Project Description
Release History
## Release History

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INTRODUCTION

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

This package implements the louvain 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 louvain algorithm

for a number of different methods. The methods currently implemented are:

* Modularity.

This method compares the actual graph to the expected graph, taking into

account the degree of the nodes [1]. The expected graph is based on a

configuration null-model. Notice that we use the non-normalized version (i.e.

we don't divide by the number of edges), so that this Modularity values

generally does not fall between 0 and 1. The formal definition is

```

H = sum_ij (A_ij - k_i k_j / 2m) d(s_i, s_j),

```

where `A_ij = 1` if there is an edge between node `i` and `j`, `k_i` is the degree of

node `i` and `s_i` is the community of node i.

* RBConfiguration.

This is an extension of modularity which includes a resolution parameter [2].

In general, a higher resolution parameter will lead to smaller communities.

The formal definition is

```

H = sum_ij (A_ij - gamma k_i k_j / 2m) d(s_i, s_j),

```

where `gamma` is the resolution value, and the other variables are the same as

for Modularity.

* RBER.

A variant of the previous method that instead of a configuration null-model

uses a Erdös-Rényi null-model in which each edge has the same probability of

appearing [2]. The formal definition is

```

H = sum_ij (A_ij - gamma p) d(s_i, s_j),

```

where `p` is the density of the graph, and the other variables are the same as

for Modularity, with `gamma` a resolution parameter.

* CPM.

This method compares to a fixed resolution parameter, so that it finds

communities that have an internal density higher than the resolution

parameter, and is separated from other communities with a density lower than

the resolution parameter [3].The formal definition is

```

H = sum_ij (A_ij - gamma ) d(s_i, s_j),

```

with `gamma` a resolution parameter, and the other variables are the same as for

Modularity.

* Significance.

This is a probabilistic method based on the idea of assessing the probability

of finding such dense subgraphs in an (ER) random graph [4]. The formal

definition is

```

H = sum_c M_c D(p_c || p)

```

where `M_c` is the number of possible edges in community `c`, i.e. `n_c (n_c - 1)/2`

for undirected graphs and twice that for directed grahs with `n_c` the size of

community `c`, `p_c` is the density of the community `c`, and `p` the general density

of the graph, and `D(x || y)` is the binary Kullback-Leibler divergence.

* Surprise.

Another probabilistic method, but rather than the probability of finding dense

subgraphs, it focuses on the probability of so many edges within communities

[5, 6]. The formal definition is

```

H = m D(q || <q>)

```

where `m` is the number of edges, `q` is the proportion of edges within

communities (i.e. `sum_c m_c / m`) and `<q>` is the expected proportion of edges

within communities in an Erdős–Rényi graph.

INSTALLATION

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

In short, for Unix: ``sudo pip install louvain``.

For Windows: download the binary installers.

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

overly complicated, and you are recommended to use the binary installation files.

There are two things that are needed by this package: the igraph c core library

and the python-igraph python package. For both, please see http://igraph.org.

There are basically two installation modes, similar to the python-igraph package

itself (from which most of the setup.py comes).

1. No C core library is installed yet. The packages will be compiled and linked

statically to an automatically downloaded version of the C core library of

igraph.

2. A C core library is already installed. In this case, the package will link

dynamically to the already installed version. This is probably also the

version that is used by the igraph package, but you may want to double check

this.

In case the python-igraph package is already installed before, make sure that

both use the **same versions**.

The cleanest setup it to install and compile the C core library yourself (make

sure that the header files are also included, e.g. install also the development

package from igraph). Then both the python-igraph package, as well as this

package are compiled and (dynamically) linked to the same C core library.

TROUBLESHOOTING

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

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

you remove the python-igraph package completely, remove the C core library and

remove the louvain package. Then, do a complete reinstall starting from ``pip

install louvain``. In case you want a dynamic library be sure to then install

the C core library from source before. Make sure you **install the same

versions**.

USAGE

=====

There is no standalone version of louvain-igraph, and you will always need

python to access it. There are no plans for developing a standalone version or R

support. So, use python. Please refer to the documentation within the python

package for more details on function calls and parameters.

To start, make sure to import the packages:

```python

import louvain

import igraph as ig

```

We'll create a random graph for testing purposes:

```python

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

```

For simply finding a partition use:

```python

part = louvain.find_partition(G, method='Modularity');

```

In case you want to use a weighted graph, you can store this in an edge

attribute:

```python

G.es['weight'] = 1.0;

part = louvain.find_partition(G, method='Modularity', weight='weight');

```

Please note that not all methods are necessarily capable of handling weighted

graphs.

