Santa Fe Institute Events Wiki - User contributions [en]

CSSS 2008 Beijing-Readings-Week-Two

2008-07-07T14:02:45Z

Haobailin: /* HAO Bai-lin */

{{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==

===Background Reading===

==HAN Zhangang==

===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.ptt | 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==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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===

File:Asd.pdf

2008-07-07T14:00:34Z

Haobailin: Applied symbolic dynamics: From 1D to 2D to ODE

Applied symbolic dynamics: From 1D to 2D to ODE

CSSS 2008 Beijing-Readings-Week-Two

2008-07-07T00:11:18Z

Haobailin: /* HAO Bai-lin */

{{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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==
* Lecture 1: [[Media:csss08a.ppt | Symbolic dynamics in action or Applied symbolic dynamics ]] (First 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.ptt | 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==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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===

File:Csss08a.ppt

2008-07-07T00:08:58Z

Haobailin: Symbolic dynamics in action or Applied symbolic dynamics, Lecture Note 1 for CSSS2008

Symbolic dynamics in action or Applied symbolic dynamics, Lecture Note 1 for
CSSS2008

CSSS 2008 Beijing-Readings-Week-Two

2008-07-06T08:08:22Z

Haobailin: /* HAO Bai-lin */

{{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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

* 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.ptt | 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==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T08:07:16Z

Haobailin: /* HAO Bai-lin */

{{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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

* 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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: [[Media: csss08b.ptt | 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==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T07:55:14Z

Haobailin: /* 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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

* 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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

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

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

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

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

==Dan Hruschka==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T07:50:02Z

Haobailin: /* HAO Bai-lin */

{{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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

* 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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: Visualization of real DNA data and a few nice math therefrom

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

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

3. [[Media:ProkBranch_jse08.pdf ]]

==Dan Hruschka==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T07:43:42Z

Haobailin: /* HAO Bai-lin */

{{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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

* [[Media:csss08b.ppt]]

===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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: Visualization of real DNA data and a few nice math therefrom

# [[Media:HaoXie_SFI.pdf]]

# [[Media:jkps07.pdf]]

# [[Media:ProkBranch_jse08.pdf]]

==Dan Hruschka==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T07:38:55Z

Haobailin: /* 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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

===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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: Visualization of real DNA data and a few nice math therefrom

1. [[Image:HaoXie_SFI.pdf]]

2. [[Image:jkps07.pdf]]

3. [[ProkBranch_jse08.pdf]]

==Dan Hruschka==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T07:34:59Z

Haobailin: /* 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 Zhengru==

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==

===Background Reading===

==HAN Zhangang==

===Background Reading===

==HAO Bai-lin==

===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, 1989,
430pp. There is one copy at SFI's Library and in ITP-CAS Library.

Lecture 2: Visualization of real DNA data and a few nice math therefrom

[[Image:HaoXie_SFI.pdf]|Bailin Hao and Huimin Xie, Factorizable language: From Dyanmics
to Biology, SFI Working Paper #07-08016]

==Dan Hruschka==

* Models of Cultural Diversity
* Simple Models of Social Learning
* Neutral Models of Language Change

===Background Reading===

==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

2008-07-06T04:16:41Z

Haobailin: /* HAO Bai-lin */

File:ProkBranch jse08.pdf

2008-07-06T04:12:20Z

Haobailin: Bailin Hao and Lei Gao, Prokaryotic branch of the tree of life, J. Systematics and Evolution, 46(3) (2008): 258-262. The uniqueness problem of protein sequence decomposition and reconstruction arose in justifying the CVTree approach of prokaryote phyloege

Bailin Hao and Lei Gao, Prokaryotic branch of the tree of life, J. Systematics and Evolution, 46(3) (2008): 258-262.
The uniqueness problem of protein sequence decomposition and reconstruction arose in justifying the CVTree approach of prokaryote phyloegeny. The latter was described briefly in this paper.

