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Uncovering rationales behind predictions of graph neural networks (GNNs) has received increasing attention over recent years. Instance-level GNN explanation aims to discover critical input elements, such as nodes or edges, that the target GNN relies upon for making predictions. Though various algorithms are proposed, most of them formalize this task by searching the minimal subgraph, which can preserve original predictions. However, an inductive bias is deep-rooted in this framework: Several subgraphs can result in the same or similar outputs as the original graphs. Consequently, they have the danger of providing spurious explanations and failing to provide consistent explanations. Applying them to explain weakly performed GNNs would further amplify these issues. To address this problem, we theoretically examine the predictions of GNNs from the causality perspective. Two typical reasons for spurious explanations are identified: confounding effect of latent variables like distribution shift and causal factors distinct from the original input. Observing that both confounding effects and diverse causal rationales are encoded in internal representations,we propose a new explanation framework with an auxiliary alignment loss, which is theoretically proven to be optimizing a more faithful explanation objective intrinsically. Concretely for this alignment loss, a set of different perspectives are explored: anchor-based alignment, distributional alignment based on Gaussian mixture models, mutual-information-based alignment, and so on. A comprehensive study is conducted both on the effectiveness of this new framework in terms of explanation faithfulness/consistency and on the advantages of these variants. For our codes, please refer to the following URL link:https://github.com/TianxiangZhao/GraphNNExplanation
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This content will become publicly available on March 1, 2026
Global Graph Counterfactual Explanation: A Subgraph Mapping Approach
Graph Neural Networks (GNNs) have been widely deployed in various real-world applications. However, most GNNs are black-box models that lack explanations. One strategy to explain GNNs is through counterfactual explanation, which aims to find minimum perturbations on input graphs that change the GNN predictions. Existing works on GNN counterfactual explanations primarily concentrate on the local-level perspective (i.e., generating counterfactuals for each individual graph), which suffers from information overload and lacks insights into the broader cross-graph relationships. To address such issues, we propose GlobalGCE, a novel global-level graph counterfactual explanation method. GlobalGCE aims to identify a collection of subgraph mapping rules as counterfactual explanations for the target GNN. According to these rules, substituting certain significant subgraphs with their counterfactual subgraphs will change the GNN prediction to the desired class for most graphs (i.e., maximum coverage). Methodologically, we design a significant subgraph generator and a counterfactual subgraph autoencoder in our GlobalGCE, where the subgraphs and the rules can be effectively generated. Extensive experiments demonstrate the superiority of our GlobalGCE compared to existing baselines.
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- PAR ID:
- 10612754
- Publisher / Repository:
- Transactions on Machine Learning Research
- Date Published:
- Journal Name:
- Transactions on machine learning research
- ISSN:
- 2835-8856
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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