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Python package for unsupervised, supervised and semi-supervised self-organizing maps (SOM)

Project description

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SuSi: SUpervised Self-organIzing maps in Python

Python package for unsupervised, supervised and semi-supervised self-organizing maps (SOM)

Description

We present the SuSi package for Python. It includes a fully functional SOM for unsupervised, supervised and semi-supervised tasks. The class structure is set up as follows:

  • SOMClustering: Unsupervised SOM for clustering

    • SOMEstimator: Base class for supervised and semi-supervised SOMs

      • SOMRegressor: Regression SOM

      • SOMClassifier: Classification SOM

License:

3-Clause BSD license

Author:

Felix M. Riese

Citation:

see Citation and in the bibtex file

Documentation:

Documentation

Installation:

Installation guidelines

Paper:

arXiv:1903.11114

Installation

pip install susi

More information can be found in the installation guidelines.

Examples

A collection of code examples can be found in the documentation. Code examples as Jupyter Notebooks can be found here:

Citation

The bibtex file including both references is available here.

Paper:

Felix M. Riese and S. Keller, “SUSI: Supervised Self-Organizing Maps for Regression and Classification in Python”, arXiv:1903.11114, 2019. Submitted to an ISPRS conference.

@article{riesekeller2019susi,
    author = {Riese, Felix~M. and Keller, Sina},
    title = {SUSI: Supervised Self-Organizing Maps for Regression and Classification in Python},
    year = {2019},
    archivePrefix = {arXiv},
    eprint = {1903.11114},
    primaryClass = {cs.LG},
    url = {https://arxiv.org/abs/1903.11114}
}

Code:

Felix M. Riese, “SuSi: SUpervised Self-organIzing maps in Python”, 10.5281/zenodo.2609130, 2019.

https://zenodo.org/badge/DOI/10.5281/zenodo.2609130.svg
@misc{riese2019susicode,
    author = {Riese, Felix~M.},
    title = {{SuSi: SUpervised Self-organIzing maps in Python}},
    year = {2019},
    DOI = {10.5281/zenodo.2609130},
    publisher = {Zenodo},
    howpublished = {\href{https://doi.org/10.5281/zenodo.2609130}{doi.org/10.5281/zenodo.2609130}}
}

Change Log

[1.0.7] - 2019-11-28

  • [ADDED] Optional tqdm visualization of the SOM training

  • [ADDED] New init_mode_supervised called random_minmax.

  • [CHANGED] Official name of package changes from SUSI to SuSi.

  • [CHANGED] Docstrings for functions are now according to guidelines.

  • [FIXED] Semi-supervised classification handling, sample weights

  • [FIXED] Supervised classification SOM initalization of n_iter_supervised

  • [FIXED] Code refactored according to prospector

  • [FIXED] Resolved bug in get_datapoints_from_node() for unsupervised SOM.

[1.0.6] - 2019-09-11

  • [ADDED] Semi-supervised abilities for classifier and regressor

  • [ADDED] Example notebooks for semi-supervised applications

  • [ADDED] Tests for example notebooks

  • [CHANGED] Requirements for the SuSi package

  • [REMOVED] Support for Python 3.4

  • [FIXED] Code looks better in documentation with sphinx.ext.napoleon

[1.0.5] - 2019-04-23

  • [ADDED] PCA initialization of the SOM weights with 2 principal components

  • [ADDED] Variable variance

  • [CHANGED] Moved installation guidelines and examples to documentation

[1.0.4] - 2019-04-21

  • [ADDED] Batch algorithm for unsupervised and supervised SOM

  • [ADDED] Calculation of the unified distance matrix (u-matrix)

  • [FIXED] Added estimator_check of scikit-learn and fixed recognized issues

[1.0.3] - 2019-04-09

  • [ADDED] Link to arXiv paper

  • [ADDED] Mexican-hat neighborhood distance weight

  • [ADDED] Possibility for different initialization modes

  • [CHANGED] Simplified initialization of estimators

  • [FIXED] URLs and styles in documentation

  • [FIXED] Colormap in Salinas example

[1.0.2] - 2019-03-27

  • [ADDED] Codecov, Codacy

  • [CHANGED] Moved decreasing_rate() out of SOM classes

  • [FIXED] Removed duplicate constructor for SOMRegressor, fixed fit() params

[1.0.1] - 2019-03-26

  • [ADDED] Config file for Travis

  • [ADDED] Requirements for read-the-docs documentation

[1.0.0] - 2019-03-26

  • Initial release

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