Add PCADecoderMetrics2 #242
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LeonStadelmann
commented
May 21, 2025
src/cellflow/training/_callbacks.py
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| for cond in conditions_adata & conditions_pred: | ||
| true_counts[name][cond] = self.validation_adata[name][ | ||
| self.validation_adata[name].obs[self.condition_id_key] == cond | ||
| ].X.toarray() |
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Could we potentially go OOM here when using real data? I was not sure @MUCDK
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should be fine, because we first subset the adata before densifying.
two things here:
- provide the option to extract any adata.X or any adata.layers[key], similar how we e.g. do it in moscot
- bear in mind that adata.X can be both sparse and dense
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@MUCDK Your suggestions have been implemented, pinged since i cant request a review right now. |
MUCDK
reviewed
May 27, 2025
src/cellflow/model/_cellflow.py
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| self._dataloader: TrainSampler | None = None | ||
| self._trainer: CellFlowTrainer | None = None | ||
| self._validation_data: dict[str, ValidationData] = {} | ||
| self._validation_adata: dict[str, ad.Anndata] = {} |
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can we make these attributes of the callbacks directly?
MUCDK
reviewed
May 27, 2025
src/cellflow/training/_callbacks.py
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| self.layers = layers | ||
| self.log_prefix = log_prefix | ||
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| def add_validation_adata( |
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this can be part of __init__, can't it?
MUCDK
reviewed
May 27, 2025
src/cellflow/training/_trainer.py
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| for callback in callbacks: | ||
| if isinstance(callback, PCADecodedMetrics2): | ||
| callback.add_validation_adata(self.validation_adata) |
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I don't think this would be needed if validation_adata was an attribute of the callback, would it?
MUCDK
requested changes
May 27, 2025
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Adressing #220.