CS 790g Seminar: Complex Networks

Course Information

Class hours	Tuesday & Thursday, 1:00 - 2:15pm
Class location	OSN 101 (Orvis School of Nursing)
Instructor	Dr. Mehmet Gunes
E-mail
Phone	(775) 784 - 4313
Web page	http://www.cse.unr.edu/~mgunes
Office	SEM 230 (Scrugham Engineering-Mines)
Office hours	Tuesday & Thursday 2:30 - 4:00 pm or by appointment

• Networks: An Introduction , by Mark Newman, (Oxford University Press - May 20, 2010).
• Dynamical Processes on Complex Networks, by Alain Barrat, Marc Barthelemy, and Alessandro Vespignani, (Cambridge University Press - November 24, 2008).
• The Structure and Dynamics of Networks, by Mark Newman, Albert-László Barabási, & Duncan J. Watts, (Princeton University Press - April 17, 2006).
• Exploratory Social Network Analysis with Pajek, by Nooy, Wouter de, Andrej Mrvar, and Vladimir Batagelj, (Cambridge University Press - January 10, 2005).

Description

This course covers theory and modeling of real-world networks such as computer, social, and biological networks where the underlying topology is a dynamically growing complex graph.

Many phenomena in nature can be modeled as a network. Researchers from many areas including biology, computer science, engineering, epidemiology, mathematics, physics, and sociology have been studying complex networks of their field.

Scale-free networks and small-world networks are well known examples of complex networks where power-law degree distribution and high clustering are their respective characteristic feature. These networks have been identified in many fundamentally different systems. Complex networks display non-trivial topological features that require an in depth study.

Objective

• a broad conceptual introduction to the modern theory and applications of complex networks,
• experience critiquing scientific papers,
• experience working with large, complex data sets,
• experience with technical writing and in class presentations.

Topics (Tentative)

• Emprical Study of Networks
  • Technological networks
  • Information networks
  • Social networks
  • Biological networks
  • Economic networks
  • Infrastructure networks
• Fundamentals of Network Theory
  • Mathematics of networks
  • Measures and metrics
  • Large-scale structure of networks
• Network Models
  • Random graphs
  • Random graphs with general degree distributions
  • Power-law
  • Small worlds
  • Network formation
• Processes on Networks
  • Percolation and network resilience
  • Epidemics on networks
  • Network dynamics
  • Network search
  • Graph data mining
• Network Visualization

Prerequisites

• Graduate level (any discipline)
• An adequate background in Calculus and Probability will be required.

Organization

• Except this web page, course materials will be posted at the WebCT. Blog page at http://UNRcs790g.blogspot.com will be actively utilized, as well. Students are encouraged to post articles, demos, web pages, and news events that are relevant to course.
   
• Presentation slides will be available on the class web page. I will try to put them up before each class meeting but no guarantees on that.
   
• Unless instructed otherwise, use of electronic devices including laptops and smart phones are not allowed during lectures.
   
• The organization of the course will evolve as the semester progresses. I'm quite confident that it will be challenging but a fun course. This is not a lecture course, but an active learning opportunity with an intense engagement in research.
   
• Class participation in terms of asking questions is highly encouraged. Please do not be afraid to ask questions no matter how simple you might think the answer could be. This type of interaction helps improve the effectiveness of the class and breaks the monotony.
   
• Attendance at all class meetings is mandatory and will affect your grade. You should arrive on time and be prepared to discuss the session's topic. The underlying notion of the class is interaction, not passivity. The success of the course depends on everyone in the class engaging the material and bringing energy, enthusiasm, and intellect to class activities.
   
• Being a seminar course, you are primarily responsible for participating in the discussion. You are expected to read indicated papers and chapters for each session and be prepared to discuss and comment on the material.
   
• Each student will write three two blog entries at http://UNRcs790g.blogspot.com for lectures he/she is assigned to. The blog should be at least two paragraphs of 100 words each and cover important points of the lecture. Everyone is welcome to add comments and add new entries.
   
• Each student will prepare a research project on a complex network of their choice. The expected outcome of the project is a research paper that can be published at a quality conference. Requiring major effort from you, the project will help in learning the culture and practice of scientific research. Late submission during project stages will be penalized by 10% per day, except holidays. Assignments will be accepted only through WebCT.
   
• The course will require students to prepare two 30 min and one 15 min in class presentations throughout the semester. You will be graded by your peers using the presentation evaluation form. However, final grade will be decided by instructor. In the first presentation, each student will carry out a thorough review of the research related to his/her project. The second presentation should cover the methodology of your research project providing details of your approach/idea. The final presentation should present your findings.
   
• You would be required to prepare reports for each of the presentations. These reports would become related work, methodology, and evaluations sections in your final paper. Your writing should be clear, engaging, technically sound, and written in an appropriate style for an academic publication.
   
