Add PCADecoderMetrics2 #242
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
LeonStadelmann
commented
May 21, 2025
src/cellflow/training/_callbacks.py
Outdated
| 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() |
There was a problem hiding this comment.
Could we potentially go OOM here when using real data? I was not sure @MUCDK
There was a problem hiding this comment.
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
|
@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
Outdated
| @@ -56,6 +56,7 @@ def __init__(self, adata: ad.AnnData, solver: Literal["otfm", "genot"] = "otfm") | |||
| self._dataloader: TrainSampler | None = None | |||
| self._trainer: CellFlowTrainer | None = None | |||
| self._validation_data: dict[str, ValidationData] = {} | |||
| self._validation_adata: dict[str, ad.Anndata] = {} | |||
There was a problem hiding this comment.
can we make these attributes of the callbacks directly?
MUCDK
reviewed
May 27, 2025
src/cellflow/training/_callbacks.py
Outdated
| self.layers = layers | ||
| self.log_prefix = log_prefix | ||
|
|
||
| def add_validation_adata( |
There was a problem hiding this comment.
this can be part of __init__, can't it?
MUCDK
reviewed
May 27, 2025
src/cellflow/training/_trainer.py
Outdated
Comment on lines
109
to
111
| for callback in callbacks: | ||
| if isinstance(callback, PCADecodedMetrics2): | ||
| callback.add_validation_adata(self.validation_adata) |
There was a problem hiding this comment.
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adressing #220.