Be Skeptical of the t-SNE Bunny

Matt Henderson on Twitter (click through for the animation):

Be skeptical of the clusters shown in t-SNE plots! Here we run t-SNE on a 3d shape - it quickly invents some odd clusters and structures that aren’t really present in the original bunny.

What would happen if every machine learning method would come with a built-in visualization of the spurious results that it found?

Never mind the the answer to that question. I think that this dimensionality reduction of a 3D bunny into two dimensions isn’t even all that bad—the ears are still pretty cute. And it’s not like the original data had a lot more global and local structure once you consider that the bunny is not much more than noise in the shape of a rectangle with two ears that human eyes ascribe meaning to.

I’m the first to admit that t-SNE, UMAP, and all kinds of other methods will produce clusters from whatever data you provide. But so will k-means always return k clusters. One shouldn’t trust any model without some kind of evaluation of its results.

If you don’t take them at face value, UMAP and Co. can be powerful tools to explore data quickly and interactively. Look no further than the cool workflows Vincent Warmerdam is building for annotating text.
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