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(PLEASE USE https://github.com/HanKruiger/tsNET) This is here for historical purpose only.

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# If you plan to use/evaluate tsnetwork, please use the code on https://github.com/HanKruiger/tsNET which is (just a little bit) less experimental.
This repository is still here because my [MSc thesis](http://fse.studenttheses.ub.rug.nl/id/eprint/14540) referred to it.

# `tsnetwork`

Graph layouts by t-distributed stochastic neighbour embedding.

This repository contains the implementation of a graph layout algorithm that makes use of the [t-SNE](https://lvdmaaten.github.io/tsne/) dimensionality reduction technique.

The exploration and evaluation of using this technique for graph layouts was done as my [MSc thesis](http://irs.ub.rug.nl/dbi/57cd44e1a5b49) project at Rijksuniversiteit Groningen, which I aim to finish in August 2016.

A large part of an essential module in this implementation is a heavily adjusted version of Paulo Rauber's [thesne](https://github.com/paulorauber/thesne), which is an implementation of dynamic t-SNE.

## Dependencies

This was developed and tested solely on ArchLinux.
For this implementation to work, you will need:

* `python3`
* [`numpy`](http://www.numpy.org/)
* [`graph-tool`](https://graph-tool.skewed.de/)
* [`theano`](http://deeplearning.net/software/theano/)
* [`graphviz`](http://www.graphviz.org/)
* [`matplotlib`](http://matplotlib.org/)
* [`scikit-learn`](http://scikit-learn.org/stable/)

For rendering fancy animations (even more heavily untested, probably only works on my system) you need:

* [`ffmpeg`](https://ffmpeg.org/)
* [`imagemagick`](https://www.imagemagick.org/)

## Benchmark layout animations

For a set of graphs that has been used as a benchmark, animations that show the state of the layout as a function of optimization time can be seen [over here](https://hankruiger.github.io/tsnetwork/animations).

## Warning

Usage of this software is at your own risk.
This utility writes and removes directories in a directory you specify, and (with me being __not__ a professional software developer) you should not trust using this if you're afraid to lose data.

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