File:HaoXie SFI.pdf

2008-07-06T03:59:34Z

Haobailin: Bailin Hao and Huimin Xie, Factorizable Language: From Dynamics to Biology, Chapter 5 in Reviews of Nonlinear Dynamics and Complexity, vol. 1, ed. by Heinz Georg Schuster, Wiley-VCH, 2008. Here is its draft as SFI Working Paper #07-08-016

Bailin Hao and Huimin Xie, Factorizable Language: From Dynamics to Biology, Chapter 5 in Reviews of Nonlinear Dynamics and Complexity, vol. 1, ed. by Heinz Georg Schuster, Wiley-VCH, 2008. Here is its draft as SFI Working Paper #07-08-016

File:Csss08b.ppt

2008-07-06T03:50:44Z

Haobailin: Powerpoint of Lecture 2 in 2nd week of CSSS2008. It contains more than what was used during the lecture.

Powerpoint of Lecture 2 in 2nd week of CSSS2008. It contains more than what was
used during the lecture.

File:Limin 2008 PNAS.pdf

2008-07-05T22:51:47Z

Haobailin: Min Li et al., Symbiotic gut microbes modulate human metabolic phenotypes, Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122

Min Li et al., Symbiotic gut microbes modulate human metabolic phenotypes, Prod. Natl. Acad. Sci. USA 105(6) (Feb 2008): 2117-2122

File:JIA 2008 NRDD.pdf

2008-07-05T22:48:15Z

Haobailin: Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery, 7 (Feb 2008): 123-129.

Wei Jia, Houkai Li, Liping Zhao, and Jeremy K. Nicholson, Got microbiota: a potential new territory for drug targeting, Nature Reviews Drug Discovery, 7 (Feb 2008): 123-129.

File:Pang 2007 ISME-J.pdf

2008-07-05T22:44:06Z

Haobailin: Pang et al., Inter-species transplatation of gut mocrobiota from human to pigs, The ISME J. 1 (2007): 156-162.

Pang et al., Inter-species transplatation of gut mocrobiota from human to pigs,
The ISME J. 1 (2007): 156-162.

CSSS 2008 Beijing-Readings-Week-Two

2008-07-02T07:47:24Z

Haobailin: /* Background Reading */

HAO Bai-Lin

2008-07-02T07:35:13Z

Haobailin:

Hao Bailin's Webpage:
http://www.itp.ac.cn/~hao/

T-Life Research Center's Webpage:
http://tlife.fudan.edu.cn/

CSSS 2008 Beijing-Readings-Week-One

2008-06-30T08:57:32Z

Haobailin: /* Lecture Notes */

{{CSSS 2008 Beijing}}



==Dave Feldman==

===Lecture Notes===



===Additional Reading===

====General Complex Systems====
* 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.


* 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].

====Entropy Rate, Excess Entropy====

*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.


====Computational Mechanics====

* C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences", ''Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference'' (UAI 2004), pp. 504--511. Best description of the CSSR algorithm. [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]

==Hao Bailin==
===Lecture Notes===

[[Media:ChineseCharacters.ppt| A Brief Introduction to Written Chinese]]

==Will Tracy==
===Lecture Notes===

===Additional Reading===

==Jon Wilkins==

===Lecture Notes===



Lecture 1: Monday, June 30
* [[Media:Wilkins_CSSS_2008_1.ppt|Adaptationism and the Adaptive Landscape]]



===Additional Reading===

'''Coalescent Theory:'''

Here are two different introductions to coalescent theory. One is a review article written by Magnus Nordborg:

* [[Media:Coalescent_Intro_-_Nordborg.pdf|Nordborg Review]]

The other is a chapter from John Wakeley's book called ''Coalescent Theory''

* [[Media:Coalescent_Intro_-_Wakeley.pdf|Wakeley Review]]

If you are interesed in learning a lot more about the subject, I recommend the rest of the book as well

'''Genomic Imprinting:'''

Here are a couple of review articles that talk about the evolution of genomic imprinting

* [[Media:Wilkins_&_Haig_2003_NRG.pdf|Wilkins & Haig Imprinting Review]] Nature Reviews Genetics, 2003
* [[Media:Wilkins_2005_TIG.pdf|Wilkins Imprinting Review]] Trends in Genetics, 2005

Here are some modeling papers on imprinting. The first two are the models that I used as an example in Wednesday's lecture

