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PyClustering
pyclustering is a Python, C++ data mining library (clustering
algorithm, oscillatory networks, neural networks). The library provides
Python and C++ implementations (via CCORE library) of each algorithm or
model. CCORE library is a part of pyclustering and supported only for
Linux, Windows and MacOS operating systems.
Version: 0.9.3.1
License: GNU General Public License
E-Mail: pyclustering@yandex.ru
Documentation: https://pyclustering.github.io/docs/0.9.3/html/index.html
Homepage: https://pyclustering.github.io/
PyClustering Wiki: https://github.com/annoviko/pyclustering/wiki
Dependencies
Required packages: scipy, matplotlib, numpy, Pillow
Python version: >=3.5 (32-bit, 64-bit)
C++ version: >= 14 (32-bit, 64-bit)
Performance
Each algorithm is implemented using Python and C/C++ language, if your platform is not supported then the Python
implementation is used, otherwise C/C++. The implementation can be chosen by ccore flag (by default it is always
'True' and it means that the C/C++ implementation is used), for example:
.. code:: python
# As by default - C/C++ is used
xmeans_instance_1 = xmeans(data_points, start_centers, 20, ccore=True);
# The same - C/C++ is used by default
xmeans_instance_2 = xmeans(data_points, start_centers, 20);
# Switch off core - Python is used
xmeans_instance_3 = xmeans(data_points, start_centers, 20, ccore=False);
ccore option runs ccore shared library (core of the pyclustering library). The core is maintained for Linux, Windows and MacOS.
Installation
Installation using pip3 tool:
.. code:: bash
$ pip3 install pyclustering
Manual installation using GCC:
.. code:: bash
# get sources of the pyclustering library, for example, from repository
$ mkdir pyclustering
$ cd pyclustering/
$ git clone https://github.com/annoviko/pyclustering.git .
# compile CCORE library (core of the pyclustering library)
# you can specify platform (32-bit: 'ccore_32bit', 64-bit: 'ccore_64bit')
$ cd ccore/
$ make ccore_64bit # compile CCORE for 64-bit
# make ccore_32bit # compile CCORE for 32-bit
# return to parent folder of the pyclustering library
cd ../
# add current folder to python path
PYTHONPATH=`pwd`
export PYTHONPATH=${PYTHONPATH}
Manual installation using Visual Studio:
- Clone repository from: https://github.com/annoviko/pyclustering.git
- Open folder pyclustering/ccore
- Open Visual Studio project ccore.sln
- Select solution platform: 'x86' or 'x64'
- Build 'ccore' project.
- Add pyclustering folder to python path.
Proposals, Questions, Bugs
In case of any questions, proposals or bugs related to the pyclustering please contact to pyclustering@yandex.ru or create an issue here.
PyClustering Status
+----------------------+------------------------------+------------------------------------+--------------------------------+
| Branch | master | 0.9.dev | 0.9.3.rel |
+======================+==============================+====================================+================================+
| Build (Linux, MacOS) | |Build Status Linux MacOS| | |Build Status Linux MacOS 0.9.dev| | |Build Status Linux 0.9.3.rel| |
+----------------------+------------------------------+------------------------------------+--------------------------------+
| Build (Win) | |Build Status Win| | |Build Status Win 0.9.dev| | |Build Status Win 0.9.3.rel| |
+----------------------+------------------------------+------------------------------------+--------------------------------+
| Code Coverage | |Coverage Status| | |Coverage Status 0.9.dev| | |Coverage Status 0.9.3.rel| |
+----------------------+------------------------------+------------------------------------+--------------------------------+
Cite the Library
If you are using pyclustering library in a scientific paper, please, cite the library:
Novikov, A., 2019. PyClustering: Data Mining Library. Journal of Open Source Software, 4(36), p.1230. Available at: http://dx.doi.org/10.21105/joss.01230.
