Santa Fe Institute Events Wiki - User contributions [en]

File:DSlecture1.pdf

2007-07-25T02:14:53Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Three

2007-07-25T01:59:46Z

Stacey: /* Raissa D'Souza */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Jia Qing-Shan (Samuel)==

===Lecture Notes===

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

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

==Han Jing==

===Lecture Notes===
*[[Media:lecture1.pdf|The Collective Behavior of Multi-Agent Systems]]

===Additional Reading===

==Jim Glazier==

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

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

===Additional Reading===

File:Lecture1.pdf

2007-07-23T01:21:39Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Three

2007-07-23T01:21:09Z

Stacey: /* Han Jing */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Han Jing==

===Lecture Notes===
*[[Media:lecture1.pdf|The Collective Behavior of Multi-Agent Systems]]

===Additional Reading===

==Jim Glazier==

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

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

CSSS 2007 Beijing-Readings-Week-Three

2007-07-23T01:19:33Z

Stacey: /* Jim Glazier */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Han Jing==

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

==Jim Glazier==

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

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

CSSS 2007 Beijing-Readings-Week-Three

2007-07-22T15:40:19Z

Stacey: /* Jim Glazier */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Han Jing==

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

==Jim Glazier==

===Lecture Notes===
*[[Media:Compucell3d_quickstartguide_0.5.pdf|CompuCell 3D Quickstart Guide]]
*[[Media:CompuCellManual.doc| 1]]
*[[Media:CompuCellPlayerManual.doc| 1]]
*[[Media:Installing_CompuCell_linux.doc | 1]]
*[[Media:Running_CompuCell3D.doc| 1]]
*[[Media:SummerSchoolExercises.doc| 1]]

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

CSSS 2007 Beijing-Readings-Week-Three

2007-07-22T15:38:59Z

Stacey: /* Jim Glazier */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Han Jing==

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

==Jim Glazier==

===Lecture Notes===
*[[Media:Compucell3d_quickstartguide_0.5.pdf| 1]]
*[[Media:CompuCellManual.doc| 1]]
*[[Media:CompuCellPlayerManual.doc| 1]]
*[[Media:Installing_CompuCell_linux.doc | 1]]
*[[Media:Running_CompuCell3D.doc| 1]]
*[[Media:SummerSchoolExercises.doc| 1]]

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

File:SummerSchoolExercises.doc

2007-07-22T15:38:27Z

Stacey:

File:Running CompuCell3D.doc

2007-07-22T15:36:49Z

Stacey:

File:Installing CompuCell linux.doc

2007-07-22T15:35:54Z

Stacey:

File:CompuCellPlayerManual.doc

2007-07-22T15:34:46Z

Stacey:

File:CompuCellManual.doc

2007-07-22T15:33:28Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Three

2007-07-22T15:32:28Z

Stacey: /* Lecture Notes */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Han Jing==

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

==Jim Glazier==

===Lecture Notes===
*[[Media:Compucell3d_quickstartguide_0.5.pdf| ]]

===Additional Reading===

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

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

</ul>

==Raissa D'Souza==

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

File:Compucell3d quickstartguide 0.5.pdf

2007-07-22T15:31:28Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-20T01:39:17Z

Stacey: /* Emily Burkhead */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are new 2007 revisions of the 2006 CSSS Beijing lectures:
<ul>
<LI>
New! [http://www.santafe.edu/~altenber/CSSS_BEIJING/2007/Lecture_1.4up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.2MB)
<LI>
New! [http://www.santafe.edu/~altenber/CSSS_BEIJING/2007/Analysis_2007_new.2up.pdf Lecture 2: Mathematical Analysis of Evolutionary Algorithms] (1 MB)
<LI>
New! [http://www.santafe.edu/~altenber/CSSS_BEIJING/2007/Lecture_3.4up.pdf Lecture 3: Higher Order Evolutionary Phenomena] (9MB)
</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]]
*[[Media:Burkhead_slides_2_4per.pdf| Symbolic Dynamics]]
*[[Media:Burkhead_slides_3_4per.pdf |A Symbolics Dynamics View of Cellular Automata]]

===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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==Van Savage==

===Lecture Notes===
*[[Media:Csss_lecture1.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]
*[[Media:Csss_lecture2.pdf| Biological Scaling Theory and Effects on Populations]]
*[[Media:Csss_lecture3.pdf| Scaling Tumor Growth and Sleep Times]]

===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:Burkhead slides 3 4per.pdf

2007-07-20T01:37:59Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-19T03:35:50Z