* [[Media:Wilkins_&_Haig_2002_PRSB.pdf|Game-Theoretic model of imprinting evolution]] Wilkins & Haig, Proc. R. Soc. B, 2002
* [[Media:Spencer_1998_Genetics.pdf|Population-Genetic model of imprinting evolution]] Spencer, Clark & Feldman, Genetics, 1998

These are some papers that look at what happens when there are more than two "players" or "genetic factions" that are co-evolving

* [[Media:Burt_&_Trivers_1998_PRSB.pdf|Genetic conflicts in genomic imprinting]] Burt & Trivers, Proc. R. Soc. B, 1998
* [[Media:Wilkins_2006a_JTB.pdf|Somatic reactivation of imprinted gene expression]] Wilkins, J. Theor. Biol., 2006
* [[Media:Wilkins_2006b_JTB.pdf|Competitive signal discrimination in imprinting]] Wilkins, J. Theor. Biol., 2006

Also, here is a paper that talks about how the level of analysis in evolutionary problems affects how you perceive the role of natural selection in evolution
It is now out it the Blackwell Companion to the Philosophy of Biology. It is the article entry on "Adaptationism" I don't have the final PDF with me, though, so I have attached the final draft that we sent to the publishers. I suspect that it is similar, though.

* [[Media:Adaptationism.pdf|Adaptationism]] Godfrey Smith and Wilkins, Blackwell Companion to the Philosophy of Biology, 1997

'''Approximate Bayesian Computation'''

Here are a few papers that describe the basic ideas of Approximate Bayesian Computation. In these papers, the applications are specifically population genetic. One warning: the techniques used in these papers to deal with the issues of correlations among statistics, etc. are completely ad hoc. The procedure that I outlined on Friday is somewhat less ad hoc. Soon, I hope to post something that provides a written description of what I talked about. Conceivably, even some code to implement these steps.

==Henry Wright==

===Lecture Notes===

===Additional Reading===

====Foragers and the Emergence of Agriculture====
*[[Media:Foragers_Biblio.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 09 July 2007)
*[[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]]

====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 (PowerPoint)
*[[Media:Reynolds_Algorithms_2002.pdf|Cultural Algorithms: A Tutorial]] Robert G. Reynolds (PDF)
*[[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]]

====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

File:ChineseCharacters.ppt

2008-06-30T08:54:20Z

Haobailin: This lecture is based on an after-dinner speech given at the Workshoip on Graph Theory and Bioinformatics and was originally entitled "Graph Theory of Chinese Characters". I hope even native Chinese students may find something new and interesting in it.

This lecture is based on an after-dinner speech given at the Workshoip on
Graph Theory and Bioinformatics and was originally entitled "Graph Theory
of Chinese Characters". I hope even native Chinese students may find something
new and interesting in it.

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T07:28:35Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<ul>
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)
</ul>

===Additional 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).

*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)

* Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. 2005. [http://http://dx.doi.org/10.1371/journal.pcbi.0010032 Evolution of Genetic Potential]. PLoS Computational Biology 1(3): e32.

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
[[Media:Burkhead1.pdf|Introduction to Discrete Dynamical Systems]]

===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
1. [[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity]], updated after the lecture on 16 July

2. [[Media:Hao4CS07b.ppt|Factorizable language: examples from biology]], for lecture on 18 July 2007

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

3. Junjie Shen, Shuyu Zhang, Hoong-Chien Lee, Bailin Hao, [[Media:SeeDNA_GPB.pdf|SeeDNA: a visualization tool for K-string content of lone DNA sequences and their randomized counterparts]]. SeeDNA runs on LINUX system with GTK support. Since .tar.gz file type is not supported on SFI wiki, please download the source code from Hao's webpage: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz

4. Bailin Hao, [[Media:physa282.pdf|Fractals from genomes: Exact solutions of a biology-inspired problem]] Goulden-Jackson cluster method and facorizable language method in action.

