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blab / pathogen-embed

Create reduced dimension embeddings for pathogen sequences
https://pypi.org/project/pathogen-embed/
MIT License
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t-sne init error #5

Closed jameshadfield closed 7 months ago

jameshadfield commented 7 months ago

Running pathogen-embed ... t-sne resulted in the error TSNE.__init__() got an unexpected keyword argument 'square_distances'. The same command but with umap or mds worked as expected. Happy to provide input data if that helps.

pathogen-embed version: 1.1.1 (via PyPi) Python 3.10.13 scikit-learn Version: 1.4.0

huddlej commented 7 months ago

Thanks for reporting this, @jameshadfield! It looks like that parameter was added in 0.24 and then removed in scikit-learn v1.3. The default behavior since 1.3 should be what we want, but we use 0.24.2 in our paper and should probably pin to that for now.