CSSS 2008 Beijing-Readings-Week-Two

CSSS 2008 Beijing Home Faculty Participants Highlights Photos 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

Aaron Clauset

Topics and Lecture Notes

• July 7: Introduction to Networks I - Structure
• July 8: Introduction to Networks II - Models & Dynamics
• July 9: Power Laws and Empirical Data

Background Reading

The following references cover background material for the three lectures.

• "The Structure and function of complex networks." M. E. J. Newman, SIAM Review 45, 167-256 (2003)
• "Power-law distributions in empirical data." A. Clauset, C. R. Shalizi and M. E. J. Newman. arXiv:0706.1062 (2007).

DI Zengru

Introduction to Weighted Networks(Lecture notes)

Background Reading

• Ying Fan, Menghui Li, Peng Zhang, Jinshan Wub, Zengru Di. Accuracy and precision of methods for community identification in weighted networks. Physica A 377 (2007) 363­372.
• S. Boccaletti, , V. Latora, Y. Moreno, M. Chavef , D.-U. Hwang. Complex networks: Structure and dynamics. Physics Reports 424 (2006) 175 ­ 308.
• Menghui Li, Ying Fan, Dahui Wang, Daqing Li, Jinshan Wu, Zengru D. Small-world effect induced by weight randomization on regular networks. Physics Letters A 364 (2007) 488­493.
• Menghui Li, Dahui Wang, Ying Fan, Zengru Di, and Jinshan Wu1. Modelling weighted networks using connection count. New Journal of Physics 8 (2006) 72.

HAN Jing

Collective Behavior of Multi-agent systems.

Lecture 1: Graph Coloring Problems – Analysis and Design. Part I Part II Part III

Lecture 2: Synchronization and “Soft Control”.

Background Reading

Soft Control on Collective Behavior of a Group of Autonomous Agents by a Shill Agent. Jing Han, Ming Li, Lei Guo. Journal of Systems Science and Complexity, 2006(19):54-62

Local Evaluation Functions and Global Evaluation Functions for Computational Evolution. Jing Han. Complex Systems, 15, Issue 4 (c) 2005, pages 307 – 347.

HAN Zhangang

• Division of Labor in an Agent System with a Market Mechanism

HAO Bai-lin

• Lecture 1: Symbolic dynamics in action or Applied symbolic dynamics (First part of the

lecture) and Applied symbolic dynamics from 1D to 2D to ODE (Second part of the lecture)

• Lecture 2: Visualization of DNA data and a few nice math therefrom (A PPT that contains more than used in class)

Background Reading

Lecture 1：Symbolic Dynamics in Action or Applied Symbolic Dynamics

1. Bailin Hao, Elementary Symbolic Dyanmics and Chaos in Dissipative Systems,

  a monograph, World Scientific, 1989. Downloadable from Hao's webpage:
  http://www.itp.ac.cn/~hao/ESDCDS-hao.pdf
  Hao's apology: Since not all figures in this book were Postscript files and
  I have not made them into .eps yet, I have put an image of my personal copy
  in my website. It is a file of more than 20MB. That is why I did not put it
  in the SFI Wiki. I hope I will be able to do it in not-distant future. The
  symbolic dynamics chapters of this book are somehow outdated. For those who
  want to learn more about symbolic dynamics I suggest the following book.

2. Bailin Hao and Weimou Zheng, Applied Symbolic Dynamics and Chaos, WSPC, 1998,

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

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

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

2. Bailin Hao and Huimin Xie, Factorizable Language: From Dyanmics to Biology

3. Xiaoli Shi et al., Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language

4. Bailin Hao and Lei Gao, Prokaryotic branch of tree of life: a composition vector approach

Dan Hruschka

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

Background Reading

• Joseph Henrich and Richard McElreath, The Evolution of Cultural Evolution , Evolutionary Anthropology 12:123­135 (2003).

LI Ming

• Introduction to Biomolecular nanomachines and related thermodynamics

ZHAO Liping

• Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology Four slides on each page.
• Top Down vs. Bottom Up: Gut Microbiota and Whole-body Systems Biology One slide on each page.

Background Reading

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

ZHOU Haijun

• Statistical physics ideas on combinatorial optimization cavity method, long-range frustration, clustering of solution spaces