Identify clusters of nodes

[mhmism]

Hello,

Thanks a lot for this wonderful mapper. I have been impressed by it so far.

Is there a way to automatically identify clusters of closely connected nodes within the TDA graph?
I have seen a few articles mentioning that they applied a Morse-clustering algorithm, but not sure how can apply it to the TDA graphs by KeplerMapper.

Any guidance in this direction will be extremely appreciated.

[sauln]

Hi @mhmism, you should be able to use any graph clustering method you'd like. For one example, you could convert the resulting graph to networkx format (using the networkx adapter), and then using sklearn's spectralclustering algorithm for your clustering.

I'm sure there are some kinks to work out around edge lengths, but this approach should work.

[mhmism]

Many thanks for your reply! this is really helpful.

Since I'm using spectral clustering already in my TDA analysis. I'm not sure if it will make sense for me to use it again for modularity detection.

I'm considering using the Louvain algorithm, https://python-louvain.readthedocs.io/en/latest/
What do you think?

Kind regards
Mahmoud

[sauln]

🤷 I'm not familiar with Louvain, but from a cursory glance at the page it seems like it would work.

fwiw, I can't think of any problem with using spectral clustering twice.