Notice that ``part`` now contains an additional variable, ``part.quality`` which

stores the quality of the partition as calculated by the used method. You can

always get the quality of the partition using another method by calling

```python

part.significance = louvain.quality(G, partition, method='Significance');

```

You can also find partition for multiplex graphs. For each layer you then

specify the objective function, and the overall objective function is simply the

sum over all layers, weighted by some weight. If we denote by ``q_k`` the quality

of layer ``k`` and the weight by ``w_k``, the overall quality is then ``q = sum_k

w_k q_k``. This can also be useful in case you have negative links. In

principle, this could also be used to detect temporal communities in a dynamic

setting, cf. [8].

For example, assuming you have a graph with positive weights ``G_positive`` and

a graph with negative weights ``G_negative``, and you want to use Modularity for

finding a partition, you can use

```python

membership, quality = louvain.find_partition_multiplex([

louvain.Layer(graph=G_positive, method='Modularity', layer_weight=1.0),

louvain.Layer(graph=G_negative, method='Modularity', layer_weight=-1.0)])

```

Notice the negative layer weight is ``-1.0`` for the negative graph, since we

want those edges to fall between communities rather than within. One particular

problem when using negative links, is that the optimal community is no longer

guaranteed to be connected (it may be a multipartite partition). You may

therefore need the options `consider_comms=ALL_COMMS` to improve the quality of

the partition. Notice that this runs much slower than only considering

neighbouring communities (which is the default).

Various methods (such as Reichardt and Bornholdt's Potts model, or CPM) support

a (linear) resolution parameter, which can be effectively bisected, cf. [5]. You

can do this by calling:

```python

res_parts = louvain.bisect(G, method='CPM', resolution_range=[0,1]);

```

Notice this may take some time to run, as it effectively calls

`louvain.find_partition` for various resolution parameters (depending on the

settings possibly hundreds of times).

Then `res_parts` is a dictionary containing as keys the resolution, and as

values a `NamedTuple` with variables `partition` and `bisect_value`, which

contains the partition and the value at which the resolution was bisected (the

value of the `bisect_func` of the `bisect` function). You could for example plot

the bisection value of all the found partitions by using:

```python

import pandas as pd

import matplotlib.pyplot as plt

res_df = pd.DataFrame({

'resolution': res_parts.keys(),

'bisect_value': [bisect.bisect_value for bisect in res_parts.values()]});

plt.step(res_df['resolution'], res_df['bisect_value']);

plt.xscale('log');

```

REFERENCES

==========

Please cite the references appropriately in case they are used.

1. Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding

of communities in large networks. J. Stat. Mech. 2008, P10008 (2008).

2. Newman, M. & Girvan, M. Finding and evaluating community structure in networks.

Physical Review E 69, 026113 (2004).

3. Reichardt, J. & Bornholdt, S. Partitioning and modularity of graphs with arbitrary

degree distribution. Physical Review E 76, 015102 (2007).

4. Traag, V. A., Van Dooren, P. & Nesterov, Y. Narrow scope for resolution-limit-free

community detection. Physical Review E 84, 016114 (2011).

5. Traag, V. A., Krings, G. & Van Dooren, P. Significant scales in community structure.

Scientific Reports 3, 2930 (2013).

6. Aldecoa, R. & Marín, I. Surprise maximization reveals the community structure

of complex networks. Scientific reports 3, 1060 (2013).

7. Traag, V.A., Aldecoa, R. & Delvenne, J.-C. Detecting communities using Asymptotical

Surprise. Forthcoming (2015).

8. Mucha, P. J., Richardson, T., Macon, K., Porter, M. A. & Onnela, J.-P.

Community structure in time-dependent, multiscale, and multiplex networks.

Science 328, 876–8 (2010).

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

This package implements the louvain 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 louvain algorithm

for a number of different methods. The methods currently implemented are:

* Modularity.

This method compares the actual graph to the expected graph, taking into

account the degree of the nodes [1]. The expected graph is based on a

configuration null-model. Notice that we use the non-normalized version (i.e.

we don't divide by the number of edges), so that this Modularity values

generally does not fall between 0 and 1. The formal definition is

```

H = sum_ij (A_ij - k_i k_j / 2m) d(s_i, s_j),

```

where `A_ij = 1` if there is an edge between node `i` and `j`, `k_i` is the degree of

node `i` and `s_i` is the community of node i.

* RBConfiguration.

