In this paper, we present a novel algorithm to address the Network Alignment problem. It is inspired from a previous message passing framework of Bayati et al. [2] and includes several modifications designed to significantly speed up the message updates as well as to enforce their convergence. Experiments show that our proposed model outperforms other state-of-the-art solvers. Finally, we propose an application of our method in order to address the Binary Diffing problem. We show that our solution provides better assignment than the reference differs in almost all submitted instances and outline the importance of leveraging the graphical structure of binary programs.