5. Xiaoli Shi, Huimin Xie, Shuyu Zhang, Bailin Hao, [[Media:jkps07.pdf|Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

==Dan Hruschka==

===Lecture Notes===
*[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
*[[Media:Hruschka_Lecture2.pdf |Simple Models of Social Learning]]

===Additional Reading===
*[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]
*[[Media:SoltisBoydRichersonCA95.pdf |Can Group-functional Behaviors Evolve by Cultural Group Selection?]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
* [[Media:Bonnie_NWB_Beijing.pdf|Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization]]

===Additional Reading===
* Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). [http://ella.slis.indiana.edu/~katy/paper/06-cishell.pdf Designing Highly Flexible and Usable Cyberinfrastructures for Convergence] In William S. Bainbridge and Mihail C. Roco (Eds.) Progress in Convergence – Technologies for Human Wellbeing. Annals of the New York Academy of Sciences, Boston, MA, Volume 1093, pp. 161-179.
* Börner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007). [http://nwb.slis.indiana.edu/papers/borner-2006-netsci.pdf Network Science: A Theoretical and Practical Framework] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology, Volume 41, Medford, NJ: Information Today, Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
* Börner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006). [http://nwb.slis.indiana.edu/papers/borner-2006-mapdifinfo.pdf Mapping the Diffusion of Scholarly Knowledge Among Major U.S. Research Institutions] Scientometrics. 68(3), pp. 415-426.
* Börner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). [http://ella.slis.indiana.edu/~katy/paper/arist02.pdf Visualizing Knowledge Domains] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology,Volume 37, Medford, NJ: Information Today. Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
* Ketan Mane and Katy Börner. (2004) [http://ella.slis.indiana.edu/~katy/paper/04-pnas-mane.pdf Mapping Topics and Topic Bursts in PNAS] PNAS, 101(Suppl. 1):5287-5290. Also available as cond-mat/0402380.
* Kevin W. Boyack, Richard Klavans , W. Bradford Paley , Katy Börner [http://ivl.slis.indiana.edu/km/pub/2007-boyack-siggraph.pdf Mapping, Illuminating, and Interacting with Science] one of the 96 accepted (out of 500 submitted) Siggraph 07 sketches.
* Holloway, Todd, Bozicevic, Miran, and Börner, Katy. (2007) [http://nwb.slis.indiana.edu/papers/holloway-0000-analvizwikipedia.pdf Analyzing and Visualizing the Semantic Coverage of Wikipedia and Its Authors] Complexity, Special issue on Understanding Complex Systems. 12(3), pp. 30-40. Also available as cs.IR/0512085.

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T07:08:04Z

Haobailin: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<ul>
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)
</ul>

===Additional 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).

*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)

* Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. 2005. [http://http://dx.doi.org/10.1371/journal.pcbi.0010032 Evolution of Genetic Potential]. PLoS Computational Biology 1(3): e32.

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
[[Media:Burkhead1.pdf|Introduction to Discrete Dynamical Systems]]

===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
1. [[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity]], updated after the lecture on 16 July

2. [[Media:Hao4CS07b.ppt|Factorizable language: examples from biology]], for lecture on 18 July 2007

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

3. Junjie Shen, Shuyu Zhang, Hoong-Chien Lee, Bailin Hao, [[Media:SeeDNA_GPB.pdf|SeeDNA: a visualization tool for K-string content of lone DNA sequences and their randomized counterparts]]. SeeDNA runs on LINUX system with GTK support. Since .tar.gz file type is not supported on SFI wiki, please download the source code from Hao's webpage: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz

4. Bailin Hao, [[Media:physa282.pdf|Exact solutions of a biology-inspired problem]] Goulden-Jackson cluster method and facorizable language method in action.

5. Xiaoli Shi, Huimin Xie, Shuyu Zhang, Bailin Hao, [[Media:jkps07.pdf|Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

==Dan Hruschka==

===Lecture Notes===
*[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
*[[Media:Hruschka_Lecture2.pdf |Simple Models of Social Learning]]

===Additional Reading===
*[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]
*[[Media:SoltisBoydRichersonCA95.pdf |Can Group-functional Behaviors Evolve by Cultural Group Selection?]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
* [[Media:Bonnie_NWB_Beijing.pdf|Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization]]

