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Self-organizing maps in Python
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Self-organizing maps in Python. This is just an alternative implementation of Kohonen's self-organzing maps. Some sort of playground. If you want to self-organizing maps in production environment I recommend to use SciPy.


In the following example we create a SOM with 4x4 nodes, weight vectors with five components. Each component is initially filled with random_fill (assigns random number between 0 and 1).

from som import SOM
from fill_functions import random_fill
from distance_functions import euclidean
from damping_functions import exponentional_damping
from neighbourhood_functions import mexican_hat_with_sigma

som = SOM(n = 4, dimensions = 5, fill = random_fill)

samples = [[random.gauss(m, 0.1) for e in range(0, 5)] 
    for m in range(0, 20) 
    for sample in range(0,10)]


The samples are pseudo random numbers with gauss distribution. We sample 10 times 20 gauss distributions with an expected value of 0,1,2...20. Variance is 0.1 for each distribution.


We train our SOM by using a for-loop iterating over the samples and train each sample as a target with a given learn-rate, distance and neighbourhood function. The learn-rate is a factor of how much the weight vectors of nodes are pulled to the sample vector. The learn-rate is given by a exponentional damping function with a start, end, t, tmax parameters. As the index of the sample to train increases the learn-rate decreases.

for index in range(0, len(samples)):
    learn_rate = exponentional_damping(start = 1.0, end = 0.1, t = float(index), tmax = len(samples)) 
    sigma = exponentional_damping(start = 1.0, end = 0.1, t = float(index), tmax = len(samples))
    mh = mexican_hat_with_sigma(sigma)

    som.train(target = samples[index], rate = learn_rate, distance = euclidean, nf = mh)

The neighbourhood function in this example is named mexican hat function. The parameter sigma of this function influences the radius of neighbourhood. Keep in mind, that the mexican hat function is continuous. See the files distance_functions and neighbourhood_functions and damping_functions for available functions to experiment with. If you want to inspect the weight matrix, you're able to retrieve the weight matrix by calling get_matrix().


Allright, lets query the trained SOM. The query method needs a given target and distance function to determine the winner node in the SOM. The returned value is a tuple which consists of i, j indices of the winner node and distance to target.

for sample in samples:
    winner = som.query(target = sample, distance = euclidean)
    print winner


This file is part of sompy.

sompy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

sompy is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with sompy. If not, see

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