Graph Neural Networks Powered by Encoder Embedding for Improved Node Learning

Abstract: Graph neural networks (GNNs) have emerged as a powerful framework for a wide range of node-level graph learning tasks. However, their performance is often constrained by reliance on random or minimally informed initial feature representations, which can lead to slow convergence and suboptimal solutions. In this paper, we leverage a statistically grounded method, one-hot graph encoder embedding (GEE), to generate high-quality initial node features that enhance the end-to-end training of GNNs. We refer to this integrated framework as the GEE-powered GNN (GG), and demonstrate its effectiveness through extensive simulations and real-world experiments across both unsupervised and supervised settings. In node clustering, GG consistently achieves state-of-the-art performance, ranking first across all evaluated real-world datasets, while exhibiting faster convergence compared to the standard GNN. For node classification, we further propose an enhanced variant, GG-C, which concatenates the outputs of GG and GEE and outperforms competing baselines. These results confirm the importance of principled, structure-aware feature initialization in realizing the full potential of GNNs.