# GNN-Ensemble: Towards Random Decision Graph Neural Networks

arXiv: https://arxiv.org/abs/2303.11376 · HTML: https://mlsanity.com/paper/2303.11376/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 51 references that are in the map.
- First posted on arXiv 20 Mar 2023.

## Builds on (most cited first, 30 of 32)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Obfuscated Gradients Give a False Sense of Security: Circumventing Defenses to Adversarial Examples](https://mlsanity.com/paper/1802.00420/) (2018)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [DropEdge: Towards Deep Graph Convolutional Networks on Node Classification](https://mlsanity.com/paper/1907.10903/) (2019)
- [GraphSAINT: Graph Sampling Based Inductive Learning Method](https://mlsanity.com/paper/1907.04931/) (2019)
- [FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling](https://mlsanity.com/paper/1801.10247/) (2018)
- [Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks](https://mlsanity.com/paper/1905.07953/) (2019)
- [Federated Machine Learning: Concept and Applications](https://mlsanity.com/paper/1902.04885/) (2019)
- [Adversarial Attacks on Neural Networks for Graph Data](https://mlsanity.com/paper/1805.07984/) (2018)
- [Graph Structure Learning for Robust Graph Neural Networks](https://mlsanity.com/paper/2005.10203/) (2020)
- [Adversarial Attack on Graph Structured Data](https://mlsanity.com/paper/1806.02371/) (2018)
- [Adversarial Attacks on Graph Neural Networks via Meta Learning](https://mlsanity.com/paper/1902.08412/) (2019)
- [Improving Adversarial Robustness via Promoting Ensemble Diversity](https://mlsanity.com/paper/1901.08846/) (2019)
- [Topology Attack and Defense for Graph Neural Networks: An Optimization Perspective](https://mlsanity.com/paper/1906.04214/) (2019)
- [Adversarial Attacks on Node Embeddings via Graph Poisoning](https://mlsanity.com/paper/1809.01093/) (2018)
- [Bayesian Graph Neural Networks with Adaptive Connection Sampling](https://mlsanity.com/paper/2006.04064/) (2020)
- [A Restricted Black-box Adversarial Framework Towards Attacking Graph Embedding Models](https://mlsanity.com/paper/1908.01297/) (2019)
- [Differentiable Scaffolding Tree for Molecular Optimization](https://mlsanity.com/paper/2109.10469/) (2021)
- [MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization](https://mlsanity.com/paper/2010.02318/) (2020)
- [HINT: Hierarchical Interaction Network for Trial Outcome Prediction Leveraging Web Data](https://mlsanity.com/paper/2102.04252/) (2021)
- [AdaGCN: Adaboosting Graph Convolutional Networks into Deep Models](https://mlsanity.com/paper/1908.05081/) (2019)
- [GraphCrop: Subgraph Cropping for Graph Classification](https://mlsanity.com/paper/2009.10564/) (2020)
- [Network Representation Learning: From Preprocessing, Feature Extraction to Node Embedding](https://mlsanity.com/paper/2110.07582/) (2021)
- [Robust Deep Learning Ensemble against Deception](https://mlsanity.com/paper/2009.06589/) (2020)
- [On Graph Neural Network Ensembles for Large-Scale Molecular Property Prediction](https://mlsanity.com/paper/2106.15529/) (2021)

## Built on by (most cited first, 4 of 4)

- [HGEN: Heterogeneous Graph Ensemble Networks](https://mlsanity.com/paper/2509.09843/) (2025)
- [Enhanced Soups for Graph Neural Networks](https://mlsanity.com/paper/2503.11612/) (2025)
- [LHGEL: Large Heterogeneous Graph Ensemble Learning using Batch View Aggregation](https://mlsanity.com/paper/2510.03432/) (2025)
- [Ensemble Graph Neural Networks for Probabilistic Sea Surface Temperature Forecasting via Input Perturbations](https://mlsanity.com/paper/2603.06153/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have enjoyed wide spread applications in graph-structured data. However, existing graph based applications commonly lack annotated data. GNNs are required to learn latent patterns from a limited amount of training data to perform inferences on a vast amount of test data. The increased complexity of GNNs, as well as a single point of model parameter initialization, usually lead to overfitting and sub-optimal performance. In addition, it is known that GNNs are vulnerable to adversarial attacks. In this paper, we push one step forward on the ensemble learning of GNNs with improved accuracy, generalization, and adversarial robustness. Following the principles of stochastic modeling, we propose a new method called GNN-Ensemble to construct an ensemble of random decision graph neural networks whose capacity can be arbitrarily expanded for improvement in performance. The essence of the method is to build multiple GNNs in randomly selected substructures in the topological space and subfeatures in the feature space, and then combine them for final decision making. These GNNs in different substructure and subfeature spaces generalize their classification in complementary ways. Consequently, their combined classification performance can be improved and overfitting on the training data can be effectively reduced. In the meantime, we show that GNN-Ensemble can significantly improve the adversarial robustness against attacks on GNNs.