I'm using an older version of SciKit-Learn, version 1.0.2, to try and OneHotEncode some data. My dataset is fairly large, 184 columns going to 311 after the OneHotEncoding, with ~500,000 rows. Despite this, I'm confident I could write code that OneHotEncodes my columns in a minute maximum.

Currently, SciKit-Learn's OneHotEncoder is on 10 minutes and counting. Why is this code so slow? Is there anything I can do to speed it all up?


1 Answer 1


If you use OneHotEncoder in a Jupyter Notebook, you can use %%prun -s "time" to profile your code. See How do I Profile a Jupyter Cell and Rank it by Cumulative Time? for more information.

Doing this with a subset of the rows shows that the function calls taking up the most time are inside the _encode module function from SciKit-Learn's utils sub-package.

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Looking inside this module you can see that _encode's _check_unknown, and _extract_missing contain inefficient list comprehensions, and this is most likely what's slowing you down.

If you want to create a OneHotEncoding of your data I suggest using Panda's get_dummies functionality, it's so much faster.

There are a couple of differences, pd.get_dummies(...) disregards any NaN values by default, this can be changed by switching dummy_na=True. It is also sometimes considered best practice to drop one of the categorical features as a column, as one of the columns can be represented by all zeros in the other columns. For more information on that try reading these articles: dummy variable trap, does the dropped column matter?


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