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Generative Topographic Mapping with Python

ugtm: Generative Topographic Mapping with Python.

Link to the package documentation: http://ugtm.readthedocs.io/en/latest/

GTM (Generative Topographic Mapping) is a dimensionality reduction algorithm (as t-SNE, LLE, etc) created by Bishop et al. (https://www.microsoft.com/en-us/research/wp-content/uploads/1998/01/bishop-gtm-ncomp-98.pdf) and a probabilistic counterpart of Kohonen maps.

ugtm is a python package implementing GTM and GTM prediction algorithms. ugtm contains the core functions and runGTM.py (in bin directory) is an easy-to-use program. The kernel version of the algorithm (kGTM) is also implemented. You can also generate regression or classification maps, or evaluate the predictive accuracy (classification) or RMSE/R2 (regression) in repeated cross-validation experiments.

Install ugtm

Simple installation:

• pip install ugtm

If you get error messages, try upgrading packages:

• pip install --upgrade pip numpy scikit-learn matplotlib scipy mpld3 jinja2
• sudo pip install --upgrade pip numpy scikit-learn matplotlib scipy mpld3 jinja2

If you have problems with anaconda packages, try to create a virtual env called "p2" for python 2.7.14:

• conda create -n p2 python=2.7.14 numpy=1.14.5 scikit-learn=0.20 matplotlib=2.2.2 scipy=0.19.1 mpld3=0.3 jinja2=2.10
• source activate p2
• pip install ugtm

Or p3 for python 3.6.6:

• conda create -n p3 python=3.6.6 numpy=1.14.5 scikit-learn=0.20 matplotlib=2.2.2 scipy=0.19.1 mpld3=0.3 jinja2=2.10
• source activate p3
• pip install ugtm

Documentation

Readthedocs

Prerequisites

Python 2.7 or + (tested on Python 3.4.6 and Python 2.7.14)

and following packages:

• scikit-learn>=0.20
• numpy>=1.14.5
• matplotlib>=2.2.2
• scipy>=0.19.1
• mpld3>=0.3
• jinja2>=2.10

Author

Héléna A. Gaspar, [email protected], https://github.com/hagax8