Bias detection module

[Zethson]

Description of feature

Pre-requisite: https://github.com/theislab/ehrapy/issues/637

This serves as a meta issue to collect ideas for a bias detection and mitigation module:

• [x] #645
• [x] Missingness per feature -> missingno stuff
• [x] IQR outliers -> https://github.com/theislab/ehrapy/issues/648 for numerical data @Zethson
• [x] value counts for categorical counts + warnings? Some things are already in tableone @Zethson
• [x] sensitivity analysis - easy with ehrapy because the API is so easy @Zethson
• [x] Imbalanced subsampling through https://imbalanced-learn.org/stable/index.html ? -> only the most important sampling features in ehrapy. Not the generation stuff. @eroell
• [ ] Propensity score matching @Lilly-May
• [x] standardized mean differences for numerical data @Lilly-May (#690)
• [x] Correlations between variables @Lilly-May (#690)
• [x] Feature importance -> requires target variable (only run if set) @Lilly-May (#690)
• [x] generate_bias_report that runs a lot of methods subsequently and summarizes things?!? @Lilly-May (#690)

[eroell]

Comment regarding balanced sampling from imbalanced-learn, I started off something small a while ago due to a discussion of how to sample things for scanpy: https://github.com/eroell/scimb

Anything like that could be helpful indeed.

[Lilly-May]

Regarding propensity score matching, we already have that implemented for causal inference with dowhy here. If we implement a causal discovery module (#619), implementing a propensity score matching algorithm would be important, but until then, I don't really see the need. However, please feel free to disagree! Should we close this issue then?

[Zethson]

Yup! Let's close

May 4, 2024 12:18:43 PM Lilly May @.***>:

Regarding propensity score matching, we already have that implemented for causal inference with dowhy here[https://github.com/theislab/ehrapy/blob/1b5165d925f87304948fffe9b76cc68669ee6ab2/ehrapy/tools/causal/_dowhy.py#L37]. If we implement a causal discovery module (#619[https://github.com/theislab/ehrapy/issues/619]), implementing a propensity score matching algorithm would be important, but until then, I don't really see the need. However, please feel free to disagree! Should we close this issue then?

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