Closed jameshadfield closed 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.
Running
pathogen-embed ... t-sne
resulted in the errorTSNE.__init__() got an unexpected keyword argument 'square_distances'
. The same command but withumap
ormds
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