This is an extension of modularity which includes a resolution parameter [2].

In general, a higher resolution parameter will lead to smaller communities.

The formal definition is

```

H = sum_ij (A_ij - gamma k_i k_j / 2m) d(s_i, s_j),

```

where `gamma` is the resolution value, and the other variables are the same as

for Modularity.

* RBER.

A variant of the previous method that instead of a configuration null-model

uses a Erdös-Rényi null-model in which each edge has the same probability of

appearing [2]. The formal definition is

```

H = sum_ij (A_ij - gamma p) d(s_i, s_j),

```

where `p` is the density of the graph, and the other variables are the same as

for Modularity, with `gamma` a resolution parameter.

* CPM.

This method compares to a fixed resolution parameter, so that it finds

communities that have an internal density higher than the resolution

parameter, and is separated from other communities with a density lower than

the resolution parameter [3].The formal definition is

```

H = sum_ij (A_ij - gamma ) d(s_i, s_j),

```

with `gamma` a resolution parameter, and the other variables are the same as for

Modularity.

* Significance.

This is a probabilistic method based on the idea of assessing the probability

of finding such dense subgraphs in an (ER) random graph [4]. The formal

definition is

```

H = sum_c M_c D(p_c || p)

```

where `M_c` is the number of possible edges in community `c`, i.e. `n_c (n_c - 1)/2`

for undirected graphs and twice that for directed grahs with `n_c` the size of

community `c`, `p_c` is the density of the community `c`, and `p` the general density

of the graph, and `D(x || y)` is the binary Kullback-Leibler divergence.

* Surprise.

Another probabilistic method, but rather than the probability of finding dense

subgraphs, it focuses on the probability of so many edges within communities

[5, 6]. The formal definition is

```

H = m D(q || <q>)

```

where `m` is the number of edges, `q` is the proportion of edges within

communities (i.e. `sum_c m_c / m`) and `<q>` is the expected proportion of edges

within communities in an Erdős–Rényi graph.

INSTALLATION

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

In short, for Unix: ``sudo pip install louvain``.

For Windows: download the binary installers.

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

overly complicated, and you are recommended to use the binary installation files.

There are two things that are needed by this package: the igraph c core library

and the python-igraph python package. For both, please see http://igraph.org.

There are basically two installation modes, similar to the python-igraph package

itself (from which most of the setup.py comes).

1. No C core library is installed yet. The packages will be compiled and linked

statically to an automatically downloaded version of the C core library of

igraph.

2. A C core library is already installed. In this case, the package will link

dynamically to the already installed version. This is probably also the

version that is used by the igraph package, but you may want to double check

this.

In case the python-igraph package is already installed before, make sure that

both use the **same versions**.

The cleanest setup it to install and compile the C core library yourself (make

sure that the header files are also included, e.g. install also the development

package from igraph). Then both the python-igraph package, as well as this

package are compiled and (dynamically) linked to the same C core library.

TROUBLESHOOTING

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

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

you remove the python-igraph package completely, remove the C core library and

remove the louvain package. Then, do a complete reinstall starting from ``pip

install louvain``. In case you want a dynamic library be sure to then install

the C core library from source before. Make sure you **install the same

versions**.

USAGE

=====

There is no standalone version of louvain-igraph, and you will always need

python to access it. There are no plans for developing a standalone version or R

support. So, use python. Please refer to the documentation within the python

package for more details on function calls and parameters.

To start, make sure to import the packages:

```python

import louvain

import igraph as ig

```

We'll create a random graph for testing purposes:

```python

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

```

For simply finding a partition use:

```python

part = louvain.find_partition(G, method='Modularity');

```

In case you want to use a weighted graph, you can store this in an edge

attribute:

```python

G.es['weight'] = 1.0;

part = louvain.find_partition(G, method='Modularity', weight='weight');

```

Please note that not all methods are necessarily capable of handling weighted

graphs.

Notice that ``part`` now contains an additional variable, ``part.quality`` which

stores the quality of the partition as calculated by the used method. You can

always get the quality of the partition using another method by calling

```python

part.significance = louvain.quality(G, partition, method='Significance');

```

You can also find partition for multiplex graphs. For each layer you then

specify the objective function, and the overall objective function is simply the

sum over all layers, weighted by some weight. If we denote by ``q_k`` the quality

of layer ``k`` and the weight by ``w_k``, the overall quality is then ``q = sum_k

w_k q_k``. This can also be useful in case you have negative links. In

principle, this could also be used to detect temporal communities in a dynamic

setting, cf. [8].