===Additional Reading===
* Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). [http://ella.slis.indiana.edu/~katy/paper/06-cishell.pdf Designing Highly Flexible and Usable Cyberinfrastructures for Convergence] In William S. Bainbridge and Mihail C. Roco (Eds.) Progress in Convergence – Technologies for Human Wellbeing. Annals of the New York Academy of Sciences, Boston, MA, Volume 1093, pp. 161-179.
* Börner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007). [http://nwb.slis.indiana.edu/papers/borner-2006-netsci.pdf Network Science: A Theoretical and Practical Framework] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology, Volume 41, Medford, NJ: Information Today, Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
* Börner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006). [http://nwb.slis.indiana.edu/papers/borner-2006-mapdifinfo.pdf Mapping the Diffusion of Scholarly Knowledge Among Major U.S. Research Institutions] Scientometrics. 68(3), pp. 415-426.
* Börner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). [http://ella.slis.indiana.edu/~katy/paper/arist02.pdf Visualizing Knowledge Domains] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology,Volume 37, Medford, NJ: Information Today. Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
* Ketan Mane and Katy Börner. (2004) [http://ella.slis.indiana.edu/~katy/paper/04-pnas-mane.pdf Mapping Topics and Topic Bursts in PNAS] PNAS, 101(Suppl. 1):5287-5290. Also available as cond-mat/0402380.
* Kevin W. Boyack, Richard Klavans , W. Bradford Paley , Katy Börner [http://ivl.slis.indiana.edu/km/pub/2007-boyack-siggraph.pdf Mapping, Illuminating, and Interacting with Science] one of the 96 accepted (out of 500 submitted) Siggraph 07 sketches.
* Holloway, Todd, Bozicevic, Miran, and Börner, Katy. (2007) [http://nwb.slis.indiana.edu/papers/holloway-0000-analvizwikipedia.pdf Analyzing and Visualizing the Semantic Coverage of Wikipedia and Its Authors] Complexity, Special issue on Understanding Complex Systems. 12(3), pp. 30-40. Also available as cs.IR/0512085.

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T07:01:50Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<ul>
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)
</ul>

===Additional 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).

*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)

* Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. 2005. [http://http://dx.doi.org/10.1371/journal.pcbi.0010032 Evolution of Genetic Potential]. PLoS Computational Biology 1(3): e32.

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
[[Media:Burkhead1.pdf|Introduction to Discrete Dynamical Systems]]

===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

3. Junjie Shen, Shuyu Zhang, Hoong-Chien Lee, Bailin Hao, [[Media:SeeDNA_GPB.pdf|SeeDNA: a visualization tool for K-string content of lone DNA sequences and their randomized counterparts]]. SeeDNA runs on LINUX system with GTK support. Since .tar.gz file type is not supported on SFI wiki, please download the source code from Hao's webpage: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz

4. Bailin Hao, [[Media:physa282.pdf|Exact solutions of a biology-inspired problem]] Goulden-Jackson cluster method and facorizable language method in action.

5. Xiaoli Shi, Huimin Xie, Shuyu Zhang, Bailin Hao, [[Media:jkps07.pdf|Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language]]

==Dan Hruschka==

===Lecture Notes===
*[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
*[[Media:Hruschka_Lecture2.pdf |Simple Models of Social Learning]]

===Additional Reading===
*[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]
*[[Media:SoltisBoydRichersonCA95.pdf |Can Group-functional Behaviors Evolve by Cultural Group Selection?]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
* [[Media:Bonnie_NWB_Beijing.pdf|Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization]]

