Documentation updates

README.md

@@ -25,8 +25,8 @@ and the natural sciences ([Physica A](https://www.journals.elsevier.com/physica-
 For additional information, take a look at the **[Documentation](https://graph-tiger.readthedocs.io/)** and our paper:
 
 [**Evaluating Graph Vulnerability and Robustness using TIGER**](https://arxiv.org/pdf/2006.05648.pdf).
-[**Freitas, Scott**](https://scottfreitas.com), and Chau, Duen Horng.
-*arXiv, 2020.*
+[**Scott Freitas**](https://scottfreitas.com), Diyi Yang, Srijan Kumar, Hanghang Tong, and Duen Horng (Polo) Chau.
+*CIKM Resource Track, 2021.*
 
 --------------------------------------------------------------------------------
 
@@ -306,4 +306,4 @@ Beygelzimer *et al.* [Improving network robustness by edge modification](https:/
 
 ### License
 
-[MIT License](LICENSE)
+[MIT License](LICENSE)

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 82321cbed95e93198b5b216869e95c20
+config: 9e145b46b235921e18164ac974e1a974
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/intro.rst.txt

@@ -1,28 +1,12 @@
-:github_url: https://github.com/safreita1/TIGER
-
 Introduction
 ============
 
-.. figure:: ../../images/tiger-logo.jpg
-   :width: 100 %
-   :align: center
-
-
-``TIGER`` is a Python **T**\ oolbox for  evaluat\ **I**\ ing  **G**\ raph vuln\ **E**\ rability and **R**\ obustness.
-TIGER contains numerous state-of-the-art methods to help users conduct graph vulnerability and robustness analysis on
-graph structured data. Specifically, ``TIGER`` helps users:
-
-- **Quantify** network vulnerability and robustness.
-- **Simulate** a variety of network attacks, cascading failures and spread of dissemination of entities.
-- **Augment** a network's structure to resist attacks and recover from failure.
-- **Regulate** the dissemination of entities on a network (e.g., viruses, propaganda).
-
-For additional information, take a look at our paper:
-
-`Evaluating Graph Vulnerability and Robustness using TIGER <https://arxiv.org/pdf/2006.05648.pdf>`_.
-`Freitas, Scott <https://scottfreitas.com>`_, and Chau, Duen Horng.
-*arXiv, 2020.*
+``TIGER`` is a Python **T**\ oolbox for  evaluat\ **I**\ ing  **G**\ raph vuln\ **E**\ rability and **R**\ obustness that allows users to (1) measure graph vulnerability and robustness, (2) attack networks using a variety of offensive techniques, (3) defend a network using a variety of heuristic and optimization based defense techniques. ``TIGER`` is specifically designed to help users:
 
+- Quantify network vulnerability and robustness.
+- Simulate a variety of network attacks, cascading failures and spread of dissemination of entities.
+- Augment a network's structure to resist attacks and recover from failure.
+- Regulate the dissemination of entities on a network (e.g., viruses, propaganda).
 
 Background & Motivation
 ***********************
@@ -36,27 +20,27 @@ Unfortunately, the nature of cross-disciplinary research also comes with signifi
 
 Installation
 ************
-To quickly get started, install TIGER using pip:
+To quickly get started, install TIGER using pip
 
-``pip install graph-tiger``
+```sh
+$ pip install graph-tiger
+```
 
-Alternatively, you can git clone `TIGER <https://github.com/safreita1/TIGER.git>`_ and create a new Anaconda environment
-using the provided `YAML <https://github.com/safreita1/TIGER/blob/master/environment.yml>`_ file.
+Alternatively, you can git clone [TIGER](https://github.com/safreita1/TIGER.git) and create a new Anaconda environment
+using the provided [YAML](environment.yml) file.
 
 
 Citing
 ******
 
+If you find **TIGER** useful in your research, please consider citing the following paper:
 
-.. code-block:: latex
-
-   @article{freitas2020evaluating,
-             title = {Evaluating Graph Vulnerability and Robustness using TIGER},
-             author = {Freitas, Scott and Chau, Duen Horng},
-             journal={arXiv preprint arXiv:2006.05648},
-             year = {2020},
-    }
-
+@article{freitas2020evaluating,
+    title={Evaluating Graph Vulnerability and Robustness using TIGER},
+    author={Freitas, Scott and Chau, Duen Horng},
+    journal={arXiv preprint arXiv:2006.05648},
+    year={2020}
+}
 
 
 Examples

docs/build/html/_sources/tutorials/tutorial-1.rst.txt

@@ -1,7 +1,6 @@
 Tutorial 1: Measuring Vulnerability and Robustness
 ********************************************************
 
-Robustness is defined as a measure of a network's ability to continue functioning when part of the network is naturally damaged or targeted for attack :cite`ellens2013graph,chan2016optimizing,beygelzimer2005improving`.
 TIGER contains numerous robustness measures, grouped into one of three categories depending on whether the measure uses the graph, adjacency, or Laplacian matrix. In the figure below, we show some common robustness measures from each category.
 
