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fix register_fields bug in tuner and add dependencies #55
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chelseabright96
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ArianAmani
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Jun 26, 2024
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# getattr(experiment.model_cls, experiment.setup_method_name)( | ||
# experiment.data, | ||
# # **experiment.setup_method_args, | ||
# ) | ||
experiment.model_cls.setup_anndata(experiment.data, **setup_anndata_kwargs) | ||
|
||
model = experiment.model_cls(experiment.data, **model_args) | ||
model.train(max_epochs=train_args.pop("max_epochs",2000), | ||
use_gpu=train_args.pop("use_gpu",True), | ||
early_stopping_patience=train_args.pop("early_stopping_patience",10), | ||
check_val_every_n_epoch=train_args.pop("check_val_every_n_epoch",5), | ||
plan_kwargs=plan_kwargs, | ||
**train_args) |
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Can we have this section similar to the part above it?
Eventually, something like this I think:
Suggested change
# getattr(experiment.model_cls, experiment.setup_method_name)( | |
# experiment.data, | |
# # **experiment.setup_method_args, | |
# ) | |
experiment.model_cls.setup_anndata(experiment.data, **setup_anndata_kwargs) | |
model = experiment.model_cls(experiment.data, **model_args) | |
model.train(max_epochs=train_args.pop("max_epochs",2000), | |
use_gpu=train_args.pop("use_gpu",True), | |
early_stopping_patience=train_args.pop("early_stopping_patience",10), | |
check_val_every_n_epoch=train_args.pop("check_val_every_n_epoch",5), | |
plan_kwargs=plan_kwargs, | |
**train_args) | |
adata = experiment.data.copy() | |
if sub_sample is not None: | |
sc.pp.subsample(adata, fraction=sub_sample) | |
experiment.model_cls.setup_anndata(adata, **setup_anndata_kwargs) | |
model = experiment.model_cls(adata, **model_args) | |
model.train(plan_kwargs=plan_kwargs, **train_args) | |
del adata | |
import gc | |
gc.collect() |
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Fixed register_fields bug in tuner:
Added dependencies and fixed compatibility issue with scipy