Bipartite-Tools

A tool for testing community detection algorithms on bipartite projected networks.

To install on Linux run:

$ sudo ./INSTALL

It is possible to use it as a python library:

import bipnet

or call the python code from bash, without install it. The code was tested only on Linux.

The module validate contains the functions for statistically validated networks. The module metrics contains other useful functions (for ex. the AWI). The code includes a wrapper to the louvain community detection method written by E. Lefebvre and released under GNU Licence. The louvain code is available separately here

Dependencies

To install the dependencies un from bash

$ sudo pip install numpy pandas python-igraph matplotlib scipy

How to use the code

Statistical Validation

In the folder example there is the simple_example.py for the python usage. To use it from bash:

$ bipnet/Validate.py -i examples/bipartite_input.net -o proj.net --side 0 --thr 0.01

the option --side can assume value 0 or 1. If it is zero it will projected with respect to the first column, otherwise it will projected with respect the second column. The option --thr is the significance level of the statistical validation. It is suggested to use 0.01.

The code will produce three networks proj_full.net proj_bonf.net proj_fdr.net.

Adjusted Wallace Index

In the folder example there is the simple_example.py for the python usage. To use it from bash:

$ bipnet/metric.py examples/awi_input.cfg 

The code will check the first column respect to the second.

Benchmark

In the folder example there is the simple_example.py for the python usage. To use it from bash:

$ bipnet/Benchmark.py -i examples/config_benchmark.cfg -o bipartite.net --noise 0.7 

Citations

if you use the code, please cite:

• Bongiorno, Christian; London, András; Miccichè, Salvatore and Mantegna, Rosario N. "Core of communities in bipartite networks", Physical review E 96.2 (2017): 022321.

• Tumminello, Michele; Micciche, Salvatore; Lillo, Fabrizio, Piilo, Jyrki and Mantegna, Rosario N. "Statistically validated networks in bipartite complex systems". PloS one, 6.3 (2011):e17994.

• Blondel, V. D.; Guillaume, J. L.; Lambiotte, R. and Lefebvre, E. "Fast unfolding of communities in large networks". Journal of statistical mechanics: theory and experiment, 2008.10 (2008): P10008.

License

The code is released under GNU license.

Authors

• Christian Bongiorno - pvofeta@gmail.com
  

See also the list of contributors:
Andras London andraslondon@gmail.com
Salvatore Miccichè salvatore.micciche@unipa.it
Rosario N Mantegna rn.mantegna@gmail.com