===Additional Reading===
* Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). [http://ella.slis.indiana.edu/~katy/paper/06-cishell.pdf Designing Highly Flexible and Usable Cyberinfrastructures for Convergence] In William S. Bainbridge and Mihail C. Roco (Eds.) Progress in Convergence – Technologies for Human Wellbeing. Annals of the New York Academy of Sciences, Boston, MA, Volume 1093, pp. 161-179.
* Börner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007). [http://nwb.slis.indiana.edu/papers/borner-2006-netsci.pdf Network Science: A Theoretical and Practical Framework] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology, Volume 41, Medford, NJ: Information Today, Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
* Börner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006). [http://nwb.slis.indiana.edu/papers/borner-2006-mapdifinfo.pdf Mapping the Diffusion of Scholarly Knowledge Among Major U.S. Research Institutions] Scientometrics. 68(3), pp. 415-426.
* Börner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). [http://ella.slis.indiana.edu/~katy/paper/arist02.pdf Visualizing Knowledge Domains] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology,Volume 37, Medford, NJ: Information Today. Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
* Ketan Mane and Katy Börner. (2004) [http://ella.slis.indiana.edu/~katy/paper/04-pnas-mane.pdf Mapping Topics and Topic Bursts in PNAS] PNAS, 101(Suppl. 1):5287-5290. Also available as cond-mat/0402380.
* Kevin W. Boyack, Richard Klavans , W. Bradford Paley , Katy Börner [http://ivl.slis.indiana.edu/km/pub/2007-boyack-siggraph.pdf Mapping, Illuminating, and Interacting with Science] one of the 96 accepted (out of 500 submitted) Siggraph 07 sketches.
* Holloway, Todd, Bozicevic, Miran, and Börner, Katy. (2007) [http://nwb.slis.indiana.edu/papers/holloway-0000-analvizwikipedia.pdf Analyzing and Visualizing the Semantic Coverage of Wikipedia and Its Authors] Complexity, Special issue on Understanding Complex Systems. 12(3), pp. 30-40. Also available as cs.IR/0512085.

File:Physa282.pdf

2007-07-17T06:56:19Z

Haobailin: Goulden-Jackson cluster method and factorizable language method applied to get the exact counting of redundant avoided strings. Detailed arithmetic carried out.

Goulden-Jackson cluster method and factorizable language method applied to get the exact counting of redundant avoided strings. Detailed arithmetic carried out.

File:Jkps07.pdf

2007-07-17T06:53:02Z

Haobailin: A paper on the protein decomposition and reconstruction problem

A paper on the protein decomposition and reconstruction problem

File:Hao4CS07b.ppt

2007-07-17T06:51:49Z

Haobailin: PPT for lecture 2 on 18 July 2007

PPT for lecture 2 on 18 July 2007

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T06:08:35Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<ul>
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)
</ul>

===Additional 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).

*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)

* Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. 2005. [http://http://dx.doi.org/10.1371/journal.pcbi.0010032 Evolution of Genetic Potential]. PLoS Computational Biology 1(3): e32.

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
[[Media:Burkhead1.pdf|Introduction to Discrete Dynamical Systems]]

===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

3. Junjie Shen, Shuyu Zhang, Hoong-Chien Lee, Bailin Hao, [[Media:SeeDNA_GPB.pdf|SeeDNA: a visualization tool for K-string content of lone DNA sequences and their randomized counterparts]]. SeeDNA runs on LINUX system with GTK support. Since .tar.gz file type is not supported on SFI wiki, please download the source code from Hao's webpage: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz

==Dan Hruschka==

===Lecture Notes===
*[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
*[[Media:Hruschka_Lecture2.pdf |Simple Models of Social Learning]]

===Additional Reading===
*[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]
*[[Media:SoltisBoydRichersonCA95.pdf |Can Group-functional Behaviors Evolve by Cultural Group Selection?]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
* [[Media:Bonnie_NWB_Beijing.pdf|Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization]]

===Additional Reading===
* Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). [http://ella.slis.indiana.edu/~katy/paper/06-cishell.pdf Designing Highly Flexible and Usable Cyberinfrastructures for Convergence] In William S. Bainbridge and Mihail C. Roco (Eds.) Progress in Convergence – Technologies for Human Wellbeing. Annals of the New York Academy of Sciences, Boston, MA, Volume 1093, pp. 161-179.
* Börner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007). [http://nwb.slis.indiana.edu/papers/borner-2006-netsci.pdf Network Science: A Theoretical and Practical Framework] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology, Volume 41, Medford, NJ: Information Today, Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
* Börner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006). [http://nwb.slis.indiana.edu/papers/borner-2006-mapdifinfo.pdf Mapping the Diffusion of Scholarly Knowledge Among Major U.S. Research Institutions] Scientometrics. 68(3), pp. 415-426.
* Börner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). [http://ella.slis.indiana.edu/~katy/paper/arist02.pdf Visualizing Knowledge Domains] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology,Volume 37, Medford, NJ: Information Today. Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
* Ketan Mane and Katy Börner. (2004) [http://ella.slis.indiana.edu/~katy/paper/04-pnas-mane.pdf Mapping Topics and Topic Bursts in PNAS] PNAS, 101(Suppl. 1):5287-5290. Also available as cond-mat/0402380.
* Kevin W. Boyack, Richard Klavans , W. Bradford Paley , Katy Börner [http://ivl.slis.indiana.edu/km/pub/2007-boyack-siggraph.pdf Mapping, Illuminating, and Interacting with Science] one of the 96 accepted (out of 500 submitted) Siggraph 07 sketches.
* Holloway, Todd, Bozicevic, Miran, and Börner, Katy. (2007) [http://nwb.slis.indiana.edu/papers/holloway-0000-analvizwikipedia.pdf Analyzing and Visualizing the Semantic Coverage of Wikipedia and Its Authors] Complexity, Special issue on Understanding Complex Systems. 12(3), pp. 30-40. Also available as cs.IR/0512085.

