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jean-pierreBoth / annembed

data embedding based on approximate nearest neighbour
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[Feature request] Python bindings #7

Open apcamargo opened 2 months ago

apcamargo commented 2 months ago

Hi,

I've been using annembed for some time now and I'm really satisfied with how fast it is. However, the workflow from Python is very cumbersome at the moment. It would be great if there were Python bindings that allowed annembed to be called from within Python, using numpy arrays as input.

jianshu93 commented 1 month ago

@jean-pierreBoth,

do you think we need to have it since it is really useful in a python environment, comparable to UMAP. @apcamargo We do have some comparison with UMPA in terms of visualization accuracy in the paper: https://www.biorxiv.org/content/10.1101/2024.01.28.577627v1.abstract

best,

Jianshu

apcamargo commented 1 month ago

I think this can be really useful both because of the advantages regarding visualization and because it is way faster than UMAP (and would require less dependencies too)

apcamargo commented 4 weeks ago

I can try to create a fork a develop Python library using PyO3. But it would be a couple of months before I have the time to start working on that.