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https://github.com/vtraag/leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
https://github.com/vtraag/leidenalg

clustering-algorithm community-detection

Last synced: 25 days ago
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Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.

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README 

        
leidenalg

==============



This package implements the Leiden algorithm in ``C++`` and exposes it to

``python``.  It relies on ``(python-)igraph`` for it to function. Besides the

relative flexibility of the implementation, it also scales well, and can be run

on graphs of millions of nodes (as long as they can fit in memory). The core

function is ``find_partition`` which finds the optimal partition using the

Leiden algorithm [1]_, which is an extension of the Louvain algorithm [2]_ for a

number of different methods. The methods currently implemented are (1)

modularity [3]_, (2) Reichardt and Bornholdt's model using the configuration

null model and the Erdös-Rényi null model [4]_, (3) the Constant Potts model

(CPM) [5]_, (4) Significance [6]_, and finally (5) Surprise [7]_. In addition,

it supports multiplex partition optimisation allowing community detection on for

example negative links [8]_ or multiple time slices [9]_. There is the

possibility of only partially optimising a partition, so that some community

assignments remain fixed [10]_. It also provides some support for community

detection on bipartite graphs. See the `documentation

`_ for more information.



.. image:: https://readthedocs.org/projects/leidenalg/badge

                :target: http://leidenalg.readthedocs.io/en/latest/

                :alt: Leiden documentation status



.. image:: https://github.com/vtraag/leidenalg/actions/workflows/build.yml/badge.svg?branch=master

                :target: https://github.com/vtraag/leidenalg/actions/workflows/build.yml

                :alt: Leiden build status (GitHub Actions)



.. image:: https://zenodo.org/badge/146722095.svg

                :target: https://zenodo.org/badge/latestdoi/146722095

                :alt: DOI



.. image:: https://anaconda.org/conda-forge/leidenalg/badges/version.svg

                :target: https://anaconda.org/conda-forge/leidenalg

                :alt: Anaconda (conda-forge)



Installation

------------



In short: ``pip install leidenalg``. All major platforms are supported on

Python>=3.6, earlier versions of Python are no longer supported. Alternatively,

you can install from Anaconda (channel ``conda-forge``).



For Unix like systems it is possible to install from source. For Windows this is

more complicated, and you are recommended to use the binary wheels. This Python

interface depends on the C++ package ``libleidenalg`` which in turn depends on

``igraph``. You will need to build these packages yourself before you are able

to build this Python interface.



Make sure you have all necessary tools for compilation. In Ubuntu this can be

installed using ``sudo apt-get install build-essential autoconf automake flex

bison``, please refer to the documentation for your specific system.  Make sure

that not only ``gcc`` is installed, but also ``g++``, as the ``leidenalg``

package is programmed in ``C++``. Note that there are build scripts included in

the ``scripts/`` directory. These are also used to build the binary wheels.



1. Compile (and install) the C core of ``igraph`` (version >= 0.10). You can use

   the file ``build_igraph.sh`` (on Unix-like systems) or ``build_igraph.bat``

   (on Windows) in the ``scripts/`` directory to do this. For more details, see

   https://igraph.org/c/doc/igraph-Installation.html.

2. Compile (and install) the C core of ``libleidenalg`` (version >= 0.10). You

   can use the file ``build_libleidenalg.sh`` (on Unix-like systems) or

   ``build_libleidenalg.bat`` (on Windows) in the ``scripts/`` directory to do

   this. For more details, see https://github.com/vtraag/libleidenalg.

3. Build the Python interface using ``python setup.py build`` and ``python

   setup.py install``, or use ``pip install .``



You can check if all went well by running a variety of tests using ``python -m

unittest``.



Troubleshooting

---------------



In case of any problems, best to start over with a clean environment. Make sure

you remove the ``igraph`` and ``leidenalg`` package completely. Then, do a

complete reinstall starting from ``pip install leidenalg``. In case you

installed from source, and built the C libraries of ``igraph`` and

``libleidenalg`` yourself, remove them completely and rebuild and reinstall

them.



