GNN Expressivity

GNN: Graph Neural Network

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6 papers in the last four weeks, up 100% on the four weeks before. 0.1% of all new papers.

Jul 13Week of Sep 28

Latest papers 36

Oct 7, 2026cs.LG

Oscillatory Neural Dynamics over Sheaves

Effective long-range propagation remains a central challenge in graph neural networks, as increasing a model's propagation depth does not guarantee that distant nodes effectively influence each other. Sheaf neural networks enrich graph propagation through matrix-valued transport between stalks; still, this expressivity alone does not automatically imply effective long-range communication. We introduce ONDA, a long-range graph learning framework based on operator-valued information waves. Stalk-valued representations evolve through second-order dynamics governed by learned sheaf transport operators, combining wave-like propagation with expressive local geometry. We characterize long-range influence through a stalk-wise sensitivity analysis and show that the cross-influence never vanishes. Across long-range propagation, severe graph bottlenecks, graph transfer, and heterophilic benchmarks, ONDA consistently improves over scalar wave propagation, diffusive sheaf baselines, and state-of-the-art models, demonstrating the benefit of coupling wave dynamics with matrix-valued transport.

Jan-Willem Van Looy, Alessandro Trenta, Alessio Gravina +5

FaBiT, University of Bologna · Department of Computer Science, University of Pisa · Department of Computer, Control and Management Engineering, Sapienza University of Rome +1

Graph Neural Networks Graph Representation Learning Sheaf Neural Networks Oscillatory Neural Networks GNN Expressivity

Sep 28, 2026cs.LG

Multi-Attractor GNNs: Set-Valued Expressivity Beyond Unique Equilibria

Recurrent and equilibrium graph neural networks (GNNs) often enforce a unique fixed point or use one training target per graph. Yet many combinatorial and scientific problems admit multiple valid solutions, with no preferred one. A designated target can then impose an arbitrary selection rule. For tasks invariant to node relabeling, a symmetric graph may have a symmetric solution set but no symmetric solution. We show that multiple equilibria enable one weight-tied message-passing GNN to represent set-valued equivariant maps: different initializations approach different valid solutions. Under stated regularity assumptions, we first construct globally Lipschitz, permutation-equivariant dynamics that converge almost surely to valid solutions and reach every solution branch with positive probability. We then establish approximate realization by recurrent message passing with continuous component maps, with arbitrarily small update and limiting errors and arbitrarily high probability. This goes beyond standard universality arguments: although message passing alone cannot distinguish symmetric nodes, the evolving state keeps nodes distinguishable at every finite step without auxiliary node identifiers. Such dynamics can be learned without solution labels using problem-specific energies. On Ising ground states, structural module detection in protein graphs, and chemical reaction steady states, the learned updates produce multiple high-quality predictions with high numerical convergence rates. They achieve better average solution quality than the tested unique-equilibrium, single-target, and feedforward baselines, while remaining competitive with much larger diffusion-based solvers.

Jialin Liu

GNN Expressivity Combinatorial Optimization Equivariant GNNs

Sep 28, 2026cs.LG

Edge-Level Automorphism in GNNs: A Quantitative Framework and Effective Designs For Link Prediction

Graph Neural Networks (GNNs) are effective for learning node and link embeddings through permutation-equivariant aggregation. However, standard GNNs collapse automorphic nodes, i.e., those with identical structural roles (or orbits) into indistinguishable representations, leading to the node automorphism problem. This collapse limits their expressive power and degrades link prediction performance. Existing approaches to characterize GNN expressiveness rely primarily on Weisfeiler-Lehman (WL) analyses, but these methods are typically qualitative and often misaligned with empirical results. To address this gap, we begin by introducing a novel quantitative framework to assess GNN expressiveness for link prediction. We first formalize edge-level automorphism through edge orbits, which capture the set of structural role pairs for nodes that share a link. Then, we introduce the edge automorphism ratio (EAR), a scalar metric that quantifies a GNN's ability to distinguish links in a given graph. We empirically demonstrate that EAR correlates strongly with performance, validating its practical benefit. Building on this insight, we design EDGE-ORBIT EQUIVARIANT GRAPH NEURAL NETWORK (EO-GNN), a GNN architecture that addresses automorphism collapse while preserving equivariance and incurring minimal computational overhead. EO-GNN accomplishes this through two core designs combined with WL-based node hashes: (i) automorphism-aware dropouts and (ii) subgraph orbit-biased aggregation. Empirical evaluations on synthetic and real graphs show improvements of up to 42.36% and 28.44%, respectively, in predicting links in scenarios with high automorphism.