BibTeX entry:
.. code::
@article{Novikov2019,
doi = {10.21105/joss.01230},
url = {https://doi.org/10.21105/joss.01230},
year = 2019,
month = {apr},
publisher = {The Open Journal},
volume = {4},
number = {36},
pages = {1230},
author = {Andrei Novikov},
title = {{PyClustering}: Data Mining Library},
journal = {Journal of Open Source Software}
}
Brief Overview of the Library Content
Clustering algorithms and methods (module pyclustering.cluster):
+------------------------+---------+-----+
| Algorithm | Python | C++ |
+========================+=========+=====+
| Agglomerative | ✓ | ✓ |
+------------------------+---------+-----+
| BANG | ✓ | |
+------------------------+---------+-----+
| BIRCH | ✓ | |
+------------------------+---------+-----+
| BSAS | ✓ | ✓ |
+------------------------+---------+-----+
| CLARANS | ✓ | |
+------------------------+---------+-----+
| CLIQUE | ✓ | ✓ |
+------------------------+---------+-----+
| CURE | ✓ | ✓ |
+------------------------+---------+-----+
| DBSCAN | ✓ | ✓ |
+------------------------+---------+-----+
| Elbow | ✓ | ✓ |
+------------------------+---------+-----+
| EMA | ✓ | |
+------------------------+---------+-----+
| Fuzzy C-Means | ✓ | ✓ |
+------------------------+---------+-----+
| GA (Genetic Algorithm) | ✓ | ✓ |
+------------------------+---------+-----+
| G-Means | ✓ | ✓ |
+------------------------+---------+-----+
| HSyncNet | ✓ | ✓ |
+------------------------+---------+-----+
| K-Means | ✓ | ✓ |
+------------------------+---------+-----+
| K-Means++ | ✓ | ✓ |
+------------------------+---------+-----+
| K-Medians | ✓ | ✓ |
+------------------------+---------+-----+
| K-Medoids | ✓ | ✓ |
+------------------------+---------+-----+
| MBSAS | ✓ | ✓ |
+------------------------+---------+-----+
| OPTICS | ✓ | ✓ |
+------------------------+---------+-----+
| ROCK | ✓ | ✓ |
+------------------------+---------+-----+
| Silhouette | ✓ | ✓ |
+------------------------+---------+-----+
| SOM-SC | ✓ | ✓ |
+------------------------+---------+-----+
| SyncNet | ✓ | ✓ |
+------------------------+---------+-----+
| Sync-SOM | ✓ | |
+------------------------+---------+-----+
| TTSAS | ✓ | ✓ |
+------------------------+---------+-----+
| X-Means | ✓ | ✓ |
+------------------------+---------+-----+
Oscillatory networks and neural networks (module pyclustering.nnet):
+--------------------------------------------------------------------------------+---------+-----+
| Model | Python | C++ |
+================================================================================+=========+=====+
| CNN (Chaotic Neural Network) | ✓ | |
+--------------------------------------------------------------------------------+---------+-----+
| fSync (Oscillatory network based on Landau-Stuart equation and Kuramoto model) | ✓ | |
+--------------------------------------------------------------------------------+---------+-----+
| HHN (Oscillatory network based on Hodgkin-Huxley model) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| Hysteresis Oscillatory Network | ✓ | |
+--------------------------------------------------------------------------------+---------+-----+
| LEGION (Local Excitatory Global Inhibitory Oscillatory Network) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| PCNN (Pulse-Coupled Neural Network) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| SOM (Self-Organized Map) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| Sync (Oscillatory network based on Kuramoto model) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| SyncPR (Oscillatory network for pattern recognition) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
| SyncSegm (Oscillatory network for image segmentation) | ✓ | ✓ |
+--------------------------------------------------------------------------------+---------+-----+
Graph Coloring Algorithms (module pyclustering.gcolor):
+------------------------+---------+-----+
| Algorithm | Python | C++ |
+========================+=========+=====+
| DSatur | ✓ | |
+------------------------+---------+-----+
| Hysteresis | ✓ | |
+------------------------+---------+-----+
| GColorSync | ✓ | |
+------------------------+---------+-----+
Containers (module pyclustering.container):
+------------------------+---------+-----+
| Algorithm | Python | C++ |
+========================+=========+=====+
| KD Tree | ✓ | ✓ |
+------------------------+---------+-----+
| CF Tree | ✓ | |
+------------------------+---------+-----+
Examples in the Library
The library contains examples for each algorithm and oscillatory network model:
Clustering examples: pyclustering/cluster/examples
Graph coloring examples: pyclustering/gcolor/examples
Oscillatory network examples: pyclustering/nnet/examples
.. image:: https://github.com/annoviko/pyclustering/blob/master/docs/img/example_cluster_place.png
:alt: Where are examples?
Code Examples
Data clustering by CURE algorithm
.. code:: python
from pyclustering.cluster import cluster_visualizer;
from pyclustering.cluster.cure import cure;
from pyclustering.utils import read_sample;
from pyclustering.samples.definitions import FCPS_SAMPLES;
# Input data in following format [ [0.1, 0.5], [0.3, 0.1], ... ].
input_data = read_sample(FCPS_SAMPLES.SAMPLE_LSUN);
# Allocate three clusters.
cure_instance = cure(input_data, 3);
cure_instance.process();
clusters = cure_instance.get_clusters();
