[2604.08890] A Closer Look at the Application of Causal Inference in Graph Representation Learning

Computer Science > Machine Learning arXiv:2604.08890 (cs) [Submitted on 10 Apr 2026] Title:A Closer Look at the Application of Causal Inference in Graph Representation Learning Authors:Hang Gao, Kunyu Li, Huang Hong, Baoquan Cui, Fengge Wu View a PDF of the paper titled A Closer Look at the Application of Causal Inference in Graph Representation Learning, by Hang Gao and 4 other authors View PDF HTML (experimental) Abstract:Modeling causal relationships in graph representation learning remains a fundamental challenge. Existing approaches often draw on theories and methods from causal inference to identify causal subgraphs or mitigate confounders. However, due to the inherent complexity of graph-structured data, these approaches frequently aggregate diverse graph elements into single causal variables, an operation that risks violating the core assumptions of causal inference. In this work, we prove that such aggregation compromises causal validity. Building on this conclusion, we propose a theoretical model grounded in the smallest indivisible units of graph data to ensure that the causal validity is guaranteed. With this model, we further analyze the costs of achieving precise causal modeling in graph representation learning and identify the conditions under which the problem can be simplified. To empirically support our theory, we construct a controllable synthetic dataset that reflects realworld causal structures and conduct extensive experiments for validation. Finally,...