Investigate whether current KNN imputation default (FKNNI) works for all sparseness and AnnData objects

theislab / ehrapy

Electronic Health Record Analysis with Python.

https://ehrapy.readthedocs.io/

Apache License 2.0

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Open Zethson opened 1 month ago

Zethson commented 1 month ago

We ran into cases in the past where users suddenly reported that it didn't impute everything and we need to understand this.

[ ] Generate a loooot of different AnnData objects with different numbers of missing data etc. A LLM can easily do that for us.
[ ] Run KNN imputation with backend=fknni (default) on all of them -> check whether any of them break

eroell commented 1 month ago

We ran into cases in the past where users suddenly reported that it didn't impute everything

Does this relate to the same reportings as #734?

Zethson commented 1 month ago

Yes! Sorry this is a duplicate now :(