Social Network Analysis for Computer Scientists

The main goal of this lab session is to ensure that your team is all set for making serious progress writing the course project paper in the coming weeks.

Course project paper
Earlier, you have made a project planning. One upcoming deadline is the first version of your paper for the peer review session in 2 weeks.

1. Template. If you have not yet done so, download the paper template, make sure you can compile it in LaTeX, and understand how to use it. Remember to fill in the meta information.
2. Related work. If you have not yet done so, spend some time at Google Scholar investigating a) what other papers exist on this topic, b) which relevant papers cite your paper, and c) what important references are presented in your paper. You will likely want to include some of these in your paper as well. At least make sure that you are aware of the major works that cite your paper, and that you reference some of these works in your introduction when you sketch the context of your work.
3. Project contribution. For the course project, you go beyond the one paper that you were assigned, comparing techniques from multiple papers, for example comparing different algorithms or methods, using different validation metrics, or testing on (a) larger (number of diverse) datasets. Try to get your intended contribution written down in the appropriate section(s) of your paper.
4. Collaboration. How will you work together on the paper? Git? Overleaf? (the university provides free pro licenses). How will you share code, data and results with each other, and ensure integration of it all?
5. What is a good paper?. What defines a good paper? Discuss with your project partner to align your expections. When are you "done"? When is the paper "sufficient"? When is it "good"? And how about "excellent"?
6. Writing. Make serious progress with writing the first 3 to 4 sections of your course project paper in the coming two weeks, so that you have something substantial for the peer review session.
7. Planning. Look at the planning you made early October. Have you reserved time to review each other's texts? Are adjustments necessary?

As always: please ask course staff for help if you are still unsure about certain aspects of your project.

Need to freshen up or improve academic writing skills? See Academic writing: a practical guide and the The academic phrasebank. There is also the Leiden Science Skills platform.

The main goal of this lab session is to get started with both the course project and with Assignment 2.

Course project
Below are some topics you can discuss and investigate together with your project team partner.

1. Project schedule. Have a look at the deadlines for the course project in the schedule on this website, and create your own sensible planning with your team partner.
2. Paper. Read your course project paper, and spend some time at Google Scholar investigating a) what other papers exist on this topic, b) which relevant papers cite your paper, and c) what important references are presented in your paper.
3. Data repositories. Check out the data repositories of real (social) networks listed in the Course Project section and think of datasets suitable for your course project.
4. Project contribution. For the course project, you have to do something original. Ideally, this goes beyond the one paper that you were assigned, comparing techniques from multiple papers, for example comparing different algorithms or methods, using different validation metrics, or testing on (a) larger (number of diverse) datasets. Write down in at most 150 words what you plan to do for your course project, and feel free to discuss this with the lecturer or an assistant for feedback, this week or the next two. Also see the generic instructions for the Course Project.

Done? Get started with Assignment 2.

The main goal of this lab session is to become familiar with NetworkX (a Python package to analyze networks for research purposes).
All relevant information on NetworkX can be found in the NetworkX online documentation.

Your Python environment

For this lab session, you need a working Python environment. For this, there are two options:

