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Updated: Sep 15, 2025

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Learning model-level explanations of graph neural networks via subgraph order embedding space
Li Liu1, Pengyu Wan2, Feiyan Zhang2
1Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China; School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China; Key Laboratory of Cyberspace Big Data Intelligent Security, Ministry of Education, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
This study introduces MOSE, a novel graph neural network (GNN) explainer that generates reliable graph patterns for better model understanding. MOSE ensures typicality and efficiency in explanations, improving GNN interpretability.
Area of Science:
- Artificial Intelligence
- Machine Learning
- Graph Neural Networks
Background:
- Model-level graph neural network (GNN) explainers identify critical graph patterns for class prediction.
- Existing methods often lack constraints, producing unreliable and atypical patterns that hinder explanation quality.
Purpose of the Study:
- To propose MOSE (MOdel-level explanations via a Subgraph order Embedding space), a novel explainer for generating reliable and typical graph patterns.
- To enhance the generalization of GNN explainability by extending MOSE to node classification tasks.
Main Methods:
- MOSE utilizes a graph encoder to create an embedding space preserving subgraph relationships.
- A score function with greedy sampling generates constrained, reliable graph pattern candidates.
- Explanation candidates are selected based on the GNN's predicted probability.
Main Results:
- MOSE demonstrates effectiveness across multiple metrics, including predictive accuracy, model utility, and efficiency.
- Experiments on synthetic and real-world datasets validate MOSE's performance.
- The extension of MOSE to node classification shows enhanced generalization.
Conclusions:
- MOSE provides a simple yet effective approach to generating reliable and typical model-level GNN explanations.
- The method addresses limitations of current explainers by incorporating subgraph order embeddings.
- MOSE offers a promising direction for improving GNN interpretability and applicability.
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