I have used tsne to visualise a large dataset and it has produced the following graph. I need help interpreting it, as I have never seen a tsne graph like this before!

I am aware that not much overlapping data is a good thing, but I have rarely seen more than a few clusters. Has something gone wrong here? Or are there just a lot of clusters in this dataset.

Thanks. P

enter image description here

  • $\begingroup$ Keep in mind that tSNE isn't the only dimensionality reduction tool out there. Use the algorithm which best fits your data. $\endgroup$
    – Alex L
    Jan 4, 2019 at 5:43
  • 1
    $\begingroup$ A bit of advice: the t-SNE output depends heavily on the perplexity parameter chosen. I'd recommend always giving the perplexity that the picture was generated at. $\endgroup$
    – Ingolifs
    Jan 30, 2019 at 21:54

2 Answers 2


t-SNE is notoriously fickle. I would advise you read this short article How to Use t-SNE Effectively before you invest too much time trying to interpret the plots. In case you don't read it, you'll find that your t-SNE plot will change considerably based on your iterations, and perplexity. You'll find that distance between clusters aren't accurate and that cluster sizes aren't accurate too. t-SNE is a cool data reduction too, but often takes multiple runs to get a "good" plot. Laurens van der Maatan even suggest that running multiple iterations and picking the one with the lowest KL-divergence is perfectly okay. This is due to the fact that t-SNE is non-convex so you won't necessarily find a global minimum.


I had a similar problem, even more extreme looking. The data is from a depression screening survey as part of the Health and Nutrition Examination Survey. It's from "2017 - March 2020 Pre-pandemic" --> "Questionnaire Data" --> "Mental Health - Depression Screener". It has eleven columns, presumably one per question, and ~8k rows. Dropping NaN's, ~5k rows. I tried filling NaN's with mean, but the same plot occurred.

curvy t-SNE plot

The fix wasn't the perplexity, but rather an index column was in the data. After dropping,

t-SNE no curvy line

No clear clusters, but looks a lot better.


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