cs.LGSep 4, 2026

A Comparative Study of Counterfactual Explainers for Graph Neural Networks Enabling Multiple Types of Graph Edit

Authors: Maria Myrto Villia, Filippos Gouidis, Theodore Patkos, Panos Trahanias

Organizations: Institute of Computer Science, Foundation for Research and Technology - Hellas (FORTH) · Computer Science Department, University of Crete Greece

Abstract

Counterfactual explanations for graph-structured data seek to determine minimal and realistic modifications required in an input graph to alter a model's prediction to a predefined output. Although counterfactual explainers that support modifying the graph by both adding and removing edges have recently emerged, there is still a lack of general and efficient methods, especially when considering the quality of the generated explanations. Moreover, the problem remains far from solved, as existing methods exhibit different strengths and weaknesses, often trading off between explanation size, coverage and quality. For this reason, it is important to identify where each method performs well and where it falls short, so as to guide future research in the field. Thus, our study compares six state-of-the-art (SOTA) models on a diverse set of real-world and synthetic datasets, covering both binary and multi-class graph and node classification tasks, and evaluates their performance using diverse quantitative and qualitative metrics.

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