# Visualize allocated clusters.
visualizer = cluster_visualizer();
visualizer.append_clusters(clusters, input_data);
visualizer.show();
Data clustering by K-Means algorithm
.. code:: python
from pyclustering.cluster.kmeans import kmeans, kmeans_visualizer
from pyclustering.cluster.center_initializer import kmeans_plusplus_initializer
from pyclustering.samples.definitions import FCPS_SAMPLES
from pyclustering.utils import read_sample
# Load list of points for cluster analysis.
sample = read_sample(FCPS_SAMPLES.SAMPLE_TWO_DIAMONDS)
# Prepare initial centers using K-Means++ method.
initial_centers = kmeans_plusplus_initializer(sample, 2).initialize()
# Create instance of K-Means algorithm with prepared centers.
kmeans_instance = kmeans(sample, initial_centers)
# Run cluster analysis and obtain results.
kmeans_instance.process()
clusters = kmeans_instance.get_clusters()
final_centers = kmeans_instance.get_centers()
# Visualize obtained results
kmeans_visualizer.show_clusters(sample, clusters, final_centers)
Data clustering by OPTICS algorithm
.. code:: python
from pyclustering.cluster import cluster_visualizer
from pyclustering.cluster.optics import optics, ordering_analyser, ordering_visualizer
from pyclustering.samples.definitions import FCPS_SAMPLES
from pyclustering.utils import read_sample
# Read sample for clustering from some file
sample = read_sample(FCPS_SAMPLES.SAMPLE_LSUN)
# Run cluster analysis where connectivity radius is bigger than real
radius = 2.0
neighbors = 3
amount_of_clusters = 3
optics_instance = optics(sample, radius, neighbors, amount_of_clusters)
# Performs cluster analysis
optics_instance.process()
# Obtain results of clustering
clusters = optics_instance.get_clusters()
noise = optics_instance.get_noise()
ordering = optics_instance.get_ordering()
# Visualize ordering diagram
analyser = ordering_analyser(ordering)
ordering_visualizer.show_ordering_diagram(analyser, amount_of_clusters)
# Visualize clustering results
visualizer = cluster_visualizer()
visualizer.append_clusters(clusters, sample)
visualizer.show()
Simulation of oscillatory network PCNN
.. code:: python
from pyclustering.nnet.pcnn import pcnn_network, pcnn_visualizer
# Create Pulse-Coupled neural network with 10 oscillators.
net = pcnn_network(10)
# Perform simulation during 100 steps using binary external stimulus.
dynamic = net.simulate(50, [1, 1, 1, 0, 0, 0, 0, 1, 1, 1])
# Allocate synchronous ensembles from the output dynamic.
ensembles = dynamic.allocate_sync_ensembles()
# Show output dynamic.
pcnn_visualizer.show_output_dynamic(dynamic, ensembles)
Simulation of chaotic neural network CNN
.. code:: python
from pyclustering.cluster import cluster_visualizer
from pyclustering.samples.definitions import SIMPLE_SAMPLES
from pyclustering.utils import read_sample
from pyclustering.nnet.cnn import cnn_network, cnn_visualizer
# Load stimulus from file.
stimulus = read_sample(SIMPLE_SAMPLES.SAMPLE_SIMPLE3)
# Create chaotic neural network, amount of neurons should be equal to amount of stimulus.
network_instance = cnn_network(len(stimulus))
# Perform simulation during 100 steps.
steps = 100
output_dynamic = network_instance.simulate(steps, stimulus)
# Display output dynamic of the network.
cnn_visualizer.show_output_dynamic(output_dynamic)
# Display dynamic matrix and observation matrix to show clustering phenomenon.
cnn_visualizer.show_dynamic_matrix(output_dynamic)
cnn_visualizer.show_observation_matrix(output_dynamic)
# Visualize clustering results.
clusters = output_dynamic.allocate_sync_ensembles(10)
visualizer = cluster_visualizer()
visualizer.append_clusters(clusters, stimulus)
visualizer.show()
Illustrations
Cluster allocation on FCPS dataset collection by DBSCAN:
.. image:: https://github.com/annoviko/pyclustering/blob/master/docs/img/fcps_cluster_analysis.png
:alt: Clustering by DBSCAN
Cluster allocation by OPTICS using cluster-ordering diagram:
.. image:: https://github.com/annoviko/pyclustering/blob/master/docs/img/optics_example_clustering.png
:alt: Clustering by OPTICS
Partial synchronization (clustering) in Sync oscillatory network:
.. image:: https://github.com/annoviko/pyclustering/blob/master/docs/img/sync_partial_synchronization.png
:alt: Partial synchronization in Sync oscillatory network
Cluster visualization by SOM (Self-Organized Feature Map)
.. image:: https://github.com/annoviko/pyclustering/blob/master/docs/img/target_som_processing.png
:alt: Cluster visualization by SOM
.. _scikit-learn: https://scikit-learn.org/stable/
.. _ELKI: https://elki-project.github.io/
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