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[FEA] Expose gamma (resolution) parameter for Louvain. #674

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jwyles opened this issue Jan 17, 2020 · 0 comments · Fixed by #1034
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[FEA] Expose gamma (resolution) parameter for Louvain. #674

jwyles opened this issue Jan 17, 2020 · 0 comments · Fixed by #1034
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@jwyles
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jwyles commented Jan 17, 2020

This is to expose the gamma parameter (in the formula for modularity score) as a parameter the user can specify.

Since currently Louvain assumes a value of 1 for gamma some of the code will need to be rewritten in order to use a different value of gamma.

Modularity and the Louvain implementation are known to suffer from a resolution issues. To address that, iGraph has an option to set a resolution limit. That same feature should be added to our version.

https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.louvain.html

Modularity is defined as
image

This modification is to allow the resolution parameter, y, to be specified in the range of 0.0001 to 1.0

@jwyles jwyles added ? - Needs Triage Need team to review and classify feature request New feature or request labels Jan 17, 2020
@BradReesWork BradReesWork removed the ? - Needs Triage Need team to review and classify label May 26, 2020
@BradReesWork BradReesWork added this to the 0.15 milestone May 26, 2020
@BradReesWork BradReesWork changed the title [FEA] Expose gamma parameter for Louvain. [FEA] Expose gamma (resolution) parameter for Louvain. Jul 28, 2020
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