Effortlessly Scale tSNE to Millions of Data Points With openTSNE

The most optimized CPU implementation of tSNE.

Nov 25, 2023

In yesterday’s post, we discussed accelerating the tSNE algorithm using GPUs for faster processing.

Here’s the visual from that post for a quick recap:

In a gist, the idea was to use tSNE-CUDA, which is an optimized CUDA version of the tSNE algorithm, which, as the name suggests, can leverage hardware accelerators.

And why is an optimized implementation needed in the first place?

It’s needed because the biggest issue with tSNE (which we also discussed here) is that its run-time is quadratically related to the number of data points.

Thus, it can get pretty difficult to use tSNE from Sklearn for large datasets.

tSNE-CUDA addressed this by providing immense speedups over the standard Sklearn implementation using a GPU.

However, after releasing that post, a few readers showed concerns about not having dedicated access to a GPU to use tSNE-CUDA.

They asked if there’s any alternative optimized implementation of tSNE that can run on a CPU?

Answer: Of course, there is!

openTSNE is another optimized Python implementation of t-SNE I discovered during my exploration, which provides massive speed improvements and enables us to scale t-SNE to millions of data points — a place where Sklearn implementation may never reach.

The effectiveness is evident from the image below:

tSNE vs. openTSNE comparison on a dataset of 70k images

As depicted above, the openTSNE implementation:

is 20 times faster than the Sklearn implementation.
produces similar quality clustering as the Sklearn implementation.

The authors have also provided the following benchmarking results:

As depicted above, openTSNE can produce low dimensional visualization of a million data points in just ~15 minutes.

However, it is clear from their benchmarks that the run-time of the Sklearn implementation has already reached a couple of hours with just ~250k data points.

Isn’t that an insane speedup, that too, without ever utilizing a GPU?

Download the notebook here to try out openTSNE: openTSNE Jupyter notebook.

👉 Over to you: What are some other ways to boost the tSNE algorithm?

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