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IEEE Transactions on Neural Networks and Learning Systems

Permutation-Invariant Quantum Graph Neural Network Based on Variational Quantum Algorithms

M Li, Wen Liu, Lei Shi, Yang-Zhi Li, Weiping Ding

Published Jan 1, 2026• 0 citations
Publisher

Abstract

Graph neural networks (GNNs) have demonstrated strong capabilities in graph representation learning but still face limitations in efficiency and scalability. Quantum GNNs (QGNNs) offer a promising alternative. However, existing approaches often fail to fully exploit edge information, require substantial quantum resources, and insufficiently account for permutation invariance in graph learning. To address these challenges, this article proposes a permutation-invariant quantum GNN (PIQGNN). The proposed model introduces a low-qubit-cost quantum encoding strategy that jointly embeds node features, edge features, and graph topology into entangled quantum states using only $n$ qubits, where $n$ denotes the number of nodes, while explicitly enforcing permutation invariance. Furthermore, a symmetry-aware variational quantum neural network (QNN) is designed to enable end-to-end permutation-invariant learning. Its hyperparameters are optimized via Bayesian optimization to alleviate barren plateau (BP) effects and enhance training stability. Experimental results on multiple graph binary classification benchmark datasets demonstrate that, compared with classical GNNs, PIQGNN achieves competitive performance with a significantly reduced number of trainable parameters. Compared with existing QGNNs, PIQGNN attains higher accuracy with lower quantum resource requirements and exhibits stronger robustness under noisy conditions. These results indicate that PIQGNN provides an efficient, scalable, and noise-resilient quantum framework for graph learning, highlighting its practical potential in the noisy intermediate-scale quantum (NISQ) era.

