What do the values in the x axis and y axis of this scatterplot correspond to? It is related to t-SNE but I don't know how.

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The plot is from:

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    $\begingroup$ Thanks for the reference. I'm going to add this to my library of examples of poor graphing practices. $\endgroup$
    – user140401
    Jan 1, 2017 at 23:47

1 Answer 1


t-SNE is a technique for visualizing high-dimensional data in a low-dimensional space (2- or 3-dimensional). It attempts to preserve local structure: in other words, points that are close (according to some metric) in high-dimensional space remain close in the new, low-dimensional space.

The mapping between the high-dimensional and low-dimensional space isn't simple, however. It's computed using an iterative procedure (for details, see here), and it ends up being highly nonlinear.

This isn't surprising; a linear mapping wouldn't help with dimensionality reduction. Quoting from the paper,

Traditional dimensionality reduction techniques such as Principal Components Analysis (PCA; Hotelling, 1933) and classical multidimensional scaling (MDS; Torgerson, 1952) are linear tech- niques that focus on keeping the low-dimensional representations of dissimilar datapoints far apart. For high-dimensional data that lies on or near a low-dimensional, non-linear manifold it is usually more important to keep the low-dimensional representations of very similar datapoints close together, which is typically not possible with a linear mapping.

Anyway, all of this is a long-winded way of saying that the axes of a t-SNE plot aren't easily interpretable in terms of the axes/units of the original, high-dimensional data. So I wouldn't try to interpret a t-SNE plot quantitatively; t-SNE is just a visualization technique, nothing more.


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