SHELLEY: Exploring Learning-Based Network Alignment on Biological Data

Global network alignment is the computational problem of determining the similarity between nodes of different networks to establish a one-to-one correspondence between them. It has important applications in the biological field, particularly for discovering similar roles between the elements of different systems or for transferring knowledge from a well-studied system to another. In this paper, we present SHELLEY, a tool that facilitates the development, testing, and combination of learning-based network alignment algorithms by providing a set of modules that allow for the recreation and combination of both representation learning methods (RLMs) and deep matching methods (DMMs). We then present a case study in which we apply this tool to a protein-protein interaction network (PPI), demonstrating how the representation phase of RLMs is crucial for model robustness against noise.The code of SHELLEY is available at: https://github.com/rickydeluca/shelley