som-pbc 1.0.2
self organizing maps with periodic boundary conditions
License: MIT
Keywords: SOM embedding machine learning chemoinformatics bioinformatics datascience descriptor similarity

som-pbc README
==============
.. image:: https://img.shields.io/pypi/v/som-pbc.svg
   :target: https://pypi.org/project/som-pbc/
   :alt: pypi version

.. image:: https://readthedocs.org/projects/som-pbc/badge/?version=latest
   :target: https://som-pbc.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

A simple self-organizing map implementation in Python with periodic
boundary conditions.

Self-organizing maps are also called Kohonen maps and were invented by
Teuvo Kohonen.[1] They are an unsupervised machine learning technique to
efficiently create spatially organized internal representations of
various types of data. For example, SOMs are well-suited for the
visualization of high-dimensional data.

This is a simple implementation of SOMs in Python. This SOM has periodic
boundary conditions and therefore can be imagined as a "donut". The
implementation uses ``numpy``, ``scipy``, ``scikit-learn`` and
``matplotlib``.

Installation
~~~~~~~~~~~~

``som-pbc`` can be installed from pypi using pip::

    pip install som-pbc

To upgrade ``som-pbc`` to the latest version, run::

    pip install --upgrade som-pbc

Usage
~~~~~

Then you can import and use the ``SOM`` class as follows:

.. code:: python

    import numpy as np
    from som import SOM

    # generate some random data with 36 features
    data1 = np.random.normal(loc=-.25, scale=0.5, size=(500, 36))
    data2 = np.random.normal(loc=.25, scale=0.5, size=(500, 36))
    data = np.vstack((data1, data2))

    som = SOM(10, 10)  # initialize a 10 by 10 SOM
    som.fit(data, 10000, save_e=True, interval=100)  # fit the SOM for 10000 epochs, save the error every 100 steps
    som.plot_error_history(filename='images/som_error.png')  # plot the training error history

    targets = np.array(500 * [0] + 500 * [1])  # create some dummy target values

    # now visualize the learned representation with the class labels
    som.plot_point_map(data, targets, ['Class 0', 'Class 1'], filename='images/som.png')
    som.plot_class_density(data, targets, t=0, name='Class 0', colormap='Greens', filename='images/class_0.png')
    som.plot_distance_map(colormap='Blues', filename='images/distance_map.png')  # plot the distance map after training

    # predicting the class of a new, unknown datapoint
    datapoint = np.random.normal(loc=.25, scale=0.5, size=(1, 36))
    print("Labels of neighboring datapoints: ", som.get_neighbors(datapoint, data, targets, d=0))

    # transform data into the SOM space
    newdata = np.random.normal(loc=.25, scale=0.5, size=(10, 36))
    transformed = som.transform(newdata)
    print("Old shape of the data:", newdata.shape)
    print("New shape of the data:", transformed.shape)

Training Error:
^^^^^^^^^^^^^^^

.. figure:: https://github.com/alexarnimueller/som/blob/master/docs/_static/som_error.png?raw=true
   :alt: Training Error

Point Map:
^^^^^^^^^^

.. figure:: https://github.com/alexarnimueller/som/blob/master/docs/_static/som.png?raw=true
   :alt: Point Map

Class Density:
^^^^^^^^^^^^^^

.. figure:: https://github.com/alexarnimueller/som/blob/master/docs/_static/class_0.png?raw=true
   :alt: Class Density Map

Distance Map:
^^^^^^^^^^^^^

.. figure:: https://github.com/alexarnimueller/som/blob/master/docs/_static/distance_map.png?raw=true
   :alt: Distance Map

The same way you can handle your own data.

Methods / Functions
~~~~~~~~~~~~~~~~~~~

The ``SOM`` class has the following methods:

- ``initialize(data, how='pca')``: initialize the SOM, either via Eigenvalues (``pca``) or randomly (``random``)
- ``winner(vector)``: compute the winner neuron closest to a given data point in ``vector`` (Euclidean distance)
- ``cycle(vector)``: perform one iteration in adapting the SOM towards the chosen data point in ``vector``
- ``fit(data, epochs=0, save_e=False, interval=1000, decay='hill')``: train the SOM on the given ``data`` for several ``epochs``
- ``transform(data)``: transform given ``data`` in to the SOM space
- ``distance_map(metric='euclidean')``: get a map of every neuron and its distances to all neighbors based on the neuron weights
- ``winner_map(data)``: get the number of times, a certain neuron in the trained SOM is winner for the given ``data``
- ``winner_neurons(data)``: for every data point, get the winner neuron coordinates
- ``som_error(data)``: calculates the overall error as the average difference between the winning neurons and the ``data``
- ``get_neighbors(datapoint, data, labels, d=0)``: get the labels of all ``data`` examples that are ``d`` neurons away from ``datapoint`` on the map
- ``save(filename)``: save the whole SOM instance into a pickle file
- ``load(filename)``: load a SOM instance from a pickle file
- ``plot_point_map(data, targets, targetnames, filename=None, colors=None, markers=None, density=True)``: visualize the som with all data as points around the neurons
- ``plot_density_map(data, filename=None, internal=False)``: visualize the data density in different areas of the SOM.
- ``plot_class_density(data, targets, t, name, colormap='Oranges', filename=None)``: plot a density map only for the given class
- ``plot_distance_map(colormap='Oranges', filename=None)``: visualize the disance of the neurons in the trained SOM
- ``plot_error_history(color='orange', filename=None)``: visualize the training error history after training (fit with ``save_e=True``)

References:
~~~~~~~~~~~

[1] Kohonen, T. Self-Organized Formation of Topologically Correct
Feature Maps. Biol. Cybern. 1982, 43 (1), 59–69.

This work was partially inspired by `ramalina's som
implementation <https://github.com/ramarlina/som>`__ and `JustGlowing's
minisom <https://github.com/JustGlowing/minisom>`__.

Documentation:
~~~~~~~~~~~~~~

Documentation for som-pbc is hosted on `readthedocs.io <https://som-pbc.readthedocs.io/en/latest>`__.