Pairwise versus multiple network alignment

Motivation: Network alignment (NA) can be pairwise (PNA) and multiple (MNA). PNA produces aligned node pairs between two networks. MNA produces aligned node clusters between more than two networks. Recently, the focus has shi‰ed from PNA to MNA, because MNA captures conserved regions between more networks than PNA (and MNA is thus considered to be more insightful), though at higher computational complexity. Œe issue is that, due to the different outputs of PNA and MNA, a PNA method is only compared to other PNA methods, and an MNAmethod is only compared to other MNA methods. Comparison of PNA against MNA must be done to evaluate whether MNA’s higher complexity is justified by its higher accuracy. Results: We introduce a framework that allows for this. We compare PNA against MNA in both a pairwise (native to PNA) and multiple (native to MNA) manner. Shockingly, we find that PNA is more accurate and faster than MNA in both cases. Œis result might guide future research efforts in the NA field. Contact: [email protected]