Chen Shao, Donald Loveland, Tobias Käfer +1

Karlsruhe Institute of Technology Karlsruhe, Germany · Department of Computer Science University of Michigan Ann Arbor, MI, USA · Computer Science & Engineering University of Michigan Ann Arbor, MI, USA

Link Prediction GNN Expressivity Equivariant GNNs

Sep 27, 2026cs.LG

Reachability is not enough: Diagnosing long-range behavior in GNNs

Graph neural networks (GNNs) are often called long-range because their architecture can connect distant nodes, but this does not show whether they use distant information correctly. We introduce a framework that measures how strongly inputs at each graph distance affect predictions and separates limitations due to architecture, finite approximation, training, and numerical execution. Our analysis shows that local message-passing can spread influence slowly, so a finite implementation may rely mainly on nearby inputs even when the ideal computation uses the whole graph. We also explain why mathematically equivalent filters can differ in how easily they are learned and how reliably they run. Across controlled tasks, models with similar architectural reach use distant information very differently, while low average error can hide failures on distant interactions. Together, these results show that long-range capability depends on learning to use information at the distances required by the task and preserving that use during computation.

Filippo Maria Bianchi

UiT The Arctic University of Norway · NORCE Norwegian Research Centre

Graph Neural Networks GNN Expressivity Message Passing Neural Networks

Sep 15, 2026cs.LG

Repurposing Unified Topological Signatures for Graph Representation Learning

Message-passing Graph Neural Networks (GNNs) iteratively propagate and aggregate local neighborhood information followed by global readout to learn graph representations. However, their discriminative power is upper-bounded by the Weisfeiler--Lehman (1-WL) graph isomorphism test. This prevents GNNs from distinguishing certain non-isomorphic graphs with identical local neighborhood structures, often leading to similar graph representations. Unified Topological Signatures (UTS) capture compact, multi-scale representation of global graph topology derived from persistent homology. We introduce two complementary UTS signatures: Graph_UTS- a static signature of the input graph topology, and Embedding_UTS- a dynamic signature of the evolving embedding topology. They encode structural information inaccessible to 1-WL-based message-passing GNNs, yet their capabilities are explored solely for post-hoc embedding-space analysis. We integrate UTS into GNN training across three architectural interventions: (i) UTS-Aug: augmenting with standard readout feature that encodes graph's true topology; (ii) UTS-Reg: topological regularizer that constrains representation collapse; (iii) UTS-Pool: topology-guided pooling that retains structurally critical nodes. We further leverage UTS as a layer-wise diagnostic to quantify oversmoothing during GNN training. Theoretically, we show that integrating UTS into GNN optimization strictly extends GNN expressivity beyond the 1-WL hierarchy. Experiments on three graph classification benchmarks show consistent benefits: Graph-UTS, Dual-UTS, and UTS-Pool improve accuracy across all three datasets, Embedding-UTS provides smaller but similarly consistent gains, and UTS-Reg's benefit varies across graph domains. Accuracy improves by up to 5.8% with Graph-UTS augmentation, by up to 1.9% with UTS-Reg, and achieves comparable performance to TOGL with UTS-Pool.

Sanyam Sanjay Jain, Anshika Krishnatray, Aditya Sharma +1

BITS Pilani, India

Graph Representation Learning GNN Expressivity Graph Classification Topological Representation Learning

Sep 14, 2026cs.SI

On the Expressive Power of Implicit Line-Graph Higher-Order Weisfeiler--Leman

Whitney's theorem allows isomorphism testing for connected simple graphs, apart from

K_3

and

K_{1,3}

, to be formulated as distinguishing their line graphs. However, the relation between fixed-dimensional Weisfeiler--Leman (WL) expressivity on line graphs and on their roots remains unresolved. We study this relation through Implicit Line-Graph WL (ILG-

k

-WL), which is exactly

k

-WL on

L(G)

