CSSS 2007 Beijing-Readings-Week-Two

CSSS 2007 Beijing Home Faculty Participants Schedule Readings and Lecture Notes Week One Week Two Week Three Week Four Projects T-Shirt Chinese Visa Information Travel Details and Logistics Final Papers Forum

Lee Altenberg

Lecture Notes

These are new 2007 revisions of the 2006 CSSS Beijing lectures:

• New! Lecture 1: Introduction to Evolutionary Computation (6.2MB)
• New! Lecture 2: Mathematical Analysis of Evolutionary Algorithms (1 MB)
• New! Lecture 3: Higher Order Evolutionary Phenomena (9MB)

Additional Reading

• Altenberg, L. , 2004. 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. 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. Neutral Evolution of Mutational Robustness. Proceedings of the National Academy of Science U.S.A. 96:9716-9720 (1999).

• Altenberg, L. , 2004. 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. 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. Evolution of Genetic Potential. PLoS Computational Biology 1(3): e32.

• Evolutionary Art at Electric Sheep

Emily Burkhead

Lecture Notes

• Introduction to Discrete Dynamical Systems
• Symbolic Dynamics
• A Symbolics Dynamics View of Cellular Automata

Hao Bai-lin

Lecture Notes

1. Coarse-graining, symbolic description, and complexity, updated after the lecture on 16 July

2. Factorizable language: examples from biology, for lecture on 18 July 2007

Additional Reading

1. Bailin Hao, Complexity, Coarse-Graining and Symbolic Description A SFI Working Paper

2. Bailin Hao and Huimin Xie, 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, 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, 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, Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language

Dan Hruschka

Lecture Notes

• Models of Cultural Diversity
• Simple Models of Social Learning

Additional Reading

• The Evolution of Cultural Evolution
• Can Group-functional Behaviors Evolve by Cultural Group Selection?
• Cultural Evolution at the Group Level

Van Savage

Lecture Notes

• Scaling and Power Laws with a Case Study in Biological Allometry
• Biological Scaling Theory and Effects on Populations
• Scaling Tumor Growth and Sleep Times

Weixia(Bonnie) Huang

Lecture Notes

• Network Workbench - A Tool For Large Scale Network Analysis, Modeling and Visualization

Additional Reading

• Herr, Bruce W., Huang, Weixia, Penumarthy, Shashikant, & Börner, Katy. (2007). 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). 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). 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). 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) 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 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) 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.