xAI-Drop: Don't Use What You Cannot Explain
Abstract
Graph Neural Networks (GNNs) have emerged as the predominant paradigm for learning from graph-structured data, offering a wide range of applications from social network analysis to bioinformatics. Despite their versatility, GNNs face challenges such as lack of generalization and poor interpretability, which hinder their wider adoption and reliability in critical applications. Dropping has emerged as an effective paradigm for improving the generalization capabilities of GNNs. However, existing approaches often rely on random or heuristic-based selection criteria, lacking a principled method to identify and exclude nodes that contribute to noise and over-complexity in the model. In this work, we argue that explainability should be a key indicator of a model's quality throughout its training phase. To this end, we introduce xAI-Drop, a novel topological-level dropping regularizer that leverages explainability to pinpoint noisy network elements to be excluded from the GNN propagation mechanism. An empirical evaluation on diverse real-world datasets demonstrates that our method outperforms current state-of-the-art dropping approaches in accuracy, and improves explanation quality.
Benchmark Results
Tested on 1 dataset 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 43 | DropEdge | 0.8900 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 440 | xAI-DropNode | 0.8280
±0.0050 | This paper |
| 507 | ExPass | 0.8220
±0.0060 | This paper |
| 551 | ENGAGE | 0.8180
±0.0040 | This paper |
| 619 | DropNode | 0.8080
±0.0055 best reported | best today: RADE: Random Add-Drop Edge as a Regularizer (ICML 2026) |
| 621 | DropMess | 0.8080
±0.0050 | This paper |
| 647 | MATE | 0.8030
±0.0040 | This paper |
| 657 | DropAggr | 0.8000
±0.0060 | This paper |
| 688 | Learn2Drop | 0.7930
±0.0110 | This paper |
| 695 | GCN Baseline | 0.7900
±0.0030 | This paper |
| 724 | MLP | 0.7768 | |
| 786 | BBGDC | 0.7420
±0.0030 | This paper |