, executed over the edges of

G

with line-graph relations derived from endpoint incidence and without explicitly constructing

L(G)

. On the Whitney-general class, the relation between root-domain and line-graph WL depends on

k

. For

k=1,2

, ILG-

k

-WL adds no distinguishing power beyond root-domain

1

-WL and misses some pairs that

1

-WL separates. For

k=3

, we prove the backward containment

L(G)\equiv_{3\text{-WL}}L(H)\Rightarrow G\equiv_{3\text{-WL}}H

. Strongly regular witness pairs, including the Shrikhande/rook pair, show that ILG-

3

-WL is strictly more expressive than

3

-WL. The backward containment also extends to disconnected graphs with no isolated vertices when every connected component is Whitney-general. Deterministic ILG-

3

-WL separates all three substructure-counting witness pairs, all

105

pairs in SR25, and

359

of

400

BREC pairs. An untrained dense ILG-

3

-GNN gives the same pairwise verdicts on these evaluations.

Fan Yang

Independent Researcher

GNN Expressivity

Sep 14, 2026cs.AI

Recurrent GraphNeural NetworkswithSet-BasedAggregation

Recurrent GNNs iterate message passing to convergence, and their logical characterizations to date rely on multi-set aggregation, graded (counting) logics, and halting or acceptance conditions that cannot be verified from the network's parameters. We study recurrent GNNs with set-based aggregation and identify sufficient conditions checkable from the weights for networks to compile into formulas and formulas into networks. The main result is an effective, two-directional equivalence between a class of networks and the Boolean closure of reachability and safety properties, the fragment B

Σ^{\circ}_1

of the modal

μ

-calculus. The fragment is not an artifact: it is the exact expressive level of stabilization over finite vocabulary, which supports fixed points of a single polarity and Boolean combinations thereof, but not the composition of fixed points of opposite polarities. The correspondence needs no counting logic, no external halting signal, and no non-effective acceptance condition, yielding a verifiable path from weights to symbolic explanations for networks meeting the conditions.

Blai Bonet

Universidad Simón Bolívar Caracas, Venezuela

Graph Neural Networks GNN Expressivity Formal Verification

Sep 1, 2026cs.LG

Edge-Girth as a Structural Edge Feature for Graph Neural Networks

Graph neural networks (GNN) based on message passing are provably no more powerful than the one-dimensional Weisfeiler--Leman colour-refinement test (1-WL): two graphs it cannot tell apart receive identical representations, however deep or wide the network. A common remedy augments node or edge features with precomputed structural descriptors, most often counts of a fixed small subgraph such as triangles or longer cycles, but such counts require committing in advance to the size of the substructure counted, a choice usually made blind to the data. We study a descriptor that avoids this choice. The edge-girth of an edge is the length of a shortest cycle through it, and its multiplicity is the number of such shortest cycles; together they form a per-edge invariant that reports cycles of arbitrary length, computable exactly by a single breadth-first search per edge. Injected into a gated message-passing architecture, EGAGNN, it reaches a test MAE a factor three below the closest gated comparator on the ZINC-12k regression benchmark at 104k parameters; against bounded cycle-counting descriptors under the same architecture, it matches only a dictionary counting cycles up to length eight, using twice as many channels, while a dictionary capped at length four performs no better than no structural information at all. On graph discrimination we prove a matching limitation: on graphs where every edge sees the same number of shortest cycles of the same length, the descriptor becomes constant and any model built on it collapses back to the 1-WL bound. This holds without exception across all 400 pairs of the BREC benchmark: not one of the 90 such pairs is distinguished.

Lilian Marey, Charlotte Laclau

LTCI, Télécom Paris, Institut Polytechnique de Paris, Palaiseau, France

Graph Neural Networks Graph Representation Learning GNN Expressivity

Sep 1, 2026cs.LG

Why Multi-Layer Message Passing Works: Completeness Theory for Graph Neural Network Interatomic Potentials

We prove that the Hypergraph Neural Network, an invariant architecture with 3-body message passing, is a universal approximator for potential energy surfaces. Our main contribution is a multi-layer completeness theory. We show that

L

layers of message passing on sparse, cutoff-based graphs achieve the same representational power as having access to the full

L

-hop neighborhood, provided the configurations are generic, satisfy an overlap condition and a connectivity condition. This provides the first rigorous justification for the common practice of using multi-layer message passing with a per-layer cutoff smaller than the physical interaction range, the setting used by virtually all practical graph neural network based machine-learned interatomic potentials. As immediate consequences, we show that both DPA3 and CHGNet architectures inherit universal approximation.

