Network alignment provides a comprehensive way to discover the similar parts between molecular systems of different species based on topological and biological similarity. With such a strong basis, one can do comparative studies at a systems level in the field of computational biology. In this survey paper, we focus on protein-protein interaction networks and review some representative algorithms for network alignment in the past two decades as well as the state-of-the-art aligners. We also introduce the most popular evaluation measures in the literature to benchmark the performance of these approaches. Finally, we address several future challenges and the possible ways to conquer the existing problems of biological network alignment.

网络对齐提供了一种基于拓扑和生物学相似性来发现不同物种的分子系统之间相似部分的综合方法。有了如此强大的基础，就可以在计算生物学领域的系统级进行比较研究。在这篇调查论文中，我们专注于蛋白质-蛋白质相互作用网络，并回顾了过去二十年中用于网络比对的一些代表性算法以及最先进的比对器。我们还将介绍文献中最受欢迎的评估方法，以对这些方法的性能进行基准测试。最后，我们解决了一些未来的挑战以及解决生物网络对齐方式存在的问题的可能方法。