ClusterEnsembles

A Python package for cluster ensembles. Cluster ensembles generate a single consensus clustering label by using base labels obtained from multiple clustering algorithms. The consensus clustering label stably achieves a high clustering performance.

This package was originally authored by Takehiro Sano but has since been removed from PyPi. This a cloned version I am maintaining. All original code and functionality is unchanged, it is just maintained, tested, and published from here.

Installation

pip install ensembleclustering

Usage

CE.cluster_ensembles is used as follows.

>> > import numpy as np

>> > import ensembleclustering as CE

>> > label1 = np.array([1, 1, 1, 2, 2, 3, 3])

>> > label2 = np.array([2, 2, 2, 3, 3, 1, 1])

>> > label3 = np.array([4, 4, 2, 2, 3, 3, 3])

>> > label4 = np.array([1, 2, np.nan, 1, 2, np.nan, np.nan])  # `np.nan`: missing value

>> > labels = np.array([label1, label2, label3, label4])

>> > label_ce = CE.cluster_ensembles(labels)

>> > print(label_ce)
[1 1 1 2 2 0 0]

Parameters

• labels: numpy.ndarray

  Labels generated by multiple clustering algorithms such as K-Means.

  Note: Assume that the length of each label is the same.

• nclass: int, default=None

  Number of classes in a consensus clustering label. If nclass=None, set the maximum number of classes in each label except missing values. In other words, set nclass=3 automatically in the above.

• solver: {'cspa', 'hgpa', 'mcla', 'hbgf', 'nmf', 'all'}, default='hbgf'

  'cspa': Cluster-based Similarity Partitioning Algorithm [1].

  'hgpa': HyperGraph Partitioning Algorithm [1].

  'mcla': Meta-CLustering Algorithm [1].

  'hbgf': Hybrid Bipartite Graph Formulation [2].

  'nmf': NMF-based consensus clustering [3].

  'all': The consensus clustering label with the largest objective function value [1] is returned among the results of all solvers.

  

  Note: Please use 'hbgf' for large-scale labels.

• random_state: int, default=None

  Used for 'hgpa', 'mcla', and 'nmf'. Please pass an integer for reproducible results.

• verbose: bool, default=False

  Whether to be verbose.

Return

• label_ce: numpy.ndarray

  A consensus clustering label generated by cluster ensembles.

Example

tsano430/egnmf: https://github.com/tsano430/egnmf

Similar Package

GGiecold/Cluster_Ensembles: https://github.com/GGiecold/Cluster_Ensembles

References

[1] A. Strehl and J. Ghosh, "Cluster ensembles -- a knowledge reuse framework for combining multiple partitions," Journal of Machine Learning Research, vol. 3, pp. 583-617, 2002.

[2] X. Z. Fern and C. E. Brodley, "Solving cluster ensemble problems by bipartite graph partitioning," In Proceedings of the Twenty-First International Conference on Machine Learning, p. 36, 2004.

[3] T. Li, C. Ding, and M. I. Jordan, "Solving consensus and semi-supervised clustering problems using nonnegative matrix factorization," In Proceedings of the Seventh IEEE International Conference on Data Mining, pp. 577-582, 2007.

[4] J. Ghosh and A. Acharya, "Cluster ensembles," Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, vol. 1, no. 4, pp. 305-315, 2011.