reconstrue / single_cell

Single cell analysis tools built to run on Jupyter, especially Colab
http://reconstrue.com
Apache License 2.0
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tSNE: autopreplexity #10

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

The 2017 pre-print on arXiv: Automatic Selection of t-SNE Perplexity Have two parameters:

Defaults to 0.0--1.0 and 0.05. But after init probing run, user will get an idea of a sub-range that looks interesting: they will then rerun the algorithm but drill down on a narrower range at smaller steps to find a roughly optimal perplexity value.

Some explanatory text of perplexity: An Introduction to t-SNE with Python Example