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Cell utils clarification #24

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Merged
cnellington merged 2 commits into from
Sep 28, 2025
Merged

Cell utils clarification #24

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2ce3439
correct cell mask id
Sep 1, 2025
2ffb0ef
update cell_utils todos
Sep 28, 2025
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3 changes: 2 additions & 1 deletion experiments/AIDO.Cell/cell_utils.py
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Expand Up @@ -28,7 +28,8 @@ def align_adata(adata: ad.AnnData) -> Tuple[ad.AnnData, np.ndarray]:
print(f'{len(new_missing_genes)} in your data that cannot be used by AIDO.Cell. Removing these.')
print(new_missing_genes)
print(f'{len(missing_genes)} genes in the AIDO.Cell pretraining set missing in your data.')
print('AIDO.Cell is trained with zero-masking. Setting these to zero for AIDO.Cell to ignore.')
print('Setting unknown genes to 0.')
# Todo: AIDO.Cell is trained with -1 as mask token, but read depth features don't work with -1 sum for read counts
print(missing_genes)
adata_missing = ad.AnnData(np.zeros((adata.shape[0], len(missing_genes))))
adata_missing.var.index = missing_genes
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