Reference: Vipin Vijayan and Tijana Milenkovic, Aligning dynamic networks with DynaWAVE, Bioinformatics, btx841, https://doi.org/10.1093/bioinformatics/btx841, 2017.

DynaWAVE is our software tool for pairwise global alignment of dynamic networks. Dynamic networks are networks that evolve over time. Until recently, existing methods for network alignment were limited to being able to only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. Thus, DynaMAGNA++ was introduced as a proof-of-concept method for aligning dynamic networks. However, DynaMAGNA++ does not necessarily scale well to larger networks. DynaWAVE, on the other hand, scales well to larger networks in terms of alignment quality and runtime compared to DynaMAGNA++. While DynaWAVE is less accurate but faster than DynaMAGNA++ for smaller networks, DynaWAVE is more accurate and faster than DynaMAGNA++ for larger networks. An example of an application domain where DynaWAVE and DynaMAGNA++ are useful is computational biology - DynaWAVE can be used for alignment of protein interaction networks that evolve over time.

DynaWAVE is an extension of WAVE. While both WAVE and DynaWAVE optimize edge as well as node conservation across the aligned networks, WAVE conserves static edges and similarity between static node neighborhoods, while DynaWAVE conserves dynamic edges (events) and similarity between evolving node neighborhoods. WAVE appears in the following publication: Yihan Sun, Joseph Crawford, Jie Tang, and Tijana Milenkovic, Simultaneous Optimization of Both Node and Edge Conservation in Network Alignment via WAVE, in Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), Atlanta, GA, USA, September 10-12, 2015, pages 16-39.

DynaWAVE, which includes its source code, example networks to test DynaWAVE on, and installation and usage instructions, are available for download.

Vipin Vijayan may be contacted via email at vvijayan [at] nd [dot] edu and Tijana Milenkovic can be contacted via email at tmilenko [at] nd [dot] edu.