/minisom

:red_circle: MiniSom is a minimalistic implementation of the Self Organizing Maps

Primary LanguagePython

MiniSom

Self Organizing Maps

MiniSom is a minimalistic and Numpy based implementation of the Self Organizing Maps (SOM). SOM is a type of Artificial Neural Network able to convert complex, nonlinear statistical relationships between high-dimensional data items into simple geometric relationships on a low-dimensional display. Minisom is designed to allow researchers to easily build on top of it and to give students the ability to quickly grasp its details.

Updates about MiniSom are posted on Twitter.

Installation

Just use pip:

pip install minisom

or download MiniSom to a directory of your choice and use the setup script:

git clone https://github.com/JustGlowing/minisom.git
python setup.py install

How to use it

In order to use MiniSom you need your data organized as a Numpy matrix where each row corresponds to an observation or as list of lists like the following:

data = [[ 0.80,  0.55,  0.22,  0.03],
        [ 0.82,  0.50,  0.23,  0.03],
        [ 0.80,  0.54,  0.22,  0.03],
        [ 0.80,  0.53,  0.26,  0.03],
        [ 0.79,  0.56,  0.22,  0.03],
        [ 0.75,  0.60,  0.25,  0.03],
        [ 0.77,  0.59,  0.22,  0.03]]

Then you can train MiniSom just as follows:

from minisom import MiniSom    
som = MiniSom(6, 6, 4, sigma=0.3, learning_rate=0.5) # initialization of 6x6 SOM
som.train(data, 100) # trains the SOM with 100 iterations

You can obtain the position of the winning neuron on the map for a given sample as follows:

som.winner(data[0])

For an overview of all the features implemented in minisom you can browse the following examples: https://github.com/JustGlowing/minisom/tree/master/examples

Export a SOM and load it again

A model can be saved using pickle as follows

import pickle
som = MiniSom(7, 7, 4)

# ...train the som here

# saving the som in the file som.p
with open('som.p', 'wb') as outfile:
    pickle.dump(som, outfile)

and can be loaded as follows

with open('som.p', 'rb') as infile:
    som = pickle.load(infile)

Note that if a lambda function is used to define the decay factor MiniSom will not be pickable anymore.

Examples

Here are some of the charts you'll see how to generate in the examples:
Seeds map Class assignment
Handwritteng digits mapping Hexagonal Topology som hexagonal toplogy
Color quantization Outliers detection

Other tutorials

How to cite MiniSom

@misc{vettigliminisom,
  title={MiniSom: minimalistic and NumPy-based implementation of the Self Organizing Map},
  author={Giuseppe Vettigli},
  note={GitHub.[Online]. Available: https://github.com/JustGlowing/minisom/},
}

Who uses Minisom?

Compatibility notes

Minisom has been tested under Python 3.8.0.

License

This program is distributed in the hope that it will be useful, but without warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

MiniSom by Giuseppe Vettigli is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/.

License