Python SpeakEasy2 package

Provides the SpeakEasy2 community detection algorithm to cluster graph's stored as igraph's data type. The algorithm is described in the Genome Biology article.

This uses a rewrite of the algorithm used in the publication, to see a comparison to the original implementation see the benchmarks

Example:

 import igraph as ig
 import speakeasy2 as se2

 g = ig.Graph.Famous("Zachary")
 memb = se2.cluster(g)

Membership is returned as an igraph.clustering.VertexClustering object. Use print to view the membership:

print(memb)

Clustering with 34 elements and 9 clusters
[0] 0, 1, 2, 3, 7, 12, 13, 17, 19, 21
[1] 14, 15, 18, 20, 22, 32, 33
[2] 8, 30
[3] 26, 29
[4] 11
[5] 23, 24, 25, 27, 31
[6] 9
[7] 28
[8] 4, 5, 6, 10, 16

Or to convert to a python list for use outside of igraph run memb.membership.

From the results, a node ordering can be computed to group nodes in a community together. This can be used as an index and works to display the community structure using a heatmap to view the adjacency matrix.

ordering = se2.order_nodes(g, memb)

SpeakEasy 2 can work with weighted graphs by either passing weights as a list with length equal to the number of edges or by using the igraph attribute table.

g.es["weight"] = [1 for _ in range(g.ecount())]
memb = se2.cluster(g)

By default, SpeakEasy 2 will check if there is an edge attribute associated with the graph named weight and use those as weights. If you want to use a different edge attribute, pass the name of the attribute.

memb = se2.cluster(g, weights="tie_strength")

Or if a graph has a weight edge attribute but you don't want to use them, explicitly pass None to the weights keyword argument.

Subclustering can be used to detect hierarchical community structure.

memb = se2.cluster(g, subcluster=2)

The number determines how many levels to perform community detection at. The default 1 means only to perform community detection at the top level (i.e. no subclustering). When subclustering, membership will be a list of igraph.VertexClustering objects, the top level membership will be the object at index 0.

A few other useful keywords arguments are max_threads, verbose, and seed. The max_thread keyword determines how many processors SpeakEasy 2 is allowed to use. By default the value returned by OpenMP is used. To prevent parallel processing, explicitly pass max_threads = 1 to the method.

The verbose option will cause the algorithm to print out some information about the process.

For reproducible results, the seed option sets the seed of the random number generator. Note: this is a random number generator managed by the underlying C library and is independent of other random number generators that might have been set in python.

Installation

speakeasy2 is available from pypi so it can be installed with pip or other package managers.

pip install --user speakeasy2

Building from source

Compilation depends on a C compiler, CMake, and (optionally) ninja.

Since the igraph package is supplied by the vendored SE2 C library, after cloning the source directory, submodules most be recursively initialized.

git clone "https://github.com/SpeakEasy-2/python-speakeasy2"
cd python-speakeasy2
git submodule update --init --recursive

The CMake calls are wrapped into the python build logic in the build_script.py (this is a poetry specific method for building C extensions). This allows the package to be built using various python build backends. Since this package uses poetry, the suggested way to build the package is invoking poetry build and poetry install, which will install in development mode.

For convenience, the provided Makefile defines the install target to do this and clean-dist to clear all generated files (as well as other targets, see the file for more).

It should now be possible to run scripts through poetry:

poetry run ipython path/to/script.py

Or enter a python repository with the private environment activate in the same way.

poetry run ipython

If you don't want to use poetry, it's possible to build with other method in their standard way. For example python -m build or pip install --editable . should both work.