Network Science: Theory, Methods, and Applications Course Syllabus


Network Science: Theory, Methods, and Applications

GRAD 700R
Spring Semester, 2013

A pdf of the syllabus is available.

Over the last two decades there has been an explosion in the use of networks to describe a variety of phenomena, modeling areas as disparate as Greek archaeology to NCAA football and almost everything in between. In addition, network scientists are rapidly compiling new insights about networks themselves, for instance, showing commonalities of patterns of networks working at levels from global (transportation networks) to that of organizations (corporate networks) to that of people (social networks) to the cellular and molecular levels (protein networks).

Network science is a vast and rich topic, and thus we cannot hope to plumb its full depth in one semester. We aim to deal with topics of immediate interest to a team of Emory faculty who are using the tools of this discipline in their current research programs. Students will have the opportunity to explore areas of particular interest to them in their research projects.

Upon completion of this class, the successful student will be able to:

  1. define key concepts of network science;
  2. apply network science theory and methods to interpret problems in their area of interest in network terms; and
  3. manipulate and analyze network data pertaining to a problem of interest. 

  • Officially, Mondays and Wednesdays, 4 – 5:15 pm.
  • Unofficially, Mondays and Wednesdays, 4:15 – 5:30 pm.

Class Organizer

Vicki Stover Hertzberg, Ph.D.
368 Grace Crum Rollins (GCR)
404-727-1881
vhertzb@emory.edu

Teacher's Assistant

Christina Mehta, MSPH
367 GCR
404-712-8405
Christina.mehta@emory.edu

Office Hours

  • Dr. Hertzberg: TR 8 – 9 am; other hours by appointment
  • Ms. Mehta: MW 2-4 pm; other hours by appointment

Students are responsible for readings and discussion each week. Part of this work will include writing short responses to questions (weekly homework), writing up the lab assignments, giving brief reports, posting and commenting on the class blog, and being responsible for leading discussion on a particular subject or reading. In addition, each student will pursue a research project on which he or she will write a term paper and make a poster presentation.

Students will be evaluated on the basis of several components, described below. Students will be expected to attend class and to participate. Homework and lab assignments will be given weekly and students must turn these in one week after assignment. There will be a class blog on which students will be expected to post twice during the semester. There will be a final project as well, with a poster presentation and term paper associated with it.

Grades will be given according to a combination of these components, weighted according to the following table:

ComponentWeightBasis of Evaluation
Class Participation6%Thoughtfulness, originality, activity
Homework assignments24%Correctness, quality of write-up
Lab assignments25%Correctness, quality of write-up
Blog entries20% (2% for each post, 1% for each comment, 2% for inviting successful guest post)Thoughtfulness, correctness, clarity
Final Project25% (5% for Milepost 1, 5% for Milepost 2, 15% for Poster presentation)Results, conclusions, thoughtfulness, content, depth, visual aids, clarity

There is no assigned textbook. Reading assignments will be made each week. However, many people feel better about having a textbook. Here are a few suggestions, two of which are free, and others that are not.

Free

  • Network Science. Albert-László Barabási (only 4 chapters available)

Alternatives (for purchase):

Written assignments must be double-spaced, single-sided, documents with font size of 12 or greater. Late assignments will not be accepted without prior arrangement. The files must be in PDF format. The naming convention is as follows:

  • For Homework assignments: yourlastname_homeworkn.pdf
  • For Mileposts: yourlastname_milepostn.pdf
  • For Lab assignments: yourlastname_labn.pdf

Assignment due dates

DateWhat is Due Then?
*Blog posts are due at 6 pm on the assigned date. Blog comments are due at 11 pm on the assigned date. Homework, lab assignments, and mileposts must be uploaded to Blackboard by 6 pm on the date indicated.
January 22Blog posts* (A-L); Blog Comments* (M-Z)
January 23Homework 1*
January 27Blog posts (M-Z); Blog Comments (A-L)
January 30Milepost 1*
February 3Blog posts (A-L); Blog Comments (M-Z)
February 4Lab 1*
February 10Blog posts (M-Z); Blog Comments (A-L)
February 11Lab 2
February 17Blog posts (A-L); Blog Comments (M-Z)
February 18Lab 3
February 24Blog posts (M-Z); Blog Comments (A-L)
February 25Lab 4
March 3Blog posts (A-L); Blog Comments (M-Z)
March 4Lab 5
March 17Blog posts (M-Z); Blog Comments (A-L)
March 20Milepost 2
March 24Blog posts (A-L); Blog Comments (M-Z)
March 27Homework 2
March 31Blog posts (M-Z); Blog Comments (A-L)
April 3Homework 3
April 7Blog posts (A-L); Blog Comments (M-Z)
April 10Homework 4
April 14Blog posts (M-Z); Blog Comments (A-L)
April 17Homework 5
April 24Homework 6
April 29Poster

