GuyAllard / markov_clustering

markov clustering in python
MIT License
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Hyperparameter Tunning #25

Open Fish-Soup opened 4 years ago

Fish-Soup commented 4 years ago

Hi

I have 2 questions. 1) In the example using the modularity only the inflation is varied. When would we vary the expansion. Is there a case where we would want a large expansion and a large inflation (as they act in the opposite fashion).

2) Is there a way of getting a rough range for this value (given an adjacency matrix). I found in my use case I needed an inflation value of 20 to get the appropriate clustering. I decided to square the adjacency matrix and then i found an inflation of about 5 was good. I am trying to build this code into a pipeline so I wont be able to over see the selection of groups so i worry if my range hyper-parameters is off I may not find optimal values (if say my data changes).

Many thanks