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T06:06:56Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<ul>
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)
</ul>

===Additional 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).

*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)

* Lauren Ancel Meyers, Fredric D. Ancel, Michael Lachmann. 2005. [http://http://dx.doi.org/10.1371/journal.pcbi.0010032 Evolution of Genetic Potential]. PLoS Computational Biology 1(3): e32.

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
[[Media:Burkhead1.pdf|Introduction to Discrete Dynamical Systems]]

===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

3. Junjie Shen, Shuyu Zhang, Hoong-Chien Lee, Bailin Hao, [[Media:SeeDNA_GPB.pdf|SeeDNA: a visualization tool for K-string content of lone DNA sequences and their randomized counterparts]]. Since .tar.gz file type is not supported on SFI wiki, please download the source code from Hao's webpage: http://www.itp.ac.cn/~hao/SeeDNA.tar.gz

==Dan Hruschka==

===Lecture Notes===
*[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
*[[Media:Hruschka_Lecture2.pdf |Simple Models of Social Learning]]

===Additional Reading===
*[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]
*[[Media:SoltisBoydRichersonCA95.pdf |Can Group-functional Behaviors Evolve by Cultural Group Selection?]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
* [[Media:Bonnie_NWB_Beijing.pdf|Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization]]

===Additional Reading===
* Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). [http://ella.slis.indiana.edu/~katy/paper/06-cishell.pdf Designing Highly Flexible and Usable Cyberinfrastructures for Convergence] In William S. Bainbridge and Mihail C. Roco (Eds.) Progress in Convergence – Technologies for Human Wellbeing. Annals of the New York Academy of Sciences, Boston, MA, Volume 1093, pp. 161-179.
* Börner, Katy, Sanyal, Soma and Vespignani, Alessandro. (2007). [http://nwb.slis.indiana.edu/papers/borner-2006-netsci.pdf Network Science: A Theoretical and Practical Framework] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology, Volume 41, Medford, NJ: Information Today, Inc./American Society for Information Science and Technology, chapter 12, pp. 537-607.
* Börner, Katy, Penumarthy, Shashikant, Meiss, Mark and Ke, Weimao. (2006). [http://nwb.slis.indiana.edu/papers/borner-2006-mapdifinfo.pdf Mapping the Diffusion of Scholarly Knowledge Among Major U.S. Research Institutions] Scientometrics. 68(3), pp. 415-426.
* Börner, Katy, Chen, Chaomei, and Boyack, Kevin. (2003). [http://ella.slis.indiana.edu/~katy/paper/arist02.pdf Visualizing Knowledge Domains] In Blaise Cronin (Ed.), Annual Review of Information Science & Technology,Volume 37, Medford, NJ: Information Today. Inc./American Society for Information Science and Technology, chapter 5, pp. 179-255
* Ketan Mane and Katy Börner. (2004) [http://ella.slis.indiana.edu/~katy/paper/04-pnas-mane.pdf Mapping Topics and Topic Bursts in PNAS] PNAS, 101(Suppl. 1):5287-5290. Also available as cond-mat/0402380.
* Kevin W. Boyack, Richard Klavans , W. Bradford Paley , Katy Börner [http://ivl.slis.indiana.edu/km/pub/2007-boyack-siggraph.pdf Mapping, Illuminating, and Interacting with Science] one of the 96 accepted (out of 500 submitted) Siggraph 07 sketches.
* Holloway, Todd, Bozicevic, Miran, and Börner, Katy. (2007) [http://nwb.slis.indiana.edu/papers/holloway-0000-analvizwikipedia.pdf Analyzing and Visualizing the Semantic Coverage of Wikipedia and Its Authors] Complexity, Special issue on Understanding Complex Systems. 12(3), pp. 30-40. Also available as cs.IR/0512085.