• There will be six five in-class quizzes. The lowest graded one will not affect your overall grade. Exact date for these quizzes will not be exposed beforehand. These quizzes will be open book/notes and extremely time-constrained, i.e., 15-20 mins. Questions in these quizzes will be designed to give you an opportunity to test and affirm your knowledge of the course content.
   
• There will be seven six lab assignments where you will have hands on experience on complex networks. The lowest graded one will not affect your overall grade. These assignments will require you to use several tools (such as Pajek and GUESS) to analyze sample networks. Late submission will be penalized by 20% per day, except holidays.
   
• You are welcome to discuss the problems or solution strategies with your class mates but the resulting work should be your own. Copying from each other or from other sources is considered as cheating. Any form of cheating such as plagiarism or ghostwriting will incur a severe penalty, usually failure in the course. Please refer to the UNR policy on Academic Standards.
   
• If you have a disability for which you will need to request accommodations, please contact the instructor or someone at the Disability Resource Center (Thompson Student Services - 101) as soon as possible.
   
• Academic Success Services: Your student fees cover usage of the Math Center (784-4433 or www.unr.edu/mathcenter) and Tutoring Center (784-6801 or www.unr.edu/tutoring). These centers support your classroom learning; it is your responsibility to take advantage of their services. Keep in mind that seeking help outside of class is the sign of a responsible and successful student.
   

Research Project

The main component of your grade is a research project that may materialize as a paper. If your project has a significant computational component (e.g., downloading and analyzing a network dataset), then you may work with a partner after consulting with the instructor. The paper will be judged on the following criteria:

• Insight: Your paper should be more than just a recapitulation of existing work, or just raw analysis of data. You should make an effort to provide insight to the reader: for example, what is the data telling us about the networked system?
• Command of relevant course material: Your paper should connect to the main themes of the course, and your coverage of the related material should demonstrate competence with the content of the project.
• Clarity: You must clearly articulate the problem(s) or question(s) you are addressing; your methodology and approach; and your insights, solutions, and remaining open questions.
• Rigor and precision: Your paper must be mathematically precise where necessary, and rigorous and logical in its reasoning throughout. Any methodology used should be justified, and limitations or assumptions should be clarified.

Following are sample project topics:

• Dataset analysis: Obtain and analyze a network dataset (e.g., by downloading a dataset online, or by crawling an online service). You may perform conceptually or theoretically new experiments with existing datasets.
• Network formation: Choose a specific applied domain, and discuss how networks form in that domain. For example, you might discuss the formation and dissolution of contracts among Internet service providers; the formation of links in social networks; or the evolution and dissolution of political alliances.
• Theory development: Propose a new theoretical direction and specify a research agenda. You might develop a new method to analyze networks (e.g., dynamic characteristics of biological networks).
• Characterization of epidemics: Study several specific examples of epidemic phenomena, such as: fads in online content; virus and worm spreading in information networks; and word-of-mouth in product marketing.

Grading (Tentative)

Grading Policy

41 - Project (Abstract:2, Related Work:9, Methodology:10, Final paper:20)
20 - Presentations (2 + 1/2)
15 - Labs (5 of 6)
12 - Quizes (4 of 5)
9 - Paper critique (9 papers total)
3 - Blog Entries (2)

Grading Scale

A : 87 - 100
B : 75 - 86
C : 63 - 74
D : 51 - 62
F : 0 - 50 (or caught cheating)

Important Note: You will have one week to appeal for your grades after the graded assignments/tests are returned. So, please keep this in mind if you think that there is a problem/issue with the grading of your work.

Tools

• Pajek: A simple network visualization tool allowing to interactively manipulate the network. (Pajek manual)
• Graphviz: A simple network visualization tool available for a variety of platforms.
• GUESS: An exploratory data analysis and visualization tool.
• JUNG: A Java Universal Network/Graph Framework.
• NetLogo: A multi-agent programmable modeling environment.
• UCINET: A social network visualization and analysis tool.
• iGraph: A software package for creating and manipulating undirected and directed graphs.
• NetworkX: A Python package for studying the structure, dynamics, and functions of complex networks.
• IVC: InfoVis Cyberinfrastructure is a collection of data analysis and visualization algorithms.
• Net: A program for the creation and statistical analysis of large networks.
• graph-tool: A python module to help with statistical analysis.

Schedule (Tentative), Notes & Assignments

This is a tentative schedule including the assignment dates. It is subject to readjustment depending on the time we actually spend in class covering the topics.

Announcements

Announcements regarding the course will be posted on this web page and UNRcs790g.blogspot.com blog site. Please check your e-mail daily.

• Aug 18 : You can access previous year's webpage at http://www.cse.unr.edu/~mgunes/cs790g/cs790f09/.
   
• Aug 18 : Paper reading list
   
• Aug 18 : You can find nice figures of complex networks at www.visualcomplexity.com.
   
• Sep 28 : Materials for Lada Adamic's course can be found at http://open.umich.edu/education/si/si508/fall2008/materials.
   
• Oct 27 : Methodology papers are posted on WebCt.