Vincent Ustach issues

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                                            Vincent Ustach

add simreg as a similarity metric

https://cran.r-project.org/package=SimReg https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827100/ should we add this as a similarity metric?

remove equals sign from filename in add_spl_to_patients.py

I noticed that the script add_spl_to_patients.py generates filenames that include an equals sign (=). https://github.com/mims-harvard/SHEPHERD/blob/e61281f0e6ee3617d1a889d90a9908454ba31e6f/data_prep/shortest_paths/add_spl_to_patients.py#L141 'mydata_agg=mean_spl_matrix.npy' While this is technically allowed, I recommend avoiding this character in filenames. There are...

KeyError: 'alpha' when executing predict.py

Hello, I am working with a small data set using the SHEPHERD checkpoint model files to do causal gene discovery. I ran the shortest paths script with no issues, and...