What Makes a Desired Graph for Relational Deep Learning?

Relational deep learning (RDL) converts relational databases (RDBs) into heterogeneous graphs, but graphs derived directly from database schemas are often not well suited for how graph neural networks (GNNs) perform relational reasoning. We study what makes a relational graph suitable for deep learning and show that schemaderived graphs suffer from two systematic failures: information overload and semantic fragmentation. Our empirical analysis reveals that the desired graph is not the raw schema, but a result of controlled structural adaptation. Performance depends on balancing two operations: mitigating information overload via filtering, and repairing semantic fragmentation via injection. Specifically, filtering serves as a bias-variance knob with nonmonotonic effects, while injection improves performance only when it explicitly restores the relational dependencies missing from the original schema. Based on these findings, we develop an end-to-end structural optimizer that applies both operations to adapt relational graphs automatically. Across 26 tasks spanning classification, regression, and recommendation, the optimized graphs consistently improve accuracy while often reducing inference cost. Code and data are available at https://github.com/cy623/ Structural_Optimizer_RDL.git .