For example, assuming you have a graph with positive weights ``G_positive`` and

a graph with negative weights ``G_negative``, and you want to use Modularity for

finding a partition, you can use

```python

membership, quality = louvain.find_partition_multiplex([

louvain.Layer(graph=G_positive, method='Modularity', layer_weight=1.0),

louvain.Layer(graph=G_negative, method='Modularity', layer_weight=-1.0)])

```

Notice the negative layer weight is ``-1.0`` for the negative graph, since we

want those edges to fall between communities rather than within. One particular

problem when using negative links, is that the optimal community is no longer

guaranteed to be connected (it may be a multipartite partition). You may

therefore need the options `consider_comms=ALL_COMMS` to improve the quality of

the partition. Notice that this runs much slower than only considering

neighbouring communities (which is the default).

Various methods (such as Reichardt and Bornholdt's Potts model, or CPM) support

a (linear) resolution parameter, which can be effectively bisected, cf. [5]. You

can do this by calling:

```python

res_parts = louvain.bisect(G, method='CPM', resolution_range=[0,1]);

```

Notice this may take some time to run, as it effectively calls

`louvain.find_partition` for various resolution parameters (depending on the

settings possibly hundreds of times).

Then `res_parts` is a dictionary containing as keys the resolution, and as

values a `NamedTuple` with variables `partition` and `bisect_value`, which

contains the partition and the value at which the resolution was bisected (the

value of the `bisect_func` of the `bisect` function). You could for example plot

the bisection value of all the found partitions by using:

```python

import pandas as pd

import matplotlib.pyplot as plt

res_df = pd.DataFrame({

'resolution': res_parts.keys(),

'bisect_value': [bisect.bisect_value for bisect in res_parts.values()]});

plt.step(res_df['resolution'], res_df['bisect_value']);

plt.xscale('log');

```

REFERENCES

==========

Please cite the references appropriately in case they are used.

1. Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding

of communities in large networks. J. Stat. Mech. 2008, P10008 (2008).

2. Newman, M. & Girvan, M. Finding and evaluating community structure in networks.

Physical Review E 69, 026113 (2004).

3. Reichardt, J. & Bornholdt, S. Partitioning and modularity of graphs with arbitrary

degree distribution. Physical Review E 76, 015102 (2007).

4. Traag, V. A., Van Dooren, P. & Nesterov, Y. Narrow scope for resolution-limit-free

community detection. Physical Review E 84, 016114 (2011).

5. Traag, V. A., Krings, G. & Van Dooren, P. Significant scales in community structure.

Scientific Reports 3, 2930 (2013).

6. Aldecoa, R. & Marín, I. Surprise maximization reveals the community structure

of complex networks. Scientific reports 3, 1060 (2013).

7. Traag, V.A., Aldecoa, R. & Delvenne, J.-C. Detecting communities using Asymptotical

Surprise. Forthcoming (2015).

8. Mucha, P. J., Richardson, T., Macon, K., Porter, M. A. & Onnela, J.-P.

Community structure in time-dependent, multiscale, and multiplex networks.

Science 328, 876–8 (2010).

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Changelog content for this version goes here.

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help | Version | File Type | Upload Date |
---|---|---|---|

louvain-0.5.3-py2.7-linux-x86_64.egg (748.9 kB) Copy SHA256 Checksum SHA256 | 2.7 | Egg | Jun 25, 2015 |

louvain-0.5.3-py3.4-linux-x86_64.egg (749.8 kB) Copy SHA256 Checksum SHA256 | 3.4 | Egg | Jun 25, 2015 |

louvain-0.5.3.tar.gz (48.1 kB) Copy SHA256 Checksum SHA256 | – | Source | Jun 25, 2015 |

louvain-0.5.3.win32-py2.7.msi (393.2 kB) Copy SHA256 Checksum SHA256 | 2.7 | Windows MSI Installer | Jun 25, 2015 |

louvain-0.5.3.win32-py3.4.msi (123.4 kB) Copy SHA256 Checksum SHA256 | 3.4 | Windows MSI Installer | Jun 25, 2015 |

louvain-0.5.3.win-amd64-py2.7.msi (423.9 kB) Copy SHA256 Checksum SHA256 | 2.7 | Windows MSI Installer | Jun 25, 2015 |

louvain-0.5.3.win-amd64-py3.4.msi (134.1 kB) Copy SHA256 Checksum SHA256 | 3.4 | Windows MSI Installer | Jun 25, 2015 |