Stacey: /* Emily Burkhead */

{{CSSS 2007 Beijing}}

__FORCETOC__

==Lee Altenberg==

===Lecture Notes===
These are new 2007 revisions of the 2006 CSSS Beijing lectures:
<ul>
<LI>
New! [http://www.santafe.edu/~altenber/CSSS_BEIJING/2007/Lecture_1.4up.pdf Lecture 1: Introduction to Evolutionary Computation] (6.2MB)
<LI>
New! [http://www.santafe.edu/~altenber/CSSS_BEIJING/2007/Analysis_2007_new.2up.pdf Lecture 2: Mathematical Analysis of Evolutionary Algorithms] (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]]
*[[Media:Burkhead_slides_2_4per.pdf| Symbolic Dynamics]]

===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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==Van Savage==

===Lecture Notes===
*[[Media:Csss_lecture1.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]
*[[Media:Csss_lecture2.pdf| Biological Scaling Theory and Effects on Populations]]
*[[Media:Csss_lecture3.pdf| Scaling Tumor Growth and Sleep Times]]

===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:Burkhead slides 2 4per.pdf

2007-07-19T03:34:27Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T13:35:10Z

Stacey: /* Van Savage */

{{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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==Van Savage==

===Lecture Notes===
*[[Media:Csss_lecture1.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]
*[[Media:Csss_lecture2.pdf| Biological Scaling Theory and Effects on Populations]]
*[[Media:Csss_lecture3.pdf| Scaling Tumor Growth and Sleep Times]]

===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:Csss lecture3.pdf

2007-07-17T13:33:32Z

Stacey:

File:Csss lecture2.pdf

2007-07-17T13:30:56Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T13:26:23Z

Stacey: /* Van Savage */

{{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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==Van Savage==

===Lecture Notes===
*[[Media:Csss_lecture1.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]
*[[Media:Csss_lecture2.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]
*[[Media:Csss_lecture3.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]

===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

2007-07-17T13:25:59Z

Stacey: /* Van Savage */

{{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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==Van Savage==

===Lecture Notes===
*[[Media:Csss_lecture1.pdf| Scaling and Power Laws with a Case Study in Biological Allometry]]

===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:Csss lecture1.pdf

2007-07-17T13:24:52Z

Stacey:

File:Bonnie NWB Beijing.pdf

2007-07-17T13:17:16Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-17T13:14:19Z

Stacey: /* Dan Hruschka */

{{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?]]
*[[Media:Hruschka_Lecture3.pdf| Cultural Evolution at the Group Level]]

==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:Hruschka Lecture3.pdf

2007-07-17T13:12:56Z

Stacey:

CSSS 2007 Beijing-Projects

2007-07-17T12:06:59Z

Stacey:

{{CSSS 2007 Beijing}}

# [[Policy Analysis for Agricultural Deforestation in the Peruvian Amazon Rainforest using an Agent – Based Model]] Federico Bert, Jaqueline Garcia – Yi, Andrea Kiraly, Thom Scott – Phillips, Wang Lan Jun and Zhao Yan Jia
#[[The Evolution From Chaos to Order in the Real Estate Market]] Yan Yan, Richard Boland, Katherine Dykes, Austin Dingwall, Zhang Jiayin and Richard Callahan
#[[Influence of Environmental Fluctuation on Strategy Evolution]]. Henry (ZhaiJixian), Emma (MuYifen),Sean (LiXin), Rachel (RuanXiao), Ronda (XiaXi), Trygve Bakken, KiKi Benzon
#[[Social Network Survey]]. Richard Callahan, Peace Ogbogbo, Pei Li-Quan, Maria Teresa Pulido, Ren Yi-Ke, Shi Yong-Ren, Wang Chen-Wei, Yuan Jing, Zhang Han-Tian, Zhang Jia-Lin
#[[Global Efficiency and Organization of Food Webs]]. Zheng Hong Ying, Tang Ao Nan, Liu Zhi Yuan, Liu Wei, Habib Talavatifard, Will Driscoll, Jordan Okie, Wang Qiao
#[[Financial nonlinear and financial time series]] Wang Chen-wei, Liu Qi, Wang Lin, Wang Qiao, Gong Guan-nan, Spencer Matthews, Rossitsa Yalamova, Chen Yu-dong
#[[Information flow in biological systems]] Sybille Haeussler, Hou Hui, Susanna Messinger
#[[investigating novel phenomena that produce changes in biological pathways between species]] Ziya Kalay, Andrew Paek, Nicole Scott, Zhang Yu-Ping

CSSS 2007 Beijing-Projects

2007-07-17T12:06:09Z

Stacey:

