GNNAnatomy: Systematic Generation and Evaluation of Multi-Level Explanations for Graph Neural Networks

Graph Neural Networks (GNNs) have proven highly effective in various machine learning (ML) tasks involving graphs, such as node/graph classification and link prediction. However, explaining the decisions made by GNNs poses challenges because of the aggregated relational information based on graph structure, leading to complex data transformations. Existing methods for explaining GNNs often face limitations in systematically exploring diverse substructures and evaluating results in the absence of ground truths. To address this gap, we introduce GNNAnatomy, a model- and dataset-agnostic visual analytics system designed to facilitate the generation and evaluation of multi-level explanations for GNNs. In GNNAnatomy, we employ graphlets to elucidate GNN behavior in graph-level classification tasks. By analyzing the associations between GNN classifications and graphlet frequencies, we formulate hypothesized factual and counterfactual explanations. To validate a hypothesized graphlet explanation, we introduce two metrics: (1) the correlation between its frequency and the classification confidence, and (2) the change in classification confidence after removing this substructure from the original graph. To demonstrate the effectiveness of GNNAnatomy, we conduct case studies on both real-world and synthetic graph datasets from various domains. Additionally, we qualitatively compare GNNAnatomy with a state-of-the-art GNN explainer, demonstrating the utility and versatility of our design.