HG-means clustering package


Keywords
clustering, optimization
License
GPL-3.0
Install
pip install hgpack==1.1.5

Documentation

HG-means

Source code of HG-means clustering, an efficient hybrid genetic algorithm proposed for the minimum sum-of-squares clustering (MSSC). This population-based metaheuristic uses K-means as a local search in combination with crossover, mutation, and diversification operators.

As HG-means algorithm uses K-means, we included the fundamental source files of the fast K-means implementation of Greg Hamerly (to whom we are grateful for making the source code available) in this repository, under the folder /hamerly. Original files and complete source code of Greg Hamerly K-means can be found at: https://github.com/ghamerly/fast-kmeans.

For the exact crossover, HG-means uses the implementation of Dlib (https://github.com/davisking/dlib) for solving an assignment problem. Dlib files are included in /dlib-master folder.

HG-means clustering is available as a C++ code, as well as a Python package.

Related Article

HG-means: A scalable hybrid genetic algorithm for minimum sum-of-squares clustering. D. Gribel and T. Vidal, 2019. Pattern Recognition, https://doi.org/10.1016/j.patcog.2018.12.022

Installation and Run

C++

To run the algorithm in C++, go to /hgmeans folder and try the following sequence of commands:

> make

> ./hgmeans 'dataset_path' pi_min n2 it [nb_clusters] 'w'

Example

> make

> ./hgmeans 'data/iris.txt' 10 5000 1 2 5 10 'w'

This script executes HG-means clustering for "iris" dataset, with 10 solutions in population, a maximum of 5000 iterations, 1 iteration (algorithm repetition), and 2, 5 and 10 clusters.

Important: You can provide a ground-truth file with the labels of clusters. In this case, make sure that a file with the same name of the dataset and '.label' extension is placed in the same folder of the dataset. If this file is provided, HG-means clustering will compute clustering performance metrics. See section Data format to check the expected data format for datasets and labels files.

Parameters of the algorithm

dataset_path: The path of dataset.

pi_min (default = 10): Population size. Determines the size of the population in the genetic algorithm.

n2 (default = 5000): Maximum number of iterations. Determines the total number of iterations the algorithm will take.

it (default = 1): The number of independent repetitions of the algorithm.

[nb_clusters]: The list with number of clusters. You can pass multiple values, separated by a single space.

w: A flag for saving the results in a file. Use 'w' if you wish to active this feature, or leave it blank. Important: the output files are saved in your current directory, within the folder hgm_out.

Python

HG-means is also available as a Python package. To install HG-means, run the following installation command:

> python -m pip install hgmeans

Important: Check your user permissions for pip installation. You may need root user credentials.

For Windows users who do not have a C++ compiler, it may be required an installation of C++ Build tools, which can be downloaded here: https://go.microsoft.com/fwlink/?LinkId=691126

That is it! Now, open your Python interface, import the package and create an instance of HG-means. To execute it, just call the function run() with the corresponding parameters. See an example below:

>>> import hgmeans

>>> demo = hgmeans.PyHGMeans()

>>> demo.run('data/iris.txt', 10, 5000, 1, [2,5,10], 'w')

This script executes HG-means clustering for the "iris" dataset, with 10 solutions in population, a maximum of 5000 iterations, 1 repetition, and 2, 5 and 10 clusters. Here the number of clusters is passed in an array, so values are separated by commas.

Data format

Dataset files. In the first line of a dataset file, the number of data points (n) and the dimensionality of the data (d) is set, separated by a single space. The remaining lines correspond to the coordinates of data points. Each line contains the values of the d features of a sample, where x_ij correspond to the j-th feature of the i-th sample of the data. Each feature value is separated by a single space, as depicted in the scheme below:

n d
x_11 x_12 x_13 ... x_1d
x_21 x_22 x_23 ... x_2d
.... .... .... ... ....
x_n1 x_n2 x_n3 ... x_nd

Some datasets are provided in /data folder in HG-means repository.

Labels files. The content of a labels file exhibits the cluster of each sample of the dataset according to ground-truth, where y_i correspond to the label of the i-th sample:

y_1

y_2

...

y_n

Important: Labels files must have the .label extension. Some labels are provided in /data folder in HG-means repository.