blab / pathogen-embed

Create reduced dimension embeddings for pathogen sequences
https://pypi.org/project/pathogen-embed/
MIT License
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Set default learning rate for t-SNE to "auto" #4

Closed huddlej closed 5 months ago

huddlej commented 8 months ago

Based on our results from applying t-SNE to simulated populations in https://github.com/blab/cartography, a more reasonable default learning rate should scale with the input sample size instead of being fixed at 200.0. The default learning rate in the scikit-learn implementation we use is already the string "auto" which allows the learning rate to scale with the sample size. We should change the default value for the tsne subcommand's --learning-rate argument to "auto". This change will require us to define a custom argparse type function, since valid values can be either a float or a string with the value of auto.

nandsra21 commented 6 months ago

issue is fixed with default-learning-rate branch