A Word about the Blog:

The purpose of the blog assignment is to stimulate a robust virtual discussion. Thus you are free to post and to comment more frequently than assigned. The blog assignments are due on Sunday evening so that everyone can read them prior to the class meetings on Monday and Wednesday.

Class Blog Posts:

Each week half of the students will be expected to post their reflections on the coming week’s readings, and half the students will be expected to comment on one or more of the current week’s posts. The next week the groups will alternate. Each blog post should be at least 250 words for undergraduate students, 400 words for graduate students. Posts should address the strengths and weaknesses of the readings and what further areas of investigation arise.

Class Blog Comments:

There is no word limit criterion for blog posts, but they are expected to be substantive. Thus rather than posting “I agree completely,” state why you agree. Posts are expected to be respectful. This does not mean that you cannot disagree with someone. Instead you should state your counterargument, rather than simply calling someone a knucklehead.

A Final Word about the Blog:

At least once in the semester you are expected to email one of the authors of the readings to invite her/him to comment on a blog post.

Sessions, Topics, and Reading Assignments
DatePresenter(s)Details
1/14Vicki Hertzberg

Course Intro; Network Science – A Brief History

Description

Professor Hertzberg will give a brief history of network science, highlighting the parallel developments in the fields of mathematics, physics, and sociology. Professor Gould will give an overview of the basic concepts of networks, establishing common vocabulary.

Reading

  • Networks, A Very Short Introduction. Guido Caldarelli and Michele Catanzaro. Chapters 2-4, 6.
  • Networks, Crowds, and Markets. David Easley and Jon Kleinberg. Chapter 2 (all), Chapter 3 (sections 1 and 2).
Ron Gould

Basic Concepts

1/16Michele Benzi

The Network Spectrum

Description

In this lecture we will cover the notions of subgraph centrality and communicability, both of which have found widespread use in the analysis of complex networks. The main underlying idea is to exploit the fact that in real-world networks, there are many routes between two nodes besides the shortest path. Taking this into account results in more robust and effective means to rank the centrality of nodes and to measure the flow of information between nodes. From the mathematical point of view, these metrics can be expressed in terms of functions of the adjacency matrix (or of the graph Laplacian) associated with the network. In turn, these can be described using spectral graph theory, i.e., in terms of the eigenvalues and eigenvectors of the various graph matrices. These concepts have been successfully applied to the study of protein-protein interaction networks and in the analysis of social conflicts. Other potential applications include the spreading of rumors, or fads, in social networks as well as the spreading of viruses over computer networks.

Reading

  • E. Estrada, The Structure of Complex Networks. Oxford U. press, 2011.
  • E. Estrada, N. Hatano and M. Benzi, "The physics of communicability in complex networks", Physics Reports, 514 (2012), pp. 89-119.
1/21MLK Day – NO CLASS
1/23M. Grigni

Network Structure and Formation

Description

Professor will continue the discussion of fundamental network structures, such as betweenness and homophily.   He will give particular attention to the algorithmic problem of partitioning such networks.

Reading

  • Networks, Crowds, and Markets. David Easley and Jon Kleinberg. Chapter 3, section 6, and Chapter 4, sections 1-4.
1/28Lab 1

Intro to Gephi

1/30Stefan BoettcherTBN
2/4Lab 2

Gephi 2

2/6Sandra Blakely

Networks in the Greek and Roman World World

Description

Network analysis is both promising and problematic for archaeological research in the Greek and Roman world.   The promise is the correlation to the intellectual models and the lived experience of our objects of study.  Plato referred to the cultures of the ancient Mediterranean as frogs around a pond; behind his metaphor was a historical reality of geographically scattered groups who relied on long-distance networks for economic, political and military success.   The challenge is the data at our disposal, which are preserved only partially and often in extremely fragmentary condition, as well as the variations in the critical application of network analysis.  We will review several of these applications, and then consider how network analysis may be brought to the Mystery cult of the Great Gods of Samothrace.

