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Serializing UMAP

See original GitHub issue

Hi! thanks for implementing UMAP it’s very handy! When serializing a trained UMAP object via pickle I had the following error:

pickle.dump(myumap, open('pickle.pkl', 'w'))
TypeError: a class that defines __slots__ without defining __getstate__ cannot be pickled

A workaround I’ve found is:

pickle.dump(myumap, open('pickle.pkl', 'w'), protocol=-1)

Do you think it is safe? Is there a better/recommended serialization approach?

Issue Analytics

State:
Created 4 years ago
Comments:6 (5 by maintainers)

Top GitHub Comments

4reactions

lefnirecommented, Aug 1, 2020

bump. I need to use loaded umap (pickle, joblib, etc) for inference (“You’ll only need [._rp_trees] it if you want to transform new data”). I think that might be a main reason people would want to serialize incidentally; future inference. Thanks for the project!

1reaction

lmcinnescommented, Jan 25, 2020

I think the simplest thing is to delete the _rp_trees attribute. You’ll only need it if you want to transform new data, and for the use cases you describe that should be fine. I’ll try to figure out a more long term fix when I get some time.

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