{{CSSS 2007 Beijing}}

# [[Policy Analysis for Agricultural Deforestation in the Peruvian Amazon Rainforest using an Agent – Based Model]] Federico Bert, Jaqueline Garcia – Yi, Andrea Kiraly, Thom Scott – Phillips, Wang Lan Jun and Zao Yan Jia
#[[The Evolution From Chaos to Order in the Real Estate Market]] Yan Yan, Richard Boland, Katherine Dykes, Austin Dingwall, Zhang Jiayin and Richard Callahan
#[[Influence of Environmental Fluctuation on Strategy Evolution]]. Henry (ZhaiJixian), Emma (MuYifen),Sean (LiXin), Rachel (RuanXiao), Ronda (XiaXi), Trygve Bakken, KiKi Benzon
#[[Social Network Survey]]. Richard Callahan, Peace Ogbogbo, Pei Li-Quan, Maria Teresa Pulido, Ren Yi-Ke, Shi Yong-Ren, Wang Chen-Wei, Yuan Jing, Zhang Han-Tian, Zhang Jia-Lin
#[[Global Efficiency and Organization of Food Webs]]. Zheng Hong Ying, Tang Ao Nan, Liu Zhi Yuan, Liu Wei, Habib Talavatifard, Will Driscoll, Jordan Okie, Wang Qiao
#[[Financial nonlinear and financial time series]] Wang Chen-wei, Liu Qi, Wang Lin, Wang Qiao, Gong Guan-nan, Spencer Matthews, Rossitsa Yalamova, Chen Yu-dong
#[[Information flow in biological systems]] Sybille Haeussler, Hou Hui, Susanna Messinger
#[[investigating novel phenomena that produce changes in biological pathways between species]] Ziya Kalay, Andrew Paek, Nicole Scott, Zhang Yu-Ping

CSSS 2007 Beijing-Projects

2007-07-17T12:02:50Z

Stacey:

{{CSSS 2007 Beijing}}

# [[Policy Analysis for Agricultural Deforestation in the Peruvian Amazon Rainforest using an Agent – Based Model]] Federico Bert, Jaqueline Garcia – Yi, Andrea Kiraly, Thom Scott – Phillips, Wang Lan Jun and Zao Yan Jia
#[[The Evolution From Chaos to Order in the Real Estate Market]] Yan Yan, Richard Boland, Katherine Dykes, Austin Dingwall, Zhang Jiayin and Richard Callahan
#[[Influence of Environmental Fluctuation on Strategy Evolution]]. Henry (ZhaiJixian), Emma (MuYifen),Sean (LiXin), Rachel (RuanXiao), Ronda (XiaXi), Trygve Bakken, KiKi Benzon
#[[Social Network Survey]]. Richard Callahan, Peace Ogbogbo, Pei Li-Quan, Maria Teresa Pulido, Ren Yi-Ke, Shi Yong-Ren, Wang Chen-Wei, Yuan Jing, Zhang Han-Tian, Zhang Jia-Lin
#[[Global Efficiency and Organization of Food Webs]]. Zheng Hong Ying, Tang Ao Nan, Liu Zhi Yuan, Liu Wei, Habib Talavatifard, Will Driscoll, Jordan Okie, Wang Qiao
#[[Financial nonlinear and financial time series]] Wang Chen-wei, Liu Qi, Wang Lin, Wang Qiao, Gong Guan-nan, Spencer Matthews, Rossitsa Yalamova, Chen Yu-dong

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T13:55:17Z

Stacey: /* 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===
[[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.

==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===
===Additional Reading===

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T13:54:34Z

Stacey: /* 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===
[[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.

==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===
===Additional Reading===

File:Hruschka Lecture2.pdf

2007-07-16T13:53:31Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T13:11:41Z

Stacey: /* Dan Hruschka */

{{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===
[[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.

==Dan Hruschka==

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

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T13:11:11Z

Stacey: /* Dan Hruschka */

{{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===
[[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.

==Dan Hruschka==

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

File:SoltisBoydRichersonCA95.pdf

2007-07-16T13:08:58Z

Stacey:

File:Burkhead1.pdf

2007-07-16T12:42:44Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T12:38:04Z

Stacey: /* Emily Burkhead */

{{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===
[[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.