1. Use your own self-installed Python environment, and choose your own editor and way of running code (via the command line, an IDE or an interactive notebook). Proceed to Instructions for today
2. Alternatively, you can use the desktop machines in the student computer rooms.
   One easy way to create a Python environment on the university computers, is to use conda. As of 2024, conda appears to be installed already. Therefore, you can likely skip step 1--3 below, and start at step 4.
   1. Download Miniconda by running the following command in your terminal:
      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   2. Install Miniconda:
      bash Miniconda3-latest-Linux-x86_64.sh
      The installer will ask you some questions. Normally, the standard location suffices and you do not have to add conda to PATH.
   3. After installation finishes, close your terminal so that the changes take effect. Upon opening a new terminal, activate the conda virtual environment with:
      source miniconda3/bin/activate
      If all goes well, you will see that (base) appears in front of your shell prompt. This means that conda's base environment is active.
   4. Create a new conda environment:
      conda create --name snacs
      And activate it with:
      conda activate snacs
      You might use conda for other courses as well, and version conflicts can arise when you install many packages. Using separate environments prevents this.
      NOTE: some packages can make your conda environment take up a lot of space. So try not to use an unnecessary number of environments with duplicate packages. You can also remove an environment that you don't need anymore, see the conda cheatsheet.
   5. Packages can easily be installed with conda. To install NetworkX, run:
      conda install networkx
   6. Getting started
      • Running code from the command line. Now you should be able to run your code from the command line by typing
        python3 scriptname.py
      • Running code in interactive Jupyter notebook from the university environment:
        conda install -c conda-forge jupyterlab
        After installing that once, the notebook/lab can be started using:
        jupyter lab
(When using Jupyter through SSH, so when it is not running on the machine that you are currently working on, make sure to use port forwarding whilst SSH-ing, using options -g -L 8888:127.0.0.1:8888. Also add options --no-browser and --port=8888 when starting up Jupyter.)

Instructions for today: Lab session on NetworkX

1. Take some time to do the NetworkX tutorial.
2. Have a look at functionality to read and write graphs from/to disk, and in particular learn how to import an edge list. Understand the input format and ways of including things like Weight and other attributes of edges.
3. A lot of the common network metrics you may want to compute are implemented as NetworkX function or NetworkX algorithm. Become familiar with these, for example by computing measures such as degree assortativity, clustering, density, diameter and average distance.
4. While at it, why not take a look at how NetworkX relates to other data formats?
5. Try to load the network from the first lab session (small-gephiready.tsv) into NetworkX, and investigate some characteristic properties of the network, such as the degree distribution and distance distribution. Use theread_edgelist function and remember to select the correct separator (tab), and pay attention to the header of the file.
6. Get the Epinions network from the SNAP repository. You may need to fiddle with the precise header, but it is already in edge list format. Compute some common characteristics such as the degree distribution, and visualize them using appropriate figures or distributions, for example using pyplot/Matplotlib.
7. What are the differences between NetworkX and Gephi in terms of visualization and analysis capabilities?

Done? Proceed with Exercise 2 of Assignment 1.

Looking for a challenge? Check out these three alternatives (that you can also use instead of NetworkX throughout the course, if you prefer (but for which there is less help available)):

• Python igraph, a Python version of the R igraph package.
• Graph-Tool, a python graph analysis toolkit that leaves the hard computation to parallel (OpenMP) C++ code.
• SNAP, which is entirely written in C++ and has many interesting features. Nowadays, there is also a Python version.

Running intro problems regarding prior knowledge on python programming? See the reading material at the bottom of this course website.

About social network analysis tools and packages. There exist different tools and packages for social network analysis. In this course, we coveR two of them, with complementary advantages:

1. Gephi, an easy-to-use tool with a graphical interface useful for visualization and quick analysis of relatively small network data (this week, see below).
   
2. NetworkX, an extensive Python package for network analysis that can handle larger network datasets and computations (next week).

Learning goals. The main goal of this lab session is to become familiar with Gephi (experimental beta-software to visualize networks for research purposes) and its input format. At the end of this session you should be able to:

• Know how to use Gephi for social network analysis
• Import and visualize raw network data with labeled nodes and labeled and/or weighted edges (directed or undirected),
• Understand how to map edge and node size and color to structural network properties such as the node degree and edge type,
• Know how to apply filters to the visualization, for example to focus only on the giant component,
• Export a vector graphic PDF of your network for reuse in for example a presentation or paper,
• Export computed node data for reuse in another program.

There is no deliverable for this lab session, but you are assumed to know the tool afterwards. Practice more at home if needed.

Instructions:

1. Walk through the Gephi tutorial.
   Note that the tutorial briefly covers topic such as centrality and communities, that will not be covered extensively until Lecture 2.

Done? Get started with the practical part of Assignment 1. You can download the smaller datafiles medium.tsv and large.tsv. If you want to analyze huge.tsv, you will have to get it from the shared folder in the ISSC Linux or LIACS DS lab environment, as stated in the assignment.