RNN DBSCAN

version 1.0.1 (1.42 MB) by Trevor Vannoy
MATLAB implementation of the RNN-DBSCAN clustering algorithm

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Updated 20 Aug 2021

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matlab-rnn-dbscan

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This repo contains a MATLAB implementation of the RNN-DBSCAN algorithm by Bryant and Cios. This implementation is based upon the graph-based interpretation presented in their paper.

RNN DBSCAN is a density-based clustering algorithm that uses reverse nearest neighbor counts as an estimate of observation density. It is based upon traversals of the directed k-nearest neighbor graph, and can handle clusters of different densities, unlike DBSCAN. For more details about the algorithm, see the original paper.

Dependencies

  • My knn-graphs MATLAB library
  • Statistics and Machine Learning Toolbox

To run the tests contained in the Jupyter notebook, you will need to install the Jupyter matlab kernel.

To use the NN Descent algorithm to construct the KNN graph used by RNN DBSCAN, you need pynndescent and MATLAB's Python language interface. I recommend using Conda to set up an environment, as MATLAB is picky about which Python versions it supports.

Installation

Install with mpm:

mpm install knn-graphs
mpm install matlab-rnn-dbscan

Manual installation

Usage

RnnDbscan is a class with a single public method, cluster. The results of the clustering operation are stored in read-only public properties.

Creating an RnnDbscan object:

% Create an RnnDbscan object using a 5-nearest-neighbor graph.
% nNeighborsIndex is how many neighbors used to create the knn index, and must be >= nNeighbors + 1
% because the index includes self-edges (each point is it's own nearest neighbor).
nNeighors = 5;
nNeighborsIndex = 6;
rnndbscan = RnnDbscan(data, nNeighbors, nNeighborsIndex);

% Use the NN Descent algorithm to create the knn index; this is much faster than an exhaustive search
rnndbscan = RnnDbscan(data, nNeighbors, nNeighborsIndex, 'Method', 'nndescent');

% Explicitly use an exhaustive search, which is the default
rnndbscan = RnnDbscan(data, nNeighbors, nNeighborsIndex, 'Method', 'knnsearch');

% Use a precomputed knn index
knnidx = knnindex(data, nNeighborsIndex);
rnndbscan = RnnDbscan(data, nNeighbors, knnidx);

Clustering:

rnndbscan.cluster();
% Or
cluster(rnndbscan);

% Inspect clusters, outliers, and labels
rnndbscan.Clusters
rnndbscan.Outliers
rnndbscan.Labels

For more details, see the help text: help RnnDbscan. RNN-DBSCAN tests.ipynb also contains many tests, which can be used as usage examples.

Contributing

All contributions are welcome! Just submit a pull request or open an issue.

Cite As

Trevor Vannoy (2022). RNN DBSCAN (https://github.com/tvannoy/matlab-rnn-dbscan/releases/tag/v1.0.1), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2020a
Compatible with R2020a and later releases
Platform Compatibility
Windows macOS Linux

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To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.