Robustness of Graph Self-Supervised Learning to Real-World Noise: A Case Study on Text-Driven Biomedical Graphs
This study addresses the vulnerability of graph self-supervised learning (GSSL) to noise inherent in real-world, text-derived biomedical knowledge graphs—a challenge overlooked by existing research that predominantly evaluates methods on clean or synthetic graphs. To bridge this gap, the authors introduce the first benchmarking framework tailored to realistic noisy settings, systematically comparing model performance on MedMentions (a noisy graph) against UMLS (a curated, clean graph). Through comprehensive analysis of pretraining tasks and GNN architectures, they find that feature reconstruction exhibits robustness under noise and that bidirectional message passing consistently outperforms unidirectional variants. The work further proposes NATD-GSSL, a unified pipeline integrating graph construction, refinement, and representation learning, which achieves up to a 7% improvement over language model baselines. Code and benchmark datasets are publicly released.