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Scalable and parallel programming implementation of Affinity Propagation clustering

Project Description

Overview

A scalable and concurrent programming implementation of Affinity Propagation clustering.

Affinity Propagation is a clustering algorithm based on passing messages between data-points.

Storing and updating matrices of ‘affinities’, ‘responsibilities’ and ‘similarities’ between samples can be memory-intensive. We address this issue through the use of an HDF5 data structure, allowing Affinity Propagation clustering of arbitrary large data-sets, where other Python implementations would return a MemoryError on most machines.

We also significantly speed up the computations by splitting them up across subprocesses, thereby taking full advantage of the resources of multi-core processors and bypassing the Global Interpreter Lock of the standard Python interpreter, CPython.

Installation and Requirements

Concurrent_AP requires Python 2.7 along with the following packages and a few modules from the Standard Python Library:

  • NumPy >= 1.9
  • psutil
  • PyTables
  • scikit-learn
  • setuptools

It is suggested that you check that the required dependencies are installed, although the pip command below should do this automatically for you. You can indeed most conveniently download Concurrent_AP from the official Python Package Index (PyPI) as follows:

  • open a terminal window;
  • type in the command pip install Concurrent_AP.

The code herewith has been tested on Fedora, OS X and Ubuntu and should work fine on any other member of the Unix-like family of operating systems.

Usage and Command Line Options

See the docstrings associated to each function of the Concurrent_AP module for more information and an understanding of how different tasks are organized and shared among subprocesses.

Usage: Concurrent_AP [options] file_name, where file_name denotes the path where the data to be processed by Affinity Propagation clustering is held. The data must consist in tab-separated rows of samples, each column corresponding to a particular feature.

  • -c or --convergence: specify the number of iterations without change in the number of clusters that signals convergence (defaults to 15);
  • -d or --damping: the damping parameter of Affinity Propagation (defaults to 0.5);
  • -f or --file: option to specify the file name or file handle of the hierarchical data format where the matrices involved in Affinity Propagation clustering will be stored (defaults to a temporary file);
  • -i or --iterations: maximum number of message-passing iterations (defaults to 200);
  • -m or --multiprocessing: the number of processes to use;
  • -p or --preference: the preference parameter of Affinity Propagation (if not specified, will be determined as the median of the distribution of pairwise L2 Euclidean distances between samples);
  • -s or --similarities: determine if a similarity matrix has been pre-computed and stored in the HDF5 data structure accessible at the location specified through the command line option -f or --file (see above);
  • -v or --verbose: whether to be verbose.

Demo of Concurrent_AP

The following few lines illustrate the use of Concurrent_AP on the ‘Iris data-set’ from the UCI Machine Learning Repository. While the number of samples is here way too small for the benefits of the present multi-tasking implementation and the use of an HDF5 data structure to come fully into play, this data-set has the advantage of being well-known and prone to a quick comparison with scikit-learn’s version of Affinity Propagation clustering.

  • In a Python interpreter console, enter the following few lines, whose purpose is to create a file containing the Iris data-set that will be later subjected to Affinity Propagation clustering via Concurrent_AP:
>>> import numpy as np
>>> from sklearn import datasets

>>> iris = datasets.load_iris()
>>> data = iris.data
>>> with open('./iris_data.txt', 'w') as f:
       np.savetxt(f, data, fmt = '%.4f', delimiter = '\t')
  • Open a terminal window.
  • Type in Concurrent_AP --preference 5.47 --v iris_data.txt or simply Concurrent_AP iris_data.txt.

The latter will automatically compute a preference parameter from the data-set.

When the rounds of message-passing among data-points have completed, a folder containing a file of cluster labels and a file of cluster centers indices both in tab-separated format is created in your current working directory.

Reference

Brendan J. Frey and Delbert Dueck. “Clustering by Passing Messages between Data Points”, Science Feb. 2007

Release History

Release History

This version
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1.4

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1.3

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1.2

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