A few months ago I realised you have to use Cython to calc pairwise dists for big data in Python, so I wrote my own:https://github.com/oliviaguest/pdist …
It's ridiculously faster. There's a file called compare.py — try it out. Be careful though.
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Big values of N my Cython copes, but be careful read the comments before running a comparison if you change the N.
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I'm not sure what's the best way to bench mark this other than what I put in compare.py —
@usethespacebar maybe knows?
End of conversation
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