Internally both the hyperedges and the vertices are stored as an AutoArrayHashmap with the associated data and the relations ( https://github.com/yamafaktory/hypergraphz/blob/9f87e705afd7...). Then the implementation diverge since a given hyperedge can hold zero to n vertices, with self-loops (ArrayList). For vertices, we just need to keep track of the hyperedges (AutoArrayHashmap).