Difference between sklearn make_pipeline and imblearn make_pipeline
The imblearn package contains a lot of different samplers for easy over- or under-sampling of data.
These samplers can not be placed in a standard sklearn pipeline. 

To allow for using a pipeline with these samplers, the imblearn package also implements an extended pipeline. This pipeline is very similar to the sklearn one with the addition of allowing samplers. 

If you want to include samplers in the pipeline, use the imblearn pipeline. Otherwise, use the sklearn one.



The code for the imblearn pipeline can be seen here and the sklearn pipeline code here. Note that make_pipeline is just a convenient method to create a new pipeline and the differnece here is actually with the pipelines themselves.