Paradigm Shift of GNN Explainer from Label Space to Prototypical Representation Space

ICLR 2026 Conference Submission858 Authors

Keywords: Graph Neural Networks, GNN Explanation Method, Vector Quantization

Abstract: Post-hoc instance-level graph neural network (GNN) explainers are developed to identify a compact subgraph (i.e., explanation) that encompasses the most influential components for each input graph. A fundamental limitation of existing methods lies in the insufficient utilization of structural information during GNN explainer optimization. They typically optimize the explainer by aligning the GNN predictions of input graph and its explanation in the graph label space which inherently lacks expressiveness to describe various graph structures. Motivated by the powerful structural expression ability of vectorized graph representations, we for the first time propose to shift the GNN explainer optimization from the graph label space to the graph representation space. However, the paradigm shift is challenging due to both the entanglement between the explanatory and non-explanatory substructures, and the distributional discrepancy between the input graph and the explanation subgraph. To this end, we meticulously design IDEA, a universal dual-stage optimization framework grounded in a prototypical graph representation space, which can generalize across diverse existing GNN explainer architectures. Specifically, in the Structural Information Disentanglement stage, a graph tokenizer equipped with a structure-aware disentanglement objective is designed to disentangle the explanatory substructures and encapsulate them into explanatory prototypes. In the Explanatory Prototype Alignment stage, IDEA aligns the representational distributions of the input graph and its explanation unified in the prototypical representation space, to optimize the GNN explainer. Comprehensive experiments on real-world and synthetic datasets demonstrate the effectiveness of IDEA, with the average improvements of ROC-AUC by 4.45% and precision by 48.71%. We further integrate IDEA with diverse explainer architectures and achieve an improvement by up to 10.70%, which verifies its generalizability.

Primary Area: interpretability and explainable AI

Submission Number: 858