Usage

-----



This is the Python interface for the C++ package ``libleidenalg``. There are no

plans at the moment for developing an R interface to the package. However, there

have been various efforts to port the package to R. These typically do not offer

all available functionality or have some other limitations, but nonetheless may

be very useful. The available ports are:



- https://github.com/cole-trapnell-lab/leidenbase

- https://github.com/TomKellyGenetics/leiden

- https://github.com/kharchenkolab/leidenAlg



Please refer to the documentation for more details

on function calls and parameters.



This implementation is made for flexibility, but ``igraph`` nowadays also

includes an implementation of the Leiden algorithm internally. That

implementation is less flexible: the implementation only works on undirected

graphs, and only CPM and modularity are supported. It is likely to be

substantially faster though.



Just to get you started, below the essential parts.

To start, make sure to import the packages:



>>> import leidenalg

>>> import igraph as ig



We'll create a random graph for testing purposes:



>>> G = ig.Graph.Erdos_Renyi(100, 0.1);



For simply finding a partition use:



>>> part = leidenalg.find_partition(G, leidenalg.ModularityVertexPartition);



Contribute

----------



Source code: https://github.com/vtraag/leidenalg



Issue tracking: https://github.com/vtraag/leidenalg/issues



See the documentation on `Implementation` for more details on how to

contribute new methods.



References

----------



Please cite the references appropriately in case they are used.



.. [1] Traag, V.A., Waltman. L., Van Eck, N.-J. (2018). From Louvain to

       Leiden: guaranteeing well-connected communities. Scientific reports, 9(1), 5233.

       `10.1038/s41598-019-41695-z `_



.. [2] Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008).

       Fast unfolding of communities in large networks. Journal of Statistical

       Mechanics: Theory and Experiment, 10008(10), 6.

       `10.1088/1742-5468/2008/10/P10008 `_



.. [3] Newman, M. E. J., & Girvan, M. (2004). Finding and evaluating community

       structure in networks. Physical Review E, 69(2), 026113.

       `10.1103/PhysRevE.69.026113 `_



.. [4] Reichardt, J., & Bornholdt, S. (2006). Statistical mechanics of

       community detection. Physical Review E, 74(1), 016110.

       `10.1103/PhysRevE.74.016110 `_



.. [5] Traag, V. A., Van Dooren, P., & Nesterov, Y. (2011). Narrow scope for

       resolution-limit-free community detection. Physical Review E, 84(1),

       016114.  `10.1103/PhysRevE.84.016114

       `_



.. [6] Traag, V. A., Krings, G., & Van Dooren, P. (2013). Significant scales in

       community structure. Scientific Reports, 3, 2930.  `10.1038/srep02930

       `_



.. [7] Traag, V. A., Aldecoa, R., & Delvenne, J.-C. (2015). Detecting

       communities using asymptotical surprise. Physical Review E, 92(2),

       022816.  `10.1103/PhysRevE.92.022816

       `_



.. [8] Traag, V. A., & Bruggeman, J. (2009). Community detection in networks

       with positive and negative links. Physical Review E, 80(3), 036115.

       `10.1103/PhysRevE.80.036115

       `_



.. [9] Mucha, P. J., Richardson, T., Macon, K., Porter, M. A., & Onnela, J.-P.

       (2010). Community structure in time-dependent, multiscale, and multiplex

       networks. Science, 328(5980), 876–8. `10.1126/science.1184819

       `_



.. [10] Zanini, F., Berghuis, B. A., Jones, R. C., Robilant, B. N. di,

        Nong, R. Y., Norton, J., Clarke, Michael F., Quake, S. R. (2019).

        northstar: leveraging cell atlases to identify healthy and neoplastic

        cells in transcriptomes from human tumors. BioRxiv, 820928.

        `10.1101/820928 `_



Licence

-------



Copyright (C) 2020 V.A. Traag



This program is free software: you can redistribute it and/or modify it under

the terms of the GNU General Public License as published by the Free Software

Foundation, either version 3 of the License, or (at your option) any later

version.



This program is distributed in the hope that it will be useful, but WITHOUT ANY

WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A

PARTICULAR PURPOSE.  See the GNU General Public License for more details.



You should have received a copy of the GNU General Public License along with

this program. If not, see http://www.gnu.org/licenses/.