The Interpretable and Effective Graph Neural Additive Networks

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.

Graph Neural Networks (GNNs) achieve strong performance on node classification tasks but remain difficult to interpret, particularly with respect to which input features drive their predictions. Existing global GNN explainers operate at the structural level identifying recurring subgraph motifs, but none explain model behaviour globally at the level of input node attributes. We propose GRAFT, a posthoc global explanation framework that identifies class-level feature importance profiles for GNNs. The method combines diversity-guided exemplar selection, Integrated Gradients-based attribution, and aggregation to construct a global view of feature influence for each class, which can be further expressed as concise natural language rules using a large language model with self-refinement. We evaluate GRAFT across multiple datasets, architectures, and experimental settings, demonstrating its effectiveness in capturing model-relevant features, supporting bias analysis, and enabling feature-efficient transfer learning. In addition, we introduce a structured human evaluation protocol to assess the interpretability of generated rules along dimensions such as accuracy and usefulness. Our results suggest that GRAFT provides a practical and interpretable approach for analysing feature-level behaviour in GNNs, bridging quantitative attribution with human-understandable explanations.

Graph Neural Additive Networks (GNANs) have emerged as effective, interpretable-by-design architectures for graph learning. They achieve transparency by combining per-feature shape functions with simple distance-based reweighting. However, GNANs have three limitations. First, node-wise relevance scores aggregate information from all graph nodes, allowing irrelevant nodes to inherit spurious relevance from relevant ones. Second, topology is represented only through shortest-path distances, so structurally distinct graphs may share identical distance profiles. Third, feature and distance information are combined multiplicatively, entangling feature, distance, and interaction effects in a single rescalable term. We introduce AMIGA, which represents topology through a vocabulary of mined motifs and decomposes each node contribution into three additive channels: feature, structure, and feature-structure interaction. The channels are centered around a graph-balanced training baseline, making the decomposition well-defined and unique under the chosen reference distribution. Across ten graph classification and regression benchmarks, AMIGA outperforms GNAN on most datasets and narrows the gap with standard black-box GNNs. Because each channel is centered and assigned to a single node, AMIGA produces node-local explanations that reconstruct the model output exactly and support interpretation at multiple levels of granularity.