File:SeeDNA GPB.pdf

2007-07-17T05:58:30Z

Haobailin: Description of the SeeDNA program

Description of the SeeDNA program

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T09:08:07Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] A SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

==Dan Hruschka==

===Lecture Notes===
[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
===Additional Reading===
[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T09:06:17Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. Bailin Hao, [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] SFI Working Paper

2. Bailin Hao and Huimin Xie, [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

==Dan Hruschka==

===Lecture Notes===
[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
===Additional Reading===
[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T09:04:44Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
1. [[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] SFI Working Paper

2. [[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

==Dan Hruschka==

===Lecture Notes===
[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
===Additional Reading===
[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T09:02:48Z

Haobailin: /* Additional Reading */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
[[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] SFI Working Paper
[[Media:HaoXieChap.pdf|Factorizable Language: from Dynamics to Biology]] A chapter written for Annual Reviews in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, page numbers tentative.

==Dan Hruschka==

===Lecture Notes===
[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
===Additional Reading===
[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T08:57:12Z

Haobailin: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
[[Media:Hao4CS07a.ppt|Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July]]

===Additional Reading===
[[Media:crossSFI.pdf|Complexity, Coarse-Graining and Symbolic Description]] SFI Working Paper

==Dan Hruschka==

===Lecture Notes===
[[Media:Hruschka_Lecture1.pdf|Models of Cultural Diversity]]
===Additional Reading===
[[Media:Henrich_20McElreathCultural_20Evo.pdf|The Evolution of Cultural Evolution]]

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

File:Hao4CS07a.ppt

2007-07-16T08:55:06Z

Haobailin: An updated version of the first lecture PPT

An updated version of the first lecture PPT

File:HaoXieChap.pdf

2007-07-16T08:52:52Z

Haobailin: A chapter written for Annual Review in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, 2007

A chapter written for Annual Review in Nonlinear Science and Complexity, ed. by Heinz G. Schuster, to be published by Wiley-VCH, 2007

File:Hao4CSSS07a.ppt

2007-07-15T02:19:57Z

Haobailin: PPT for Lecture 1 on 16th July 2007 Monday

PPT for Lecture 1 on 16th July 2007 Monday

CSSS 2007 Beijing-Readings-Week-Two

2007-07-13T21:04:10Z

Haobailin: This is a science-popular style narration on coarse-graining, symbolic description and complexity with a number of further references.

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are from the 2006 CSSS Beijing, and will have some revisions for this year:
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_1.2up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.15MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_2.2up.pdf Lecture 2: Analysis of Evolutionary Dynamics] (1 MB)
<LI>
[http://www.santafe.edu/~altenber/CSSS_BEIJING/2006/Altenberg_Lecture_3.2up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (2.51MB)

===Additional 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).

*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)

* Evolutionary Art at [http://electricsheep.org/ Electric Sheep]

==Emily Burkhead==

===Lecture Notes===
===Additional Reading===

==Hao Bai-lin==

===Lecture Notes===
1. Bailin Hao, Coarse-graining, symbolic description, and complexity [[image:crossSFI.pdf]]

==Dan Hruschka==

===Lecture Notes===
===Additional Reading===

==Van Savage==

===Lecture Notes===
===Additional Reading===

==Weixia(Bonnie) Huang==

===Lecture Notes===
===Additional Reading===

File:CrossSFI.pdf

2007-07-13T20:57:58Z

Haobailin: This is a very brief and general account with the same title as the first lecture at CSSS2007, i.e., Coarse-Graining, Symbolic Descritption, and Complexity

This is a very brief and general account with the same title as the first lecture at CSSS2007, i.e., Coarse-Graining, Symbolic Descritption, and Complexity