 .. _fig-coordsys-rect:

docs/build/html/attacks.html

@@ -53,13 +53,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 
@@ -479,7 +476,7 @@
 <dl class="py function">
 <dt id="graph_tiger.attacks.get_node_ns">
 <code class="sig-prename descclassname"><span class="pre">graph_tiger.attacks.</span></code><code class="sig-name descname"><span class="pre">get_node_ns</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#graph_tiger.attacks.get_node_ns" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get k nodes to attack based on the Netshield algorithm :cite`tong2010vulnerability`.</p>
+<dd><p>Get k nodes to attack based on the Netshield algorithm: <a class="reference external" href="http://tonghanghang.org/pdfs/icdm10_netshield.pdf">http://tonghanghang.org/pdfs/icdm10_netshield.pdf</a></p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
@@ -496,7 +493,7 @@
 <dl class="py function">
 <dt id="graph_tiger.attacks.get_node_pr">
 <code class="sig-prename descclassname"><span class="pre">graph_tiger.attacks.</span></code><code class="sig-name descname"><span class="pre">get_node_pr</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#graph_tiger.attacks.get_node_pr" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get k nodes to attack based on top PageRank entries :cite`page1999pagerank`.</p>
+<dd><p>Get k nodes to attack based on top PageRank entries</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

docs/build/html/bibliography.html

@@ -52,13 +52,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 

docs/build/html/cascading.html

@@ -53,13 +53,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 
@@ -201,7 +198,7 @@
 <dt id="graph_tiger.cascading.Cascading">
 <em class="property"><span class="pre">class</span> </em><code class="sig-prename descclassname"><span class="pre">graph_tiger.cascading.</span></code><code class="sig-name descname"><span class="pre">Cascading</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">runs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#graph_tiger.cascading.Cascading" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference internal" href="simulations.html#graph_tiger.simulations.Simulation" title="graph_tiger.simulations.Simulation"><code class="xref py py-class docutils literal notranslate"><span class="pre">graph_tiger.simulations.Simulation</span></code></a></p>
-<p>This class simulates cascading failures on a network :cite`crucitti2004model`.</p>
+<p>This class simulates cascading failures on a network</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

docs/build/html/defenses.html

@@ -53,13 +53,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 
@@ -427,7 +424,7 @@
 <dl class="py function">
 <dt id="graph_tiger.defenses.get_node_ns">
 <code class="sig-prename descclassname"><span class="pre">graph_tiger.defenses.</span></code><code class="sig-name descname"><span class="pre">get_node_ns</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#graph_tiger.defenses.get_node_ns" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get k nodes to defend based on the Netshield algorithm <span id="id9">[<a class="reference internal" href="bibliography.html#id2"><span>17</span></a>]</span>.</p>
+<dd><p>Get k nodes to defend based on the Netshield algorithm <span id="id9">[<a class="reference internal" href="bibliography.html#id2"><span>17</span></a>,<a class="reference internal" href="bibliography.html#id37"><span>5</span></a>]</span>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

docs/build/html/diffusion.html

@@ -53,13 +53,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 
@@ -201,7 +198,7 @@
 <dt id="graph_tiger.diffusion.Diffusion">
 <em class="property"><span class="pre">class</span> </em><code class="sig-prename descclassname"><span class="pre">graph_tiger.diffusion.</span></code><code class="sig-name descname"><span class="pre">Diffusion</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'SIS'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">runs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.00208</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">d</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">c</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#graph_tiger.diffusion.Diffusion" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference internal" href="simulations.html#graph_tiger.simulations.Simulation" title="graph_tiger.simulations.Simulation"><code class="xref py py-class docutils literal notranslate"><span class="pre">graph_tiger.simulations.Simulation</span></code></a></p>
-<p>Simulates the propagation of a virus using either the SIS or SIR model :cite`kermack1927contribution`.</p>
+<p>Simulates the propagation of a virus using either the SIS or SIR model</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

docs/build/html/genindex.html

@@ -51,13 +51,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 

docs/build/html/graphs.html

@@ -53,13 +53,10 @@
 
 
 
-            <a href="index.html">
+            <a href="index.html" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>
 
 

docs/build/html/index.html

@@ -52,13 +52,10 @@
 
 
 
-            <a href="#">
+            <a href="#" class="icon icon-home"> TIGER
 
 
 
-
-            <img src="_static/tiger-logo.jpg" class="logo" alt="Logo"/>
-
           </a>