This repository contains all non-confidential data that is required to reproduce the results of our paper *Clique Community Persistence: A Topological Visual Analysis for Complex Networks*. The following sections will briefly discuss the necessary steps to reproduce the results. If you have any question, please scroll below for contact information. # Setup Most of our results were obtained using *Aleph*, a library for exploring persistent homology. Please refer to the build steps in the associated GitHub repository to build the project. Assuming that you built the project in `/home/user/Projects/Aleph/build`, please adjust your `$PATH` variable as follows: path+=($HOME/Projects/Aleph/build/examples) path+=($HOME/Projects/Aleph/build/src/tools) This makes the scripts and tools available on the command-line. # Scripts The `Scripts/` folder contains scripts for the individual data sets to reproduce the steps. They are briefly documented in order to explain the necessary steps. Here is a short summary: - `make_clique_persistence_diagrams_arXiv.sh`: creates all clique community persistence diagrams for the condensed matter collaboration networks. This script also demonstrates how to obtain the centrality values. - `make_clique_persistence_diagrams_lesmis.sh`: creates all clique community persistence diagrams for the Les Misérables network. Please run this script in the folder that contains the file `lesmis.gml` - `make_clique_persistence_diagrams_shakespeare.sh`: creates all clique community persistence diagrams for the Shakespeare networks. Please run this script in the data folder that contains all graphs. # Creating persistence indicator functions Assuming that you have a working installation of *Aleph* (see above), please use the tool `persistence_indicator_function` to create persistence indicator functions. The function accepts the filename of a persistence diagram as a parameter. If the current directory contains all persistence diagrams, the following is sufficient to create *all* persistence indicator functions: persistence_indicator_function *.txt The generated functions will be placed in `/tmp`. # Calculating topological distances To reproduce the distance matrices that we depicted in the paper, please use the tool `topological_distance` that is shipped with *Aleph*. The tool is sufficiently smart to detect common suffixes of persistence diagrams belonging to the *same* data set automatically. To calculate the first Wasserstein distance between all of Shakespeare's plays, go into the directory that contains the persistence diagrams and call topological_distance -w -p 1 *.txt or topological_distance --wasserstein --power 1 *.txt to create a distance matrix. This matrix can be visualized in gnuplot, for example, by calling `plot FILE matrix with image`. Alternatively, it can be transformed with the `transform_matrix.py` to de displayed using the TikZ or pgfplots packages for LaTeX. # Nested Tracking Graphs For the graph visualization, please refer to an [example provided by Jonas Lukasczyk](http://jluk.de/blog/NestedGraphs/index.html). # Contact Please contact [Bastian Rieck](mailto:bastian.rieck@iwr.uni-heidelberg.de) for any further inquiries regarding the data, the results, or Aleph.