feat: scib-autotune #3168
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feat: scib-autotune #3168
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canergen
reviewed
Jan 28, 2025
| from lightning.pytorch.callbacks import Callback, ModelCheckpoint | ||
| from lightning.pytorch.callbacks.early_stopping import EarlyStopping | ||
| from lightning.pytorch.utilities import rank_zero_info | ||
| from scib_metrics.benchmark import ( # TODO: Need to be installed by default if we put it here |
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Needs to go into the CallBack. Don’t make it default.
canergen
reviewed
Jan 28, 2025
| batch = outputs["batch"].numpy() | ||
| labels = outputs["labels"].numpy() | ||
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| adata = AnnData(X=x, obs={"batch": batch, "labels": labels}, obsm={"z": z}) |
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Doesn’t need X. We should be able to run it on some custom indices. It’s otherwise to expensive quickly.
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This is just an initial draft. No need to review yet.
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re open the scib-autotune branch
see: #2593
#2517