zachwill / hdbscan

A high performance implementation of HDBSCAN clustering.

HDBSCAN

HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection.

Based on the paper:

R. Campello, D. Moulavi, and J. Sander, Density-Based Clustering Based on Hierarchical Density Estimates In: Advances in Knowledge Discovery and Data Mining, Springer, pp 160-172. 2013

How to use HDBSCAN

The hdbscan package inherits from sklearn classes, and thus drops in neatly next to other sklearn clusterers with an identical calling API. Similarly it supports input in a variety of formats: an array (or pandas dataframe, or sparse matrix) of shape (num_samples x num_features); an array (or sparse matrix) giving a distance matrix between samples.

import hdbscan

clusterer = hdbscan.HDBSCAN(min_cluster_size=10)
cluster_labels = clusterer.fit_predict(data)

Note that clustering larger datasets will require significant memory (as with any algorithm that needs all pairwise distances). Support for low memory/better scaling is planned but not yet implemented.

Installing

Fast install

pip install hdbscan

For a manual install get this package:

wget https://github.com/lmcinnes/hdbscan/archive/master.zip
unzip master.zip
rm master.zip
cd hdbscan-master

Install the requirements

sudo pip install -r requirements.txt

Install the package

python setup.py install

Licensing

The hdbscan package is BSD licensed. Enjoy.