Immune BioGraphy: A tale of graphical approaches in systems and virtual immunology

We discuss how graph-based machine learning (Graph ML) can guide discovery in the next era of systems immunology. The multi-scale complexity of the immune system makes it ideal for graph-based models, which can integrate disparate, high-resolution datasets while focusing on biological interpretability. Graph ML uniquely models how individual perturbations cascade into systemic disruptions across biological scales. Graph ML can be fused with recent advances in knowledge graphs and language models to help build a virtual cell, test therapeutic strategies, and accelerate translational discovery.