Reading

  • Brughmans, T.  Connecting the Dots: Towards Archaeological Network Analysis, Oxford Journal of Archaeology 29(3) (2010) 277-303;
  • Burkert, W.  Concordia Discors: the literary and the archaeological evidence on the sanctuary of Samothrace, 179-191 in N. Marinatos, R. Hagg, ed.s Greek Sanctuaries: New Approaches (Routledge 1993).
2/11Lab 3

Gephi 3

2/13TBA
2/18Lab 4

Gephi 4

2/20Mike PrietulaTBN
2/25Lab 5

Gephi 5

2/27Monica Capra

Complex Networks in Economics

Description

Not surprisingly, recent theoretical and methodological advances in Complex Networks have impacted how we model and analyze economic interactions.  There are applications of Complex Networks to a variety of areas in economics including Industrial Organization, Information Economics, International Trade, Finance, and Labor Economics.  Yet, the area that may be most impacted by these new theories and methods is Development Economics.  In this session, Professor Capra will present an overview of the main applications of Complex Networks in economics, emphasizing how CN has impacted how we see economic development.

Reading

  • C. Hidalgo, B. Klinger, A.L. Barabasi, R. Hausmann. The product space conditions the development of nations. Science, 317 (2007), pp. 482–487
  • César A. Hidalgo and Ricardo Hausmann. The building blocks of economic complexity. PNAS June 30, 2009 vol. 106 no. 26 10570-10575
  • Reyes, Javier, Stefano Schiavo, and Giorgio Fagiolo. 2010. Using Complex Networks Analysis to Assess the Evolution of International Economic Integration: The Cases of East Asia and Latin America. Journal Of International Trade And Economic Development 19, no. 2: pp. 215-239
3/4David DavisTBN
3/6Roberto FranzosiTBN
3/11Spring Break – NO CLASS
3/13Spring Break – NO CLASS
3/18A. VenezianiTBN
3/20Brad Pearce

Application of network analysis software and web-based databanks in molecular pathophysiology research

Description

Human disease typically involves disruption of molecular networks as opposed to isolated abnormalities in an individual gene or protein. Advances in  “-omics” technologies holds the promise to measure molecular differences between individual people, and discern underlying pathways of disease causation. However, this requires bioinformatic approaches to elucidate complex multilevel interactions between molecules, cells, and tissues. We will overview web-based software designed to facilitate this understanding, and work-through examples with one of these tools using data from a case-control study.

Reading

  • Gene Set Analysis and Network Analysis for Genome-Wide Association Studies. Inti Pedroso and Gerome Breen. Cold Spring Harb Protoc 2011; doi: 10.1101/pdb.top065581
3/25Ned WallerTBN
3/27Doug Lowery

Interpersonal Social Contacts in the ED

4/1Gonzalo VazquezTBN
4/3Lance Waller

Adding geographic location to network analysis: Examples from veterinary outbreaks

Description

Social networks provide a powerful way to assess contacts between infectious and susceptible individuals and influence the subsequent spread of infection.   However, social interactions also occur in geographic space.  In this session, we will explore how spatial locations can influence network analyses.  The three papers explore this with respect to infectious disease in animals and illustrate how to incorporate geographic and social distance in attempts to control the spread of an outbreak.

Reading

  • Firestone SM, Ward MP, Christley RM, and Dhand NK (2011) The importance of location in contact networks: Describing early epidemic spread using spatial social network analysis. 
  • Preventive Veterinary Medicine 102, 185-195.  Doi: 10.1016/j.prevetmed.2011.07.006
  • Firestone SM, Christley RM, Ward MP, and Dhand NK (2012) Adding the spatial dimension to the social network analysis of an epidemic:  Investigation of the 2007 outbreak of equine influenza in Australia. Preventive Veterinary Medicine 106, 123-135.  Doi: 10.1016/j.prevetmed.2012.01.020
  • Bajardi P, Barrat A, Savini L, and Colizza V (2012) Optimizing surveillance for livestock disease spreading through animal movements.  Journal of the Royal Society Interface 9, 2814-2825. doi: 10.1098/rsif.2012.0289
4/8Hannah CooperTBN
4/10Ralph DiClementeTBN
4/15Julia PainterTBN
4/17Claire SterkTBN
4/22Solveig Argeseanu

Friendships, health, and health behaviors

4/24Vicki Hertzberg

More on Interpersonal Contacts

4/29Student GroupsTBN

Please remember that the Emory University Honor Code applies to all work in this class.