Before revision:  Finally, using three real-world examples of metabolic networks , we show that the degenerate solutions can fundamentally disagree on the composition of even the largest modules. Together, these results significantly extend and clarify our understanding of this popular method. In particular, they explain why so manyheuristics perform well in practice at finding high-scoring partitions, why these heuristics can disagree on the composition of the identified modules , and how the estimated value of Q_max should be interpreted.
After revision:  Finally, using three real-world examples of metabolic networks , we show that the degenerate solutions can fundamentally disagree on many, but not all, partition properties such as the composition of the identified modules , and how the estimated value of Q_max should be interpreted.