It seems that the only class that implements GraphModel (found by “implements*GraphModel*” regular expression) is: DHNS (Durable Hierarchical Network Structure): https://github.com/gephi/gephi/blob/master/DHNSGraph/src/org/gephi/graph/dhns/core/Dhns.java
Update: I have created a jgrapht-gephi library that works well for algorithm-centric tasks.
Keywords:
Gephi graph model graphmodel implementation source java class implements class provides an implementation of GraphModel in Gephi
