Network-Integrated Reverse Vaccinology Using Biomni-Prioritized Features and Graph Neural Networks in Flavobacterium

Rational vaccine design against emerging and understudied pathogens is hindered by incomplete protein–protein interaction (PPI) maps and limited integration of computational prioritization with network-based inference. Here, we present a unified framework that couples Biomni, a biomedical AI agent providing vaccine-priority and virulence-aware annotations, with graph neural network (GNN) based link prediction on STRING-derived PPIs to systematically identify candidate vaccine targets in Flavobacterium. Starting from the complete Flavobacterium proteome, Biomni-derived antigenicity, subcellular, and virulence features were integrated with high-confidence STRING associations into a unified PPI graph in which isolated and weakly connected proteins were explicitly retained. We evaluated three representative GNN architectures Graph Convolutional Network (GCN), Graph Attention Network (GAT), and GraphSAGE under a consistent three-fold cross-validation scheme and performed priorityaware assessment of predicted high-confidence links (posterior probability ≥ 0.90). GraphSAGE achieved the highest best-fold ROC-AUC (0.5585), followed by GAT (0.5536) and GCN (0.5000), reflecting modest yet meaningful discriminative performance in this sparse, single-species setting. Class-pair analyses revealed that GCN predominantly reconstructed links among lower-priority nodes, while GAT modestly increased coverage of interactions involving High-priority proteins but 1 remained biased toward low-tier combinations. In contrast, GraphSAGE produced a more balanced distribution of predicted links across Biomni priority tiers, including enriched High–Medium and High–Low connections, indicating more effective use of antigenicity and virulence features for inductive generalization to under-characterized proteins. Collectively, these results demonstrate that integrating AI-driven prioritization with inductive GNNs enables biologically informed exploration of missing PPIs and highlights previously overlooked Flavobacterium proteins as plausible vaccine candidates. The proposed Biomni–STRING–GNN framework is modular and transferable, offering a principled template for priority-aware, network-based vaccine target discovery in data-sparse pathogen systems.