Pingbing Ming, Han Wang

SKLMS, Institute of Computational Mathematics and Scientific/Engineering Computing, AMSS, Chinese Academy of Sciences, No. 55, East Road Zhong-Guan-Cun, Beijing 100190, China · National Key Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, P.R. China, and HEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, P.R. China

Machine Learning Interatomic Potentials GNN Expressivity Message Passing Neural Networks Hypergraph Neural Networks Neural Network Approximation Theory

Aug 12, 2026cs.LG

The Boolean Power of ReLU

We prove that, on finite simple undirected graphs equipped with a single Boolean node feature, the Boolean queries expressible in

Σ

-MPLang, for any collection

Σ

of eventually constant activation functions and with arbitrary real coefficients, form a strict subclass of the Boolean queries expressible in ReLU-MPLang. We thereby settle a recently posed open problem: whether ReLU-MPLang is more powerful than trReLU-MPLang when it comes to Boolean queries. In particular, this implies that ReLU-GNNs are strictly more expressive than {TrReLU,id}-GNNs with respect to Boolean queries on Boolean-featured graphs.

Pablo Barceló, Floris Geerts, Matthias Lanzinger +2

Pontifical Catholic University · IMFD & CENIA, Chile · University of Antwerp +4

ReLU Neural Networks GNN Expressivity Neural Network Expressivity

Aug 7, 2026cs.LG

When GNNs Fail: Quantifying and Overcoming Temporal Correlation Volatility in Time Series

Modeling multivariate time series by representing them as graphs, where individual series act as nodes and pairwise temporal corre- lations serve as edges, has gained significant traction. Recent advances in Graph Neural Networks (GNNs) have demonstrated strong perfor- mance by assuming a static graph topology and aggregating information from neighboring series. In this work, we investigate the representa- tional power of GNNs for forecasting under both static and dynamic settings (i.e., when pairwise correlations evolve drastically over time) and identify critical limitations in current architectures. To formalize this, we first propose Temporal Correlation Volatility (TCV), a model- agnostic metric designed to quantify the distributional evolution of these latent structures. We establish a clear connection between TCV and performance degradation, demonstrating that many popular models, including Transformers, generalize poorly in high-TCV settings and are often outperformed by simple structure-agnostic baselines. To address these limitations, we propose Graph Layer for Inference in Dynamic En- vironments (GLIDE), a novel GNN layer enhanced by two theoretically grounded design mechanisms: (D1) Path-based Message Passing, which captures path-based neighborhoods and (D2) Static and Dynamic Propagation Separation, which identifies optimal dynamics via local static approximation. These components significantly improve learning under dynamic topology while preserving robustness in static scenarios. Ex- tensive experiments on synthetic and real-world benchmarks show that GLIDE improves average performance by up to 45.6% across static and dynamic settings, with the largest gain reaching 85.7%. The source code is available at https://github.com/ChenS676/GLIDE.

Chen Shao, Yue Wang, Zhenyi Zhu +4

Karlsruhe Institute of Technology, Germany · The Hong Kong University of Science and Technology, Hong Kong SAR · East China Normal University, China +1

Multivariate Time Series Forecasting Temporal GNNs GNN Expressivity Dynamic Graph Learning

Aug 5, 2026cs.LG

Tropical Algebraic Geometry for Neuronal Representations: An Arakelov-Green Measure Based Descriptor for Graph Learning

