Predicting protein complexes in protein interaction networks using Mapper and graph convolution networks

Protein complexes are groups of interacting proteins that are central to multiple biological processes. Studying protein complexes can enhance our understanding of cellular functions and malfunctions and thus support the development of effective disease treatments. High-throughput experimental techniques allow the generation of large-scale protein-protein interaction datasets. Accordingly, various computational approaches to predict protein complexes from protein-protein interactions were presented in the literature. They are typically based on networks in which nodes and edges represent proteins and their interactions, respectively. State-of-the-art approaches mainly rely on clustering static networks to identify complexes. However, since protein interactions are highly dynamic in nature, recent approaches seek to model such dynamics by typically integrating gene expression data and identifying protein complexes accordingly. We propose MComplex, a method that utilizes time-series gene expression with interaction data to generate a temporal network which is passed to a generative adversarial network whose generator is a graph convolutional network. This creates embeddings which are then analyzed using a modified graph-based version of the Mapper algorithm to predict corresponding protein complexes. We test our approach on multiple benchmark datasets and compare identified complexes against gold-standard protein complex datasets. Our results show that MComplex outperforms existing methods in several evaluation aspects, namely recall and maximum matching ratio as well as a composite score covering aggregated evaluation measures. The code and data are available for free download from https://github.com/LeonardoDaou/MComplex.