Organizations: Nantes University, LS2N, Nantes, 44300, France. · National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku,2026 Tokyo 101-8430 Japan. · Institute of Science Tokyo, Tokyo 152-8550 Japan.
Graph Self-Supervised Learning (GSSL) offers a powerful paradigm for learning graph representations without labeled data. However, existing work assumes clean, manually curated graphs. Recent advances in NLP enable the large-scale automatic extraction of knowledge graphs from text, opening new opportunities for GSSL while introducing substantial real-world noise. This type of noise remains largely unexplored, as prior robustness studies typically rely on synthetic perturbations. To address this gap, we present the first comprehensive evaluation of GSSL methods on text-driven graphs for unsupervised term typing. We introduce Noise-Aware Text-Driven Graph GSSL (NATD-GSSL), a unified framework that combines automatic graph construction, graph refinement, and GSSL. Our evaluation follows a dual-graph protocol that contrasts a noisy graph derived from MedMentions with a clean Unified Medical Language System (UMLS) reference graph, aligned through a shared gold standard. Our results reveal variability in robustness across both pretext tasks and Graph Neural Network (GNN) architectures. Relation reconstruction is highly sensitive to noise and benefits from well-defined schemas, whereas feature reconstruction is considerably more robust, achieving performance comparable to clean-graph settings. Contrastive objectives are generally less affected by noise but depend strongly on alignment with downstream tasks. GNN architecture also plays a critical role: bidirectional relational message-passing designs are better suited to noisy, text-driven graphs, while unidirectional relational ones perform best on clean graphs. Overall, NATD-GSSL provides practical guidance for applying GSSL to real-world, noisy graphs and achieves up to a 7% improvement over pretrained language model baselines. All code and benchmarks are publicly available at https://github.com/OthmaneKabal/MC2GAE.
Knowledge graphs automatically constructed from text are increasingly used in real-world applications. However, their inherent noise, fragmentation, and semantic inconsistencies significantly affect the performance of Graph Neural Networks (GNNs) on downstream tasks. Assessing their performance and robustness remains difficult, as it is often unclear whether observed results stem from the learning model or from the quality of the constructed graph itself. In this work, we introduce a dual-purpose benchmark designed to jointly evaluate (i) the performance of GNNs on noisy, text-derived graphs and (ii) the effectiveness of graph construction methods on a downstream task. The benchmark is built in the biomedical domain from a single textual corpus and includes two automatically constructed graphs generated using different extraction methods, alongside a high-quality reference graph curated by experts that serves as an upper performance bound. This design enables controlled comparison of construction methods and systematic evaluation of GNN robustness through semi-supervised node classification. We further provide a standardized, reproducible, and extensible evaluation framework, facilitating the integration of new graph extraction methods and learning models.
Graph self-supervised learning can reduce the need for labeled graph data and has been widely used in recommendation, social networks, and other web applications. However, existing methods often underuse high-frequency signals and may overfit to specific local patterns, which limits representation quality and generalization. We propose Frequency-Corrupt Based Graph Self-Supervised Learning (FC-GSSL), a method that builds corrupted graphs biased toward high-frequency information by corrupting nodes and edges according to their low-frequency contributions. These corrupted graphs are used as inputs to an autoencoder, while low-frequency and general features are reconstructed as supervision targets, forcing the model to fuse information from multiple frequency bands. We further design multiple sampling strategies and generate diverse corrupted graphs from the intersections and unions of the sampling results. By aligning node representations from these views, the model can discover useful frequency combinations, reduce reliance on specific high-frequency components, and improve robustness. Experiments on 14 datasets across node classification, graph prediction, and transfer learning show that FC-GSSL consistently improves performance and generalization.
Self-supervised Continual Graph Learning (CGL) aims to successively learn from a graph sequence with different tasks without label supervision - a paradigm that has attracted widespread attention. Most existing self-supervised CGL methods rely on instance-level consistency objectives that enforce stability of individual node (or node-pair) embeddings. Due to optimizing nodes in isolation, these methods fail to maintain global relational structure, causing inter-node correspondences to progressively distort under continual learning. To this end, we propose a novel Structure-Aware Optimal Transport (SAOT) framework that explicitly captures and preserves relational structure within graph representations across sequential tasks. Specifically, SAOT leverages optimal transport theory to capture global inter-node correspondences, thereby facilitating and enhancing graph representation learning. Simultaneously, SAOT incorporates a cross-task knowledge distillation mechanism to preserve the previous structural knowledge. Extensive experiments on four CGL benchmark datasets demonstrate that SAOT outperforms existing self-supervised baselines. In particular, SAOT achieves significant performance gains, improving average accuracy by up to 5% on CoraFull-CL and over 15% on Products-CL compared with state-of-the-art methods in the Class-IL setting.