The quantitative analysis of 3D neuronal morphologies requires capturing both graph topology and spatial geometry. Current message-passing Graph Neural Networks (GNNs) are bounded by the 1-Weisfeiler-Lehman (1-WL) test, limiting their ability to capture cycles induced by spatial proximities. To address this, we propose a training-free geometric prior based on tropical algebraic geometry. We apply the recently established tropical Abel-Jacobi transform and polarization distances to machine learning on tree-structured data. We introduce a structural transformation pipeline, comprising cycle space augmentation and quotient space construction, to convert spatial trees into cyclic metric graphs suitable for embedding into the Tropical Jacobian. Computing exact tropical polarization distances requires solving the NP-Hard Closest Vector Problem (CVP) on integer lattices. Instead of relying on explicit approximations with quantization errors (e.g., Babai's rounding), we adopt a continuous relaxation on the universal cover of the Albanese torus. We show that the discrete Arakelov-Green measure, computed in closed form via the graph Laplacian's generalized inverse, decomposes exactly into the intrinsic path metric minus the unquantized polarization distance on this cover, avoiding integer lattice searches. This metric yields two descriptors: eigenvectors provide node-level structural coordinates, and the permutation-invariant eigenvalue spectrum provides a graph-level signature. On the BREC benchmark, the eigenvector formulation demonstrates expressivity beyond the 1-WL limit. On 3D morphology datasets (ACT-4, JML-4, BIL-6), the spectrum seamlessly integrates into standard architectures (VAEs, GNNs, Tree-LSTMs) without additional trainable parameters, outperforming explicit lattice approximations and improving classification accuracy over existing spatial models.

Yuyang Zhang, Weihan Xu, Xuehai Zhou +2

McGill University

Graph Representation Learning GNN Expressivity Geometric Representation Learning

Aug 3, 2026cs.LG

Designing a Good Virtual Node: Addressable and Cardinality-Preserving Global Memory for Message Passing Architectures

Virtual nodes give message-passing neural networks a simple global communication route, but the standard node--VN--node pipeline compresses the graph into one homogeneous state and broadcasts it identically to every node. Building on the Two-Radius analysis of Mishayev et al., we ask how auxiliary virtual memory can relieve this finite-capacity bottleneck without self-attention. We identify two requirements. First, the global memory should be factorized into independently writable and readable states: this can be achieved using addressable cross-attention slots. Second, addressability alone does not preserve multiplicity, because softmax attention is invariant to uniform replication. Inserting each slot query as a private key/value anchor recovers the discarded normalization mass and yields, on bounded color domains, an injective multiset representation able to implement a 1-WL refinement. Experiments on multiplicity-aware Two-Radius, motif counting, and constrained link-set prediction support this addressable and cardinality-preserving virtual memory at (O(nMd)) arithmetic cost.

Félix Marcoccia

Cross-Attention GNN Expressivity Message Passing Neural Networks

Jul 29, 2026cs.LG

Universality and Approximation Rates of Graph Neural Networks with Random Features

We investigate message-passing graph neural networks with random node features. Random node features are known to enhance the expressiveness of graph neural networks (GNNs) both theoretically and empirically. Here, we establish a novel universality result focusing on permutation-equivariant neural networks (PENNs), a class of GNNs built from feedforward neural network components that subsumes many prominent GNN architectures. We show that PENNs, combined with partially random node features, can approximate arbitrarily well in probability any measurable permutation-invariant or permutation-equivariant function on directed graphs of fixed size with multidimensional node and edge features. For

k

-times continuously differentiable functions,

k\geq 2

, we also derive upper bounds on the approximation rates, relating the complexity of the feedforward components of a PENN in terms of layer depth and number of nonzero weights to the desired approximation accuracy.

Lukas Gonon, Thilo Meyer-Brandis, Niklas Weber

School of Computer Science University of St. Gallen St. Gallen, 9000, Switzerland · Department of Mathematics LMU Munich Munich, 80333, Germany

Graph Neural Networks Equivariant Neural Networks GNN Expressivity Message Passing Neural Networks Neural Network Approximation Theory

Jul 28, 2026cs.LG

CondPSE: A Polynomial-Filtered Structural Encoder with Conditional Modulation for Graphs

