theislab / scarches

Reference mapping for single-cell genomics
https://docs.scarches.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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hlca_map_classify.ipynb missing early_stopping_kwarg #213

Open c-westhoven opened 9 months ago

c-westhoven commented 9 months ago

Hi, I noticed that in the hlca_map_classify tutorial, the early stopping is not actually activated, because the early_stopping is not set to true, and so the training goes through all 500 surgery epochs.

From tutorial:

surgery_epochs = 500
early_stopping_kwargs_surgery = {
    "early_stopping_monitor": "elbo_train",
    "early_stopping_patience": 10,
    "early_stopping_min_delta": 0.001,
    "plan_kwargs": {"weight_decay": 0.0},
}