What Makes a Desired Graph for Relational Deep Learning?

Yao Cheng, Siqiang Luo
Proceedings of the 43rd International Conference on Machine Learning, PMLR 306:18979-18996, 2026.

Abstract

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. Through an empirical analysis on real-world databases, we find that effective graphs arise from a task-dependent balance between removing task-irrelevant structure and injecting task-aligned relational connectivity. Filtering exhibits a non-monotonic effect on performance, while structural injection is beneficial only when it reflects the logic of the downstream task. Based on these findings, we develop an end-to-end structural optimizer that applies both operations to adapt relational graphs automatically. Across 23 tasks spanning classification, regression, and recommendation, the optimized graphs consistently improve accuracy while often reducing inference cost.

Cite this Paper

BibTeX
@InProceedings{pmlr-v306-cheng26j, title = {What Makes a Desired Graph for Relational Deep Learning?}, author = {Cheng, Yao and Luo, Siqiang}, booktitle = {Proceedings of the 43rd International Conference on Machine Learning}, pages = {18979--18996}, year = {2026}, editor = {Zhang, Tong and Dudik, Miroslav and Jaggi, Martin and Agarwal, Alekh and Li, Sharon and Schuurmans, Dale and Zhu, Jerry and Berkenkamp, Felix and Dong, Hanze and Bietti, Alberto}, volume = {306}, series = {Proceedings of Machine Learning Research}, month = {06--11 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v306/main/assets/cheng26j/cheng26j.pdf}, url = {https://proceedings.mlr.press/v306/cheng26j.html}, abstract = {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. Through an empirical analysis on real-world databases, we find that effective graphs arise from a task-dependent balance between removing task-irrelevant structure and injecting task-aligned relational connectivity. Filtering exhibits a non-monotonic effect on performance, while structural injection is beneficial only when it reflects the logic of the downstream task. Based on these findings, we develop an end-to-end structural optimizer that applies both operations to adapt relational graphs automatically. Across 23 tasks spanning classification, regression, and recommendation, the optimized graphs consistently improve accuracy while often reducing inference cost.} }
Endnote
%0 Conference Paper %T What Makes a Desired Graph for Relational Deep Learning? %A Yao Cheng %A Siqiang Luo %B Proceedings of the 43rd International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2026 %E Tong Zhang %E Miroslav Dudik %E Martin Jaggi %E Alekh Agarwal %E Sharon Li %E Dale Schuurmans %E Jerry Zhu %E Felix Berkenkamp %E Hanze Dong %E Alberto Bietti %F pmlr-v306-cheng26j %I PMLR %P 18979--18996 %U https://proceedings.mlr.press/v306/cheng26j.html %V 306 %X 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. Through an empirical analysis on real-world databases, we find that effective graphs arise from a task-dependent balance between removing task-irrelevant structure and injecting task-aligned relational connectivity. Filtering exhibits a non-monotonic effect on performance, while structural injection is beneficial only when it reflects the logic of the downstream task. Based on these findings, we develop an end-to-end structural optimizer that applies both operations to adapt relational graphs automatically. Across 23 tasks spanning classification, regression, and recommendation, the optimized graphs consistently improve accuracy while often reducing inference cost.
APA
Cheng, Y. & Luo, S.. (2026). What Makes a Desired Graph for Relational Deep Learning?. Proceedings of the 43rd International Conference on Machine Learning, in Proceedings of Machine Learning Research 306:18979-18996 Available from https://proceedings.mlr.press/v306/cheng26j.html.

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