Message-passing graph neural networks are bounded by the 1-WL test and can miss topological structure that distinguishes non-isomorphic graphs. Positional and structural encodings (PSE) inject such topology-derived signals, and learned PSE encoders such as GPSE pretrain a single encoder to produce these signals from random node probes, which can then be frozen and reused as inputs across downstream graph models. We present CondPSE, a learned PSE encoder that applies a learnable polynomial graph filter bank to standard Gaussian node probes and refines the resulting structural-response branches through FiLM-style modulation conditioned on cross-filter, local message-passing, and graph-level signals. CondPSE is pretrained to reconstruct node-level positional/structural targets and graph-level invariants, and is then frozen for use as a downstream input encoding. On synthetic structural-discrimination benchmarks, CondPSE separates graph structures that 1-WL-bounded message passing cannot: it raises CSL accuracy from 42.9% to 97.3% and EXP accuracy from 68.3% to 99.9% relative to GPSE, and ablations show that the polynomial filter bank accounts for most of this gain. On real molecular property prediction, the picture is more limited. With a hybrid local-message-passing/global-attention backbone, CondPSE performs comparably to GPSE without surpassing it, and a ZINC backbone sweep shows no consistent ordering between the two encoders. We report these results and discuss why strong synthetic structural discrimination does not, on its own, yield a downstream advantage for frozen learned PSE encoders, including the role of downstream integration and possible mismatch between structural pretraining targets and molecular property labels.

Woohyun Lee, Hogun Park

Sungkyunkwan University Suwon, Republic of Korea

Graph Representation Learning Graph SSL GNN Expressivity

Jul 20, 2026cs.LG

A Weisfeiler-Leman Characterization of Global-Attention Graph Transformers for Mixed-Integer Linear Programs

Graph foundation models (GFMs) with global attention are increasingly used to represent mixed-integer linear programs (MILPs), aiming to capture structure beyond the locality of standard graph neural networks. We study their expressive power through graph isomorphism testing, asking which MILP instances they map to identical representations. We prove that a broad class of hierarchical graph transformers combining global linear attention, edge-weighted cross-attention, and bipartite message passing is bounded by the one-dimensional Weisfeiler-Leman (1-WL) test: under any parameter setting, 1-WL-equivalent MILP graphs receive identical graph embeddings. Our compositional proof shows that each architectural component is a symmetric multiset function and thus preserves 1-WL equivalence. We validate this characterization across ten diverse graph encoders, including Graphormer-, GraphGPS-, Set-Transformer-, and Gasse-style models. Across model capacities, graph scales, and pooling operators, every tested encoder maps 1-WL-equivalent non-isomorphic graph pairs to numerically identical embeddings. Consequently, graph invariants that vary within a 1-WL equivalence class cannot be recovered from these representations. We further show that expressiveness beyond 1-WL arises from input encoding rather than attention: random-walk positional encodings separate the constructed pairs, while additional constructions expose the limits of this remedy. These results characterize the expressive power of global-attention GFMs and provide an encoder-agnostic diagnostic for detecting 1-WL-induced representation equivalence.

Md Abrar Jahin, Craig A. Knoblock, Jay Pujara

University of Southern California, Los Angeles, CA 90089, USA · USC Information Sciences Institute, Marina del Rey, CA 90292, USA

Mixed-Integer Linear Programming GNN Expressivity Graph Foundation Models Graph Transformer

Jul 1, 2026cs.DC

Scaling Weisfeiler-Leman Expressiveness Analysis to Massive Graphs with GPUs

The stable coloring of the Weisfeiler-Leman (1-WL) test is a cornerstone of Graph Neural Networks because it provides an upper bound to the expressive power of message-passing architectures. Unfortunately, computing it presents two fundamental bottlenecks. First, classic algorithms are inherently sequential and cannot exploit modern massively parallel hardware. Second, these are \emph{global} algorithms, i.e., they require availability in memory of the full graph, severely limiting applicability to real-world instances. We leverage a linear-algebraic interpretation of 1-WL stable coloring and introduce two key contributions: (i)~a randomized refinement algorithm with tight probabilistic guarantees and (ii)~a correctness-preserving batching scheme that decomposes the graph into independently processable subgraphs while provably returning a stable coloring of the original graph. This approach maps directly to GPU-efficient primitives. In numerical experiments, our CUDA implementation delivers speedups up to two orders of magnitude over classical CPU-based partition refinement and, for the first time, successfully computes stable colorings on web-scale graphs with over 30 billion edges, where CPU baselines time out or fail.

