How can I examine the subnetworks of a nearly fully connected graph?
It sounds like you don't need to be talking about this as a &quot;graph&quot; data structure.. you have points in R3 and you want to partition them into clusters based on their distances (or their pairwise weight matrix). This is more a statistical clustering problem than a graph clustering problem.
Here are some python functions to accomplish these:
https://scikit-learn.org/stable/modules/clustering.html