==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-Projects

2007-07-16T06:28:49Z

Stacey:

{{CSSS 2007 Beijing}}

[[Policy Analysis for Agricultural Deforestation in the Peruvian Amazon Rainforest using an Agent – Based Model]] <br/>Federico Bert, Jaqueline Garcia – Yi, Andrea Kiraly, Thom Scott – Phillips, Wang Lan Jun and Zao Yan Jia

CSSS 2007 Beijing-Projects

2007-07-16T06:28:12Z

Stacey:

{{CSSS 2007 Beijing}}

[[Policy Analysis for Agricultural Deforestation in the Peruvian Amazon Rainforest using an Agent – Based Model]] (Federico Bert, Jaqueline Garcia – Yi, Andrea Kiraly, Thom Scott – Phillips, Wang Lan Jun and Zao Yan Jia)

CSSS 2007 Beijing-Projects

2007-07-16T06:18:12Z

Stacey:

Template:CSSS 2007 Beijing

2007-07-16T06:17:41Z

Stacey:

{| align="right" border="0" style="margin: 0px 0px 0px 10px; background: #f9f9f9; border: solid #aaa 1px;"
|'''CSSS 2007 Beijing'''
*[[CSSS 2007 Beijing|Home]]
*[[CSSS 2007 Beijing-Faculty|Faculty]]
*[[CSSS 2007 Beijing-Participants|Participants]]
*[[CSSS 2007 Beijing-Schedule|Schedule]]
*Readings and Lecture Notes
** [[CSSS 2007 Beijing-Readings-Week-One|Week One]]
** [[CSSS 2007 Beijing-Readings-Week-Two|Week Two]]
** [[CSSS 2007 Beijing-Readings-Week-Three|Week Three]]
** [[CSSS 2007 Beijing-Readings-Week-Four|Week Four]]
*[[CSSS 2007 Beijing-Projects|Projects]]
*[[CSSS 2007 Beijing-Visa|Chinese Visa Information]]
*[[CSSS 2007 Beijing-Details|Travel Details and Logistics]]
*[http://www.santafe.edu/forums/forumdisplay.php?f=31 Forum]
|}

Template:CSSS 2007 Beijing

2007-07-16T06:17:14Z

Stacey:

{| align="right" border="0" style="margin: 0px 0px 0px 10px; background: #f9f9f9; border: solid #aaa 1px;"
|'''CSSS 2007 Beijing'''
*[[CSSS 2007 Beijing|Home]]
*[[CSSS 2007 Beijing-Faculty|Faculty]]
*[[CSSS 2007 Beijing-Participants|Participants]]
*[[CSSS 2007 Beijing-Schedule|Schedule]]
*Readings and Lecture Notes
** [[CSSS 2007 Beijing-Readings-Week-One|Week One]]
** [[CSSS 2007 Beijing-Readings-Week-Two|Week Two]]
** [[CSSS 2007 Beijing-Readings-Week-Three|Week Three]]
** [[CSSS 2007 Beijing-Readings-Week-Four|Week Four]]
*[[CSSS 2007 Beijing-Content|Content]]
*[[CSSS 2007 Beijing-Projects|Projects]]
*[[CSSS 2007 Beijing-Visa|Chinese Visa Information]]
*[[CSSS 2007 Beijing-Details|Travel Details and Logistics]]
*[http://www.santafe.edu/forums/forumdisplay.php?f=31 Forum]
|}

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T03:45:03Z

Stacey: /* Dan Hruschka */

{{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:Hao4CSSS07a.ppt|Coarse-graining, symbolic description, and complexity]]

===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:Henrich 20McElreathCultural 20Evo.pdf

2007-07-16T03:40:38Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-16T02:50:41Z

Stacey: /* Dan Hruschka */

{{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:Hao4CSSS07a.ppt|Coarse-graining, symbolic description, and complexity]]

===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===

==Van Savage==

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

==Weixia(Bonnie) Huang==

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

File:Hruschka Lecture1.pdf

2007-07-16T02:49:15Z

Stacey:

CSSS 2007 Beijing-Readings-Week-Two

2007-07-15T03:38:17Z

Stacey: /* Hao Bai-lin */

{{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:Hao4CSSS07a.ppt|Coarse-graining, symbolic description, and complexity]]

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

==Dan Hruschka==

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

==Van Savage==

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

==Weixia(Bonnie) Huang==

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

CSSS 2007 Beijing-Readings-Week-Two

2007-07-15T03:37:51Z

Stacey: /* Hao Bai-lin */

{{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:Hao4CSSS07a.ppt|Coarse-graining, symbolic description, and complexity]]

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

==Dan Hruschka==

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

==Van Savage==

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

==Weixia(Bonnie) Huang==

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

CSSS 2007 Beijing-Readings-Week-Two

2007-07-15T03:36:23Z

Stacey: /* Hao Bai-lin */

{{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:Hao4CSSS07a.ppt|Coarse-graining, symbolic description, and complexity]]

===Additional Reading===
[[Media:crossSFI.pdf]]

==Dan Hruschka==

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

==Van Savage==

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

==Weixia(Bonnie) Huang==

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