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arXiv:2606.26873

Scalable Message-Passing Quantum Graph Neural Networks in the Weisfeiler-Leman Hierarchy

Snehal Raj, Brian Coyle, Léo Monbroussou, André J. Ferreira-Martins, Renato M. S. Farias, Elham Kashefi

quant-phcs.LGSubmitted Jun 25, 2026• Announced Jun 26, 2026• 0 citations• Revised Oct 27, 2026 (v2)
v1 · Jun 25, 2026v2 · Oct 27, 2026
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Abstract

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.

Comments
10 pages, 4 figures (main text); 35 pages, 9 figures, 14 tables including Supplementary Information. Code available at https://github.com/SnehalRaj/mp-qgnns

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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 powerful machine learning models that excel at analyzing structured data represented as graphs, demonstrating remarkable performance in applications like social network analysis and recommendation systems. However, classical GNNs face scalability challenges when dealing with large-scale graphs. This paper proposes frameworks for implementing GNNs on quantum computers to potentially address the challenges. We devise quantum algorithms corresponding to the three fundamental types of classical GNNs: Graph Convolutional Networks, Graph Attention Networks, and Message-Passing GNNs. A complexity analysis of our quantum implementation of the Simplified Graph Convolutional (SGC) Network shows potential quantum advantages over its classical counterpart, with significant improvements in time and space complexities. Our complexities can have trade-offs between the two: when optimizing for minimal circuit depth, our quantum SGC achieves logarithmic time complexity in the input sizes (albeit at the cost of linear space complexity). When optimizing for minimal qubit usage, the quantum SGC exhibits space complexity logarithmic in the input sizes, offering an exponential reduction compared to classical SGCs, while still maintaining better time complexity. These results suggest our Quantum GNN frameworks could efficiently process large-scale graphs. This work paves the way for implementing more advanced Graph Neural Network models on quantum computers, opening new possibilities in quantum machine learning for analyzing graph-structured data.
Graph Neural Networks (GNNs) achieve state-of-the-art performance on graph-structured data, but training and inference on large graphs are often bottlenecked by memory constraints and sparse linear-algebra workloads. Quantum computing offers an alternative set of primitives that may improve scalability for graph learning. Building on the quantum graph neural network (QGNN) framework of Liao \textit{et al.}, this work implements two representative architectures --- the Simplified Graph Convolution (SGC) and Linear Graph Convolution (LGC) models --- and evaluates them on open benchmark graph datasets and semi-supervised learning tasks using quantum simulation. We compare predictive performance and optimization behavior against classical baselines, showing that the quantum models achieve competitive performance with fewer parameters. Finally, we present a cost gradient analysis that identifies the tasks for which the models showcased are trainable. This is followed by a classical simulability study to find regimes in which the proposed circuits remain robust during training.
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.
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.
Graph Neural Networks (QGNNs) offer a promising approach to combining quantum computing with graph-structured data processing. While classical Graph Neural Networks (GNNs) are scalable and robust, existing QGNNs often lack flexibility due to graph-specific quantum circuit designs, limiting their applicability to diverse real-world problems. To address this, we propose a versatile QGNN framework inspired by GraphSAGE, using quantum models as aggregators to generate quantum-native node embeddings. We integrate inductive representation learning techniques with parameterized quantum convolutional and pooling layers, bridging classical and quantum paradigms. The convolutional layer is flexible, allowing tailored designs for specific tasks. Benchmarked on a node regression task with the QM9 dataset, our framework, using a single minimal circuit for all aggregation steps, handles molecules with varying numbers of atoms without changing qubits or circuit architecture. While classical GNNs achieve higher training performance, our quantum approach remains competitive and often shows enhanced generalization as molecular complexity increases. We also observe faster learning in early training epochs. To mitigate trainability limitations of a single-circuit setup, we extend the framework with multiple quantum aggregators on QM9. Assigning distinct circuits to each hop substantially improves training performance across all cases. Additionally, we numerically demonstrate the absence of barren plateaus as qubit numbers increase, suggesting that the proposed model remains trainable to larger, more complex graph-based problems.
Graph Neural Networks (GNNs) are eminently suitable for wireless resource management, thanks to their scalability, but they still face computational challenges in large-scale, dense networks in classical computers. The integration of quantum computing with GNNs offers a promising pathway for enhancing computational efficiency because they reduce the model complexity. This is achieved by leveraging the quantum advantages of parameterized quantum circuits (PQCs), while retaining the expressive power of GNNs. However, existing pure quantum message passing models remain constrained by the limited number of qubits, hence limiting the scalability of their application to the wireless systems. As a remedy, we conceive a Scalable Quantum Message Passing Graph Neural Network (SQM-GNN) relying on a quantum message passing architecture. To address the aforementioned scalability issue, we decompose the graph into subgraphs and apply a shared PQC to each local subgraph. Importantly, the model incorporates both node and edge features, facilitating the full representation of the underlying wireless graph structure. We demonstrate the efficiency of SQM GNN on a device-to-device (D2D) power control task, where it outperforms both classical GNNs and heuristic baselines. These results highlight SQM-GNN as a promising direction for future wireless network optimization.