Get hands-on with t-SNE plots

With the growing popularity of single-cell RNA-Seq analysis, the t-SNE projection of multi-dimensional data is appearing more often in publications and online.  If you’ve ever wanted to develop a better intuitive feel for what exactly t-SNE does and where it can go wrong, this interactive tutorial (by Martin Wattenberg and Fernanda Viegas) is extremely compelling and useful.

A screen capture of the interactive t-SNE interface.

In addition to providing a wonderful, interactive plotting function, the authors go on to provide an informative tutorial explains the pitfalls and challenges of the optimization and hyper-parameter tuning of t-SNE projections and how to get the most from the plots.  Here is an example:

An example of how hyperparameter tuning affects the final plot.

In the example above, tuning the “perplexity” of the t-SNE projection causes the correct reconstruction of the data when values are between 30-50, but the same method fails when the parameter falls outside those ranges (i.e., too small or too large).

Go check out this distill.pub site.  It’s worth your time.

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