Accumulated local effects and graph neural networks for link prediction
Paulina Kaczyńska1,2, Julian Sienkiewicz3,4, Dominik Ślęzak5
1Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland. pm.kaczynska@student.uw.edu.pl.
Scientific Reports
|February 12, 2026
Summary
We adapted Accumulated Local Effects (ALE) for Graph Neural Networks (GNNs) in link prediction. An approximate method speeds up analysis, offering similar explanations to the exact method with improved computational efficiency.
Area of Science:
- Artificial Intelligence
- Machine Learning
- Graph Neural Networks
Background:
- Graph Neural Networks (GNNs) are powerful for link prediction.
- Model-agnostic explanation methods like Accumulated Local Effects (ALE) are crucial for understanding GNNs.
- Directly applying ALE to GNNs is computationally intensive due to complex node interactions.
Purpose of the Study:
- To adapt the Accumulated Local Effects (ALE) method for visualizing node feature influence in GNN-based link prediction.
- To address the computational challenges of applying ALE to GNNs by proposing an approximate method.
Main Methods:
- Investigated the adaptation of Accumulated Local Effects (ALE) for GNNs (Graph Convolutional Networks and Graph Attention Networks).
- Developed and evaluated an approximate method to mitigate the computational cost of ALE in GNNs.
- Analyzed the impact of parameter variations on ALE estimation accuracy for both exact and approximate methods.
Main Results:
- The approximate ALE method significantly improves computational efficiency compared to the exact method.
- The exact ALE method provides more stable explanations, especially with smaller datasets.
- Explanations from the approximate method are comparable to those from the exact method.
Conclusions:
- The approximate ALE method is a viable and efficient approach for explaining GNNs in link prediction tasks.
- Trade-offs between computational efficiency and explanation stability exist, but the approximate method offers a practical solution.
- Further analysis of parameter effects is important for accurate ALE estimation in GNNs.
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