Am 19.02.20 um 19:28 schrieb Davide Cittaro: > I’m testing and implementing NABM for a specific research field (single cell > biology) in which graph partitioning is the standard way to identify groups > of cells, and this is done with Louvain (and more recently Leiden) > approaches. We already have collected some evidences that NSBM works well and > overcomes the issue of setting resolution (as a matter of fact one of the FAQ > is “where should I set the threshold). Now, given a partition with those > algorithms would it make sense to compare to NSBM using entropy? I could > create a PropertMap from Leiden partitions and set it into a BlockState, > would it work? >
If you do this kind of comparison, the NSBM approach will virtually always produce results with a smaller description length, since it is designed to minimize this quantity. It's true that the description length is a meaningful quantity on its own, and it can be used to do model selection, i.e. two models can be compared by how much they compress the data, and the one with the shortest description length should be selected. However, I'm afraid that results obtained from modularity maximization cannot be properly regarded as an inference outcome, so they cannot really be meaningfully compared to anything else, which itself is another problem with the method. If you want to determine the usefulness of modularity maximization in a particular context, there is a simple test you can do: Just randomize the data, keeping the same degree sequence, and run the algorithm again. Almost always it will find many "communities" which are completely meaningless as explanations of the data. This should be enough to convince serious researchers that this approach is unreliable. Best, Tiago -- Tiago de Paula Peixoto <[email protected]> _______________________________________________ graph-tool mailing list [email protected] https://lists.skewed.de/mailman/listinfo/graph-tool
