Bayesian-Optimized Learning on Heterogeneous Multipartite Graphs: A Framework for Multi-Level Relational Data
Year: 2025
Type: article
Abstract: Real-world systems frequently exhibit hierarchical multipartite graph structures, yet existing graph neural network (GNN) approaches lack systematic frameworks for hyperparameter optimization in heterogeneous multi-level architectures, limiting their practical applicability. This study proposes a Bayesian optimization framework specifically designed for heterogeneous GNNs operating on three-level graph structures, addressing the computational challenges of configuring partition-aware architecture. Four GNN architectures—Graph Convolutional Networks (GCNs), Graph Attention Networks (GATs), Graph Isomorphism Networks (GINs), and GraphSAGE—were systematically evaluated using Gaussian Process-based Bayesian hyperparameter optimization with inter-partition message-passing mechanisms. The framework was validated on the TIMSS 2023 dataset (10,000 students, 789 schools, 25 countries), demonstrating that Bayesian-optimized GraphSAGE achieved the highest explained variance (R2 = 0.6187, RMSE = 71.73, MAE = 64.32) compared to seven baseline methods. Bayesian optimization substantially improved model performance, revealing that two-layer architectures optimally capture cross-partition dependencies in three-level structures. GNNExplainer was used to identify the most influential student-level features learned by the model, providing explanatory insight into how the model represents individual characteristics. The optimization framework is broadly applicable to other heterogeneous and multi-level graph settings; however, the empirical findings, such as the optimal architecture depth, are specific to hierarchical graphs with structural properties like the TIMSS topology.
Source: Symmetry
DOI: 10.3390/sym17122082
Authors: Tuba Koç, Mehmet Ali Cengiz, Haydar Koç
Language: English
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,896
Award: G300740676
OpenAlex ID: W7108469312