An official website of the United States government
In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE.
more »
« less
This content will become publicly available on May 31, 2026
DyExplainer: Self-explainable Dynamic Graph Neural Network with Sparse Attentions
Graph Neural Networks (GNNs) resurge as a trending research subject owing to their impressive ability to capture representations from graph-structured data. However, the black-box nature of GNNs presents a significant challenge in terms of comprehending and trusting these models, thereby limiting their practical applications in mission-critical scenarios. Although there has been substantial progress in the field of explaining GNNs in recent years, the majority of these studies are centered on static graphs, leaving the explanation of dynamic GNNs less explored. Dynamic GNNs, with their ever-evolving graph structures, pose a unique challenge and require additional efforts to effectively capture temporal dependencies and structural relationships. To address this challenge, we present DyExplainer, a novel approach to explaining dynamic GNNs on the fly. DyExplainer trains a dynamic GNN backbone to extract representations of the graph at each snapshot, while simultaneously exploring structural relationships and temporal dependencies through a sparse attention technique. To preserve the desired properties of the explanation, such as structural consistency and temporal continuity, we augment our approach with contrastive learning techniques to providea priori-guided regularization. To model longer-term temporal dependencies, we develop a buffer-based live-updating scheme for training. The results of our extensive experiments on various datasets demonstrate the superiority of DyExplainer, not only providing faithful explainability of the model predictions but also significantly improving the model prediction accuracy, as evidenced in the link prediction task.
more »
« less
- Award ID(s):
- 2331908
- PAR ID:
- 10632899
- Publisher / Repository:
- ACM
- Date Published:
- Journal Name:
- ACM Transactions on Knowledge Discovery from Data
- Volume:
- 19
- Issue:
- 4
- ISSN:
- 1556-4681
- Page Range / eLocation ID:
- 1 to 21
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Despite recent progress in Graph Neural Networks (GNNs), explaining predictions made by GNNs remains a challenging and nascent problem. The leading method mainly considers the local explanations, i.e., important subgraph structure and node features, to interpret why a GNN model makes the prediction for a single instance, e.g. a node or a graph. As a result, the explanation generated is painstakingly customized at the instance level. The unique explanation interpreting each instance independently is not sufficient to provide a global understanding of the learned GNN model, leading to the lack of generalizability and hindering it from being used in the inductive setting. Besides, training the explanation model explaining for each instance is time-consuming for large-scale real-life datasets. In this study, we address these key challenges and propose PGExplainer, a parameterized explainer for GNNs. PGExplainer adopts a deep neural network to parameterize the generation process of explanations, which renders PGExplainer a natural approach to multi-instance explanations. Compared to the existing work, PGExplainer has better generalization ability and can be utilized in an inductive setting without training the model for new instances. Thus, PGExplainer is much more efficient than the leading method with significant speed-up. In addition, the explanation networks can also be utilized as a regularizer to improve the generalization power of existing GNNs when jointly trained with downstream tasks. Experiments on both synthetic and real-life datasets show highly competitive performance with up to 24.7% relative improvement in AUC on explaining graph classification over the leading baseline.more » « less
-
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.more » « less
-
Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models and explaining predictions made by GNNs remains unsolved. Here we propose GNNEXPLAINER, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNEXPLAINER identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN’s prediction. Further, GNNEXPLAINER can generate consistent and concise explanations for an entire class of instances. We formulate GNNEXPLAINER as an optimization task that maximizes the mutual information between a GNN’s prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms alternative baseline approaches by up to 43.0% in explanation accuracy. GNNEXPLAINER provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.more » « less
-
Graph neural networks (GNNs) have shown great potential in learning on graphs, but they are known to perform sub-optimally on link prediction tasks. Existing GNNs are primarily designed to learn node-wise representations and usually fail to capture pairwise relations between target nodes, which proves to be crucial for link prediction. Recent works resort to learning more expressive edge-wise representations by enhancing vanilla GNNs with structural features such as labeling tricks and link prediction heuristics, but they suffer from high computational overhead and limited scalability. To tackle this issue, we propose to learn structural link representations by augmenting the message-passing framework of GNNs with Bloom signatures. Bloom signatures are hashing-based compact encodings of node neighborhoods, which can be efficiently merged to recover various types of edge-wise structural features. We further show that any type of neighborhood overlap-based heuristic can be estimated by a neural network that takes Bloom signatures as input. GNNs with Bloom signatures are provably more expressive than vanilla GNNs and also more scalable than existing edge-wise models. Experimental results on five standard link prediction benchmarks show that our proposed model achieves comparable or better performance than existing edge-wise GNN models while being 3-200 × faster and more memory-efficient for online inference.more » « less
