oit.umass.edu/~gintis web site.]]

== 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].

CSSS 2006 Beijing-Readings

2006-07-26T07:18:20Z

Hanjing: /* Week Two */

{{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]]
*[http://hornacek.coa.edu/dave/Wright/csss_foragers1_rev_06.ppt PowerPoint presentation of Part 1] (Updated 21 July 2006)
*[[Media:Foragrs_talk.doc|Talk Outline]] (Updated 21 July 2006)
*[[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]]
*[http://hornacek.coa.edu/dave/Wright/csss_villages2_rev_06.ppt Revised PowerPoint presentation of Part 2] (Updated 21 July 2006)
*[[Media:Villages_talk.doc|Talk Outline]] (Updated 21 July 2006)
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds
*[[Media:Gumerman_etal_.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:States_talk_06.doc|Talk Outline]] (Updated 21 July 2006)
*[[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 ===

'''Li Shuzhuo & Marcus W.Feldman ''July 17, Morning '''''

[[Media:Population dynamics introduction.pdf|Population dynamics introduction]].

'''Marcus W.Feldman & Li Shuzhuo ''July 17, Afternoon '''''

[[Media:Rural-urban Migration in China Social Networks and Socio-demography.pdf|Rural-urban Migration in China Social Networks and Socio-demography]].

'''Marcus W.Feldman ''July 18, Morning '''''

[[Media:Niche construction A new dimension for biological and cultural evolution.pdf|Niche construction A new dimension for biological and cultural evolution]].

'''Jing Han'''
lecture notes 1, 2, 3.
About [http://complex.amss.ac.cn/hanjing/softcontrol/paper.html, Soft-control].

'''Jim Crutchfield'''

Background for lecture two:
* O. Goenernup and J. P. Crutchfield, [http://cse.ucdavis.edu/~cmg/papers/hsofps.pdf Hierarchical Self-Organization in the Finitary Process Soup], Proceedings of Artificial Life X (2006) submitted.
* J. P. Crutchfield and Olof Görnerup, [http://cse.ucdavis.edu/~cmg/papers/otmo.pdf Objects That Make Objects: The Population Dynamics of Structural Complexity].

=== Week Three ===

'''Hao Bai-lin'''

*[[Media:Asd_hao.pdf|Applied Symbolic Dynamics: From 1D to 2D to ODEs]]

'''Lee Altenberg'''

'''Lecture Slides'''
*[[http://www.santafe.edu/~altenber/CSSS_BEIJING/Altenberg_Lecture_1.4up.pdf Lecture 1: Overview]][6MB]
*[[http://www.santafe.edu/~altenber/CSSS_BEIJING/Altenberg_Lecture_2.4up.pdf Lecture 2: Spectral Analysis of Evolutionary Dynamics]][1MB]

'''Background Reading'''

*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. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.
*Erik van Nimwegen, James P. Crutchfield, and Martijn Huynen [http://www.santafe.edu/~evca/Papers/nemr.pdf Neutral Evolution of Mutational Robustness.] Proceedings of the National Academy of Science U.S.A. 96:9716-9720 (1999).

'''Additional Reading'''

*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.
*Erik van Nimwegen and James P. Crutchfield. [http://www.santafe.edu/~evca/Papers/med.pdf Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths?]
Bulletin of Mathematical Biology 62:5:799-848 (Sep 2000)

'''William S-Y. Wang & James W. Minett, ''July 24 & 25, 10:30-11:45 '''''

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_notes.pdf Notes to Lectures 1 and 2].

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_bibliography.pdf Bibliography to Lectures 1 and 2].

'''William S-Y. Wang & James W. Minett, ''July 26, 10:30-11:45 '''''

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_intro.pdf Introduction to Lectures 3 to 5].

[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_bib.pdf Bibliography to Lectures 3 to 5].

Lecture 3: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_acquisition.pdf Modeling the ontogenetic emergence of language using recurrent neural networks].

'''William S-Y. Wang & James W. Minett, ''July 27, 10:30-11:45 '''''

Lecture 4: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_4_emergence.pdf Modeling the phylogenetic emergence of language using agent-based modeling].

'''William S-Y. Wang & James W. Minett, ''July 28, 10:30-11:45 '''''

Lecture 5: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_5_competition.pdf Modeling language competition and death using differential equations and agent-based modeling].

=== Week Four ===

'''Herbert 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. The rest will be based on various papers available from his[[http://www-unix.oit.umass.edu/~gintis web site.]]

== 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].

Jing Han

2006-03-22T08:14:37Z

Hanjing:

Hello, everyone, just a test.