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1. Rationalizing Graph Neural Networks with Data Augmentation

   https://doi.org/10.1145/3638781  

   Liu, Gang; Inae, Eric; Luo, Tengfei; Jiang, Meng (May 2024, ACM Transactions on Knowledge Discovery from Data)

   Graph rationales are representative subgraph structures that best explain and support the graph neural network (GNN) predictions. Graph rationalization involves the joint identification of these subgraphs during GNN training, resulting in improved interpretability and generalization. GNN is widely used for node-level tasks such as paper classification and graph-level tasks such as molecular property prediction. However, on both levels, little attention has been given to GNN rationalization and the lack of training examples makes it difficult to identify the optimal graph rationales. In this work, we address the problem by proposing a unified data augmentation framework with two novel operations on environment subgraphs to rationalize GNN prediction. We define the environment subgraph as the remaining subgraph after rationale identification and separation. The framework efficiently performs rationale–environment separation in therepresentation spacefor a node’s neighborhood graph or a graph’s complete structure to avoid the high complexity of explicit graph decoding and encoding. We conduct experiments on 17 datasets spanning node classification, graph classification, and graph regression. Results demonstrate that our framework is effective and efficient in rationalizing and enhancing GNNs for different levels of tasks on graphs. 

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2. GStarX: Explaining Graph Neural Networks with Structure-Aware Cooperative Games

   Zhang, Shichang; Liu, Yozen; Shah, Neil; Sun, Yizhou (January 2022, 36th Conference on Neural Information Processing Systems (NeurIPS 2022))

   Explaining machine learning models is an important and increasingly popular area of research interest. The Shapley value from game theory has been proposed as a prime approach to compute feature importance towards model predictions on images, text, tabular data, and recently graph neural networks (GNNs) on graphs. In this work, we revisit the appropriateness of the Shapley value for GNN explanation, where the task is to identify the most important subgraph and constituent nodes for GNN predictions. We claim that the Shapley value is a non-ideal choice for graph data because it is by definition not structure-aware. We propose a Graph Structure-aware eXplanation (GStarX) method to leverage the critical graph structure information to improve the explanation. Specifically, we define a scoring function based on a new structure-aware value from the cooperative game theory proposed by Hamiache and Navarro (HN). When used to score node importance, the HN value utilizes graph structures to attribute cooperation surplus between neighbor nodes, resembling message passing in GNNs, so that node importance scores reflect not only the node feature importance, but also the node structural roles. We demonstrate that GStarX produces qualitatively more intuitive explanations, and quantitatively improves explanation fidelity over strong baselines on chemical graph property prediction and text graph sentiment classification. 

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3. Learning Graph Neural Networks with Positive and Unlabeled Nodes

   https://doi.org/10.1145/3450316  

   Wu, Man; Pan, Shirui; Du, Lan; Zhu, Xingquan (June 2021, ACM Transactions on Knowledge Discovery from Data)

   null (Ed.)

   Graph neural networks (GNNs) are important tools for transductive learning tasks, such as node classification in graphs, due to their expressive power in capturing complex interdependency between nodes. To enable GNN learning, existing works typically assume that labeled nodes, from two or multiple classes, are provided, so that a discriminative classifier can be learned from the labeled data. In reality, this assumption might be too restrictive for applications, as users may only provide labels of interest in a single class for a small number of nodes. In addition, most GNN models only aggregate information from short distances ( e.g. , 1-hop neighbors) in each round, and fail to capture long-distance relationship in graphs. In this article, we propose a novel GNN framework, long-short distance aggregation networks, to overcome these limitations. By generating multiple graphs at different distance levels, based on the adjacency matrix, we develop a long-short distance attention model to model these graphs. The direct neighbors are captured via a short-distance attention mechanism, and neighbors with long distance are captured by a long-distance attention mechanism. Two novel risk estimators are further employed to aggregate long-short-distance networks, for PU learning and the loss is back-propagated for model learning. Experimental results on real-world datasets demonstrate the effectiveness of our algorithm. 

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4. Global Graph Counterfactual Explanation: A Subgraph Mapping Approach

   He, Yinhan; Zheng, Wendy; Zhu, Yaochen; Ma, Jing; Mishra, Saumitra; Raman, Natraj; Liu, Ninghao; Li, Jundong (March 2025, Transactions on machine learning research)

   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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5. H^2GNN: Graph Neural Networks with Homophilic and Heterophilic Feature Aggregations

   Jing, Shixiong; Chen, Lingwei; Li, Quan; Wu, Dinghao (July 2024, International Conference on Database Systems for Advanced Applications, Springer Nature Singapore)

   Graph neural networks (GNNs) rely on the assumption of graph homophily, which, however, does not hold in some real-world scenarios. Graph heterophily compromises them by smoothing node representations and degrading their discrimination capabilities. To address this limitation, we propose H^2GNN, which implements Homophilic and Heterophilic feature aggregations to advance GNNs in graphs with homophily or heterophily. H^2GNN proceeds by combining local feature separation and adaptive message aggregation, where each node separates local features into similar and dissimilar feature vectors, and aggregates similarities and dissimilarities from neighbors based on connection property. This allows both similar and dissimilar features for each node to be effectively preserved and propagated, and thus mitigates the impact of heterophily on graph learning process. As dual feature aggregations introduce extra model complexity, we also offer a simplified implementation of H^2GNN to reduce training time. Extensive experiments on seven benchmark datasets have demonstrated that H^2GNN can significantly improve node classification performance in graphs with different homophily ratios, which outperforms state-of-the-art GNN models. 

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