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Cluster t-SNE plot [message #500]

Sat, 16 March 2019 07:28

amorrison
Messages: 38
Registered: March 2016

Member

Hi,

I'm really liking the t-SNE visualisation. If I wanted to bin the compounds based on their t-SNE positions is this possible and how would I go about it? So similar to the cluster compounds but using t-SNE to a certain distance.

Thanks,

Angus

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Re: Cluster t-SNE plot [message #506 is a reply to message #500]

Wed, 20 March 2019 23:29

thomas
Messages: 731
Registered: June 2014

Senior Member

Hi Angus,

this is currently not possible. I would suggest to always cluster compounds on a chemical descriptor, because that would reflect compound similarity much better than the reduced 2 or three dimensions after t-SNE. Of course, clusters based on the t-SNE positions would look perfectly nice in the t-SNE view, but would be far from perfect groups of similar compounds.

Thomas

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