AIMing for Standardised Explainability Evaluation in GNNs: A Framework and Case Study on Graph Kernel Networks
Authors: Magdalena Proszewska, N. Siddharth
Organizations: School of Informatics, University of Edinburgh
Abstract
Graph Neural Networks (GNNs) have advanced significantly in handling graph-structured data, but a comprehensive framework for evaluating explainability remains lacking. Existing evaluation frameworks primarily involve post-hoc explanations, and operate in the setting where multiple methods generate a suite of explanations for a single model. This makes comparison of explanations across models difficult. Evaluation of inherently interpretable models often targets a specific aspect of interpretability relevant to the model, but remains underdeveloped in terms of generating insight across a suite of measures. We introduce AIM, a comprehensive framework that addresses these limitations by measuring Accuracy, Instance-level explanations, and Model-level explanations. AIM is formulated with minimal constraints to enhance flexibility and facilitate broad applicability. Here, we use AIM in a pipeline, extracting explanations from inherently interpretable GNNs such as graph kernel networks (GKNs) and prototype networks (PNs), evaluating these explanations with AIM, identifying their limitations and obtaining insights to their characteristics. Taking GKNs as a case study, we show how the insights obtained from AIM can be used to develop an updated model, xGKN, that maintains high accuracy while demonstrating improved explainability. Our approach aims to advance the field of Explainable AI (XAI) for GNNs, providing more robust and practical solutions for understanding and improving complex models.
Graph eXplainable AI (G-XAI) is increasingly important for making Graph Neural Networks interpretable and accountable. While a growing number of explainers are available, choosing the right method and assessing the trustworthiness of its outputs remains unclear. Consistent evaluation practices and actionable guidance are still missing, hindering practical adoption. In this paper, we introduce a unified, quantitative benchmarking framework for G-XAI that requires no ground-truth assumptions. We formalize tabular explainability metrics for graph data, evaluating topological structure and node features as independent components. Our large-scale benchmarking study identifies explainers that consistently lie on the Pareto front across metric pairs and tasks, establishing robustly non-dominated solutions - while confirming that no single explainer achieves universal superiority. We distill our findings into actionable G-XAI usability guidelines to support Machine Learning practitioners in evaluating and deploying trustworthy GNN-based pipelines.
Francesco Paolo Nerini, Mirko Zaffaroni, Paolo Baracco +2
Explainable Artificial Intelligence aims to make black-box models more trustworthy by presenting, in a human-understandable manner, the elements that lead to the model's output. This involves both (i) identifying components and connections with genuine causal influence on outputs and (ii) translating such structures into an interpretable representation. For the former, we introduce CIExplainer, a novel perturbation-based method grounded in causal inference for explaining Graph Neural Networks (GNNs). CIExplainer identifies the subgraph with the highest causal effects on GNN predictions using the Potential Outcome Framework. We evaluate and compare CIExplainer on various GNN architectures (GCN, GraphSAGE, GAT, GIN) and datasets. To bridge subgraph explanations with human interpretability, we further propose G2TeXplainer, a method that transforms causal subgraphs into natural language explanations that capture both feature-level and relational information.
Francisco Caldas, Sahil Satish Kumar, Ruben Belo +1
Graph Neural Networks (GNNs) have demonstrated remarkable performance across a range of applications involving graph-structured data, particularly in high-stakes domains. However, the opaque nature of their decision-making processes limits their trustworthiness and broader adoption. Existing post-hoc explanation methods aim to improve explainability by identifying subgraphs that influence GNN predictions and adopt mixup strategies to alleviate the out-of-distribution (OOD) issue caused by using subgraphs for prediction. Yet, these approaches typically rely on soft masks, which are inherently unable to fully eliminate label-irrelevant information, allowing redundant structures to leak into the mixup process and hindering the resolution of the OOD problem, thereby degrading explanation fidelity. In this work, we propose HPME, a Hard-Perturbation Mixup Explanation framework grounded in a generalized Graph Information Bottleneck, which leverages graph pooling to extract discrete explanatory subgraphs and to yield an information-capacity bound to thoroughly compress label-irrelevant components. Furthermore, we introduce a novel mixup strategy built upon structure-level replacement, generating in-distribution explanations to effectively mitigate the distribution shift. Extensive experiments on diverse tasks demonstrate that HPME achieves state-of-the-art performance in generating robust and interpretable explanations across both synthetic and real-world datasets.