PPI-Net connects molecular protein interactions to functional processes in disease

ArXi:2605.07838v1 Announce Type: cross Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect structured biological relationships or lack interpretability across scales. Here we present PPI-Net, a hierarchical graph neural network that integrates protein-protein interaction (PPI) networks with pathway-level representations to model disease from molecular interactions to functional processes.