DOI
10.1109/tnnls.2026.3709916

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Graph neural networks (GNNs) have demonstrated strong capabilities in graph representation learning but still face limitations in efficiency and scalability. Quantum GNNs (QGNNs) offer a promising alternative. However, existing approaches often fail to fully exploit edge information, require substantial quantum resources, and insufficiently account for permutation invariance in graph learning. To address these challenges, this article proposes a permutation-invariant quantum GNN (PIQGNN). The proposed model introduces a low-qubit-cost quantum encoding strategy that jointly embeds node features, edge features, and graph topology into entangled quantum states using only nnn qubits, where nnn denotes the number of nodes, while explicitly enforcing permutation invariance. Furthermore, a symmetry-aware variational quantum neural network (QNN) is designed to enable end-to-end permutation-invariant learning. Its hyperparameters are optimized via Bayesian optimization to alleviate barren plateau (BP) effects and enhance training stability. Experimental results on multiple graph binary classification benchmark datasets demonstrate that, compared with classical GNNs, PIQGNN achieves competitive performance with a significantly reduced number of trainable parameters. Compared with existing QGNNs, PIQGNN attains higher accuracy with lower quantum resource requirements and exhibits stronger robustness under noisy conditions. These results indicate that PIQGNN provides an efficient, scalable, and noise-resilient quantum framework for graph learning, highlighting its practical potential in the noisy intermediate-scale quantum (NISQ) era.
The integration of symmetry, such as permutation equivariance, into Quantum Graph Neural Networks (QGNNs), referred to as Equivariant Quantum Graph Neural Networks (EQGNNs), markedly improves the model's generalization performance on graph-structured data. Despite this advancement, current research has not yet extended rotational equivariance to QGNN frameworks. Furthermore, processing large-scale graph data increases computational complexity due to numerous inter-node connections, significantly raising the required number of qubits. To address these challenges, a novel Rotationally Equivariant Quantum Graph Neural Network (REQGNN) with trainable compression encoder and entanglement-enhanced aggregation mechanism is proposed. By adopting quantum fidelity as the evaluation metric, we design a quantum autoencoder to effectively compress feature dimensionality, substantially lowering the qubit requirements of the model while preserving essential global structural details. To achieve rotational equivariance in the model, we propose an entanglement-enhanced layer that incorporates distance and angle information between nodes. This layer performs entanglement by extracting diverse edge information, thereby further refining edge feature extraction. Additionally, an auxiliary entanglement layer is introduced to mitigate the over-smoothing issue. Experiment results demonstrate REQGNN is significantly better for graph classification tasks than GIN, Gra+QSVM, and Gra+QCNN on four datasets in all metrics and achieves better results than egoGQNN in accuracy on PTC dataset, and it also has advantage for graph regression tasks over the classical models, including EGNN and EquiformerV2, and reduces the MAE of CvC_vCv​ task unit by 20\% on average compared with a previous quantum model QGCNN. Our approach offers an effective solution for achieving rotational equivariance while providing a novel perspective for exploring symmetry in graph neural networks (GNNs).
Graph neural networks (GNNs) are a powerful framework for learning representations from graph-structured data, but their direct implementation on near-term quantum hardware remains challenging due to circuit depth, multi-qubit interactions, and qubit scalability constraints. In this work, we introduce a hybrid quantum graph learning architecture designed explicitly for unsupervised learning in the noisy intermediate-scale quantum (NISQ) regime. Our approach combines a variational quantum feature extraction layer with an edge-local and qubit-efficient quantum message-passing mechanism inspired by the Quantum Alternating Operator Ansatz (QAOA) framework. The message-passing operation is decomposed into pairwise interactions along graph edges using standard single- and two-qubit gates. For a graph with NNN nodes and nnn-qubit feature registers, this reduces the number of qubits required at one time from NnNnNn to at most 2n2n2n. We train the model using the Deep Graph Infomax objective to perform unsupervised node representation learning. The external class labels are not used during graph construction or training and are used only to evaluate the learned embeddings. Experiments on the Cora citation network and the Phase 3 release of the 1000 Genomes Project show that the quantum edge interaction contributes to the quality of the learned node representations.
Quantum computing has been a prominent research area for decades, inspiring transformative fields such as quantum simulation, quantum teleportation, and quantum machine learning (QML), which are undergoing rapid development. Within QML, hybrid classical-quantum algorithms like Quantum Neural Networks (QNNs) and Variational Quantum Classifiers (VQCs) have shown promise in leveraging quantum circuits and classical optimizers to classify classical data efficiently. Simultaneously, classical machine learning has made significant strides in graph classification, employing Graph Neural Networks (GNNs) to analyze systems ranging from large-scale structures like the Large Hadron Collider to molecular and biological systems like proteins and DNA. Combining the advancements in quantum computing and graph classification presents a unique opportunity to develop quantum algorithms capable of extracting features from graphs and performing their classification effectively. In this paper, we propose a novel quantum encoding framework for graph classification using VQCs. Unlike existing approaches such as PCA-VQC, which rely on dimensionality reduction techniques like Principal Component Analysis (PCA) and may lead to information loss, our method preserves the integrity of graph data. Furthermore, our encoding approach is optimized for Noise-Intermediate Scale Quantum (NISQ) devices, requiring a limited number of qubits while achieving comparable or superior classification performance to PCA-VQC. By constructing slightly more complex circuits tailored for graph encoding, we demonstrate that VQCs can effectively classify graphs within the constraints of current quantum hardware.
Graph Neural Networks (GNNs) are now one of the key tools to model relational and non-Euclidean data in multiagent systems, infrastructure networks and even molecular modeling applications. Nevertheless, in very dense or noisy graph topologies, classical message-passing architectures may experience scalability and representational degeneration, especially due to over-smoothing and insufficient higher-order dependency information. The recent developments in quantum machine learning indicate that hybrid quantum-classical models can also provide an alternative feature representation by projecting relational data to parameterized quantum circuits. This article presents a Quantum-Enhanced Graph Neural Network (QGNN) architecture that extends variational quantum circuits with graph learning pipelines, based on classical learning. Parameters are represented as parameterized qubits, and relational dependencies are represented as structured entanglement mappings. We benchmark the regimes where quantum-enhanced relational encoding proves to be more robust and stable through the swarm coordination, molecular property prediction, and financial transaction network. We also elaborate on the issue of scalability, hardware issues, and practical aspects of near-term hybrid implementations and give a critical view of the changing role of quantum methods in computational intelligence systems.
Graphs provide a natural language for relational data in chemistry, biology and optimisation. Graph neural networks (GNNs) have driven much of the recent progress in learning from such data through message passing, a single primitive that generalises convolution and attention. Quantum counterparts have been proposed, but with limited connection to message passing and few guarantees on performance or scalability. More broadly, the trainability of variational quantum circuits is a recognised bottleneck for their wide applicability, and pre-training has emerged as one way to address it. Yet for a quantum model to be useful, it must offer expressivity guarantees along with demonstrable scalability. Here we show how a quantum graph neural network can be built to perform message passing, to be permutation equivariant, and to sit at a chosen level of the Weisfeiler-Leman hierarchy, the standard measure of how finely a model can tell graphs apart. We show that, as for classical GNNs, the training can be done first on small graph instances, allowing for a pre-training that can mitigate usual training issues, and its output can be read out at a cost that stays low as the graph grows. We validate the framework in large-scale simulations of up to 56 qubits across three datasets, on synthetic graphs that ordinary message passing cannot separate, on molecular property prediction, and on the travelling salesperson problem. Our framework opens a path for near-term quantum algorithms with theoretical guarantees and practical scalability, bringing the principles of graph learning into quantum circuit design.
Graph Neural Networks (GNNs) are now one of the key tools to model relational and non-Euclidean data in multiagent systems, infrastructure networks and even molecular modeling applications. Nevertheless, in very dense or noisy graph topologies, classical message-passing architectures may experience scalability and representational degeneration, especially due to over-smoothing and insufficient higher-order dependency information. The recent developments in quantum machine learning indicate that hybrid quantum-classical models can also provide an alternative feature representation by projecting relational data to parameterized quantum circuits. This article presents a Quantum-Enhanced Graph Neural Network (QGNN) architecture that extends variational quantum circuits with graph learning pipelines, based on classical learning. Parameters are represented as parameterized qubits, and relational dependencies are represented as structured entanglement mappings. We benchmark the regimes where quantum-enhanced relational encoding proves to be more robust and stable through the swarm coordination, molecular property prediction, and financial transaction network. We also elaborate on the issue of scalability, hardware issues, and practical aspects of near-term hybrid implementations and give a critical view of the changing role of quantum methods in computational intelligence systems.