Towards Foundation Models for Relational Databases with Language Models and Graph Neural Networks
Authors: Jingcheng Wu, Ratan Bahadur Thapa, Mojtaba Nayyeri, Lucas Etteldorf, Max Finkenbeiner, Fabian Leeske, Steffen Staab
Organizations: University of Stuttgart, Stuttgart, Germany · Web and Internet Science Research Group, University of Southampton, Southampton, United Kingdom
Relational databases store much of the world's structured information, and they are essential for driving complex predictive applications. However, deep learning progress on relational data remains limited, as conventional approaches flatten databases into single tables via manual feature engineering, discarding relational context. Relational deep learning (RDL) addresses this by modeling databases as relational entity graphs (REGs) for graph neural networks (GNNs), but remains task- and database-specific. To combine the strengths of both paradigms, we propose a hybrid architecture combining a fine-tuned BART encoder to capture intra-row semantics with a GraphSAGE-based GNN over REGs to inject relational context. Experiments on RelBench show that the GNN substantially enriches BART's row embeddings, achieving a ROC-AUC of 67.40 on the driver-dnf task from the rel-f1 dataset. This performance is competitive with supervised baselines such as LightGBM (68.86) and narrows the gap to RDL (72.62) to within 5.22 points, though a substantial gap remains to state-of-the-art foundation models such as KumoRFM (82.63). These results suggest that lightweight hybrid LM-GNN architectures offer a promising and resource-efficient path towards foundation models for relational databases.
Relational databases (RDBs) are the primary data infrastructure in many enterprises, yet recent deep learning methods designed for RDBs have been evaluated under inconsistent experimental protocols, making fair comparison difficult. We present one of the first systematic benchmarking studies of recently released deep learning methods for RDBs, evaluating them across five relational databases, with one classification and one regression task for each. We refactor all deep RDB models to allow the full range of experimental procedures to be applied consistently across all methods. Our findings indicate that the relational transformer (RT) approach delivers the strongest overall performance on both classification and regression tasks compared to the state-of-the-art graph-based modeling and learning of RDBs. Even for single-table learning tasks, deep learning methods designed for RDBs outperform the leading tabular foundation model, TabPFN 2.5. Extending learning from a single table (hop = 0) to multiple tables (hop = 1, 2) by connecting neighboring tables in relational databases enhances performance, but the additional benefit from higher hops diminishes as computational overhead grows. Deep RDB learning methods have the potential to challenge state-of-the-art tabular foundation models, especially on large-scale enterprise data. The source code for this benchmarking study is publicly available.
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 schema-derived 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 non-monotonic 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.
Relational databases underpin modern enterprise, scientific, and healthcare systems, yet predictive machine learning on such data remains challenging due to their multi-table, heterogeneous, and temporal structure. Relational Deep Learning (RDL) addresses this by representing databases as heterogeneous graphs and applying graph neural networks (GNNs) directly. RelBench v2 recently introduced autocomplete tasks -- a practically motivated task type where the goal is to predict an existing column value from relational context, analogous to an intelligent form-filling assistant. We propose RelGT-AC (Relational Graph Transformer for Autocomplete), extending the RelGT architecture with three targeted contributions: (1) a column masking strategy that prevents trivial solutions by masking the target column during subgraph encoding; (2) a unified task head supporting binary classification, multiclass classification, and regression autocomplete tasks within a single model; and (3) a TF-IDF text encoder that automatically detects and encodes free-text columns, recovering strong lexical signal that categorical encoders discard. Across 7 tasks spanning 3 RelBench v2 datasets (rel-trial, rel-f1, rel-stack), RelGT-AC outperforms the GraphSAGE baseline on all 3 regression autocomplete tasks and achieves up to +10 AUROC points on text-heavy eligibility tasks via the TF-IDF encoder.