Filippo Biondi, Mirco Tribastone, Max Tschaikowski

IMT Lucca, Italy · Sapienza University Rome, Italy

GPU Acceleration High-Performance Computing GNN Expressivity

Jun 25, 2026cs.LG

Graph Neural Networks Applications Across Domains: All Insights You Need

Graph neural networks have moved from a niche representation-learning technique to the default model class wherever data carry relational structure. The interesting question is no longer whether message passing helps on a given dataset, but where graph structure earns its computational cost and where it does not. This survey organises the field around a single design space, derives the spectral and spatial formulations from shared first principles, and connects expressive power to the Weisfeiler-Leman hierarchy with explicit statements of what current architectures can and cannot separate. Against that methodological backbone we examine twelve application domains, among them recommendation and social networks, knowledge graphs and language-model integration, drug discovery and molecular property learning, healthcare and neuroscience, computer vision, traffic and urban computing, power and renewable-energy systems, wireless and sixth-generation networks, fraud and cybersecurity, industrial prognostics, materials science, and climate modelling. For each domain we specify the graph-construction choices and their costs, identify which architecture families dominate and why, and separate reported gains from artefacts of weak baselines or favourable splits. A cross-domain comparison exposes recurring patterns: heterophily and scale undercut the same models almost everywhere, temporal graphs remain harder than their static counterparts, and the architectures that top public leaderboards are seldom the ones that reach deployment. We treat over-smoothing, over-squashing, robustness, distribution shift, fairness, and explainability not as a closing checklist but as the constraints that decide adoption.

Abderaouf Bahi

Computer Science and Applied Mathematics Laboratory (LIMA), Faculty of Science and Technology, Chadli Bendjedid University, P.O. Box 73, El Tarf 36000, Algeria

Graph Neural Networks Over-Squashing GNN Expressivity

Jun 25, 2026quant-ph

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

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.

Snehal Raj, Brian Coyle, Léo Monbroussou +3

1LIP6, CNRS, Sorbonne Universit´e, Paris, France · 2QC Ware, Palo Alto, USA and Paris, France · School of Informatics, University of Edinburgh, Edinburgh, UK +3

GNN Expressivity Message Passing Neural Networks Quantum Neural Networks

Jun 16, 2026cs.AI

Structural Preservation and the Logical Expressiveness of Graph Neural Networks

Bridges between graph neural networks (GNNs) and logical formalisms have been established by fixing architectural choices, such as the types of aggregation, combination, and activation functions. These choices define restricted classes of GNNs for which tight correspondences with logical formalisms can be obtained, by showing that logical formulae can be translated into equivalent GNNs and, conversely, that GNNs can be translated into equivalent formulae. In this paper we take a semantic perspective by establishing the logical expressiveness of classes of GNN classifiers that are preserved under structural properties: embeddings (extensions), injective homomorphisms, and homomorphisms. We show that, for each such property, there exists a fragment of graded modal logic characterising the class of GNNs. In particular, preservation under embeddings, injective homomorphisms, and homomorphisms corresponds to existential graded modal logic, its existential-positive fragment, and existential-positive modal logic, respectively. These results characterise the expressiveness of broad classes of GNNs independently of specific architectural choices, but we also show that each of these classes admits a GNN architecture of the same expressiveness. Technically, our approach uses a new well-quasi-order result for trees of bounded height, yielding finite representations of unravelling-invariant classes.

Przemysław Andrzej Wałęga, Bernardo Cuenca Grau

Queen Mary University of London · University of Oxford

GNN Expressivity

Jun 11, 2026cs.LG

Understanding Truncated Positional Encodings for Graph Neural Networks

Positional encodings (PEs) enhance the power of graph neural networks (GNNs), both theoretically and empirically. Two of the most popular families of PEs - spectral (e.g., Laplacian eigenspaces, effective resistance) and walk-based (polynomials of the adjacency matrix) - are theoretically equivalent in expressive power, with expressivity between the 1-WL and 3-WL tests. However, this equivalence assumes the GNN uses the "complete" version of these PEs, which requires

O(n^3)

time and space complexity. Instead, practitioners commonly use truncated variants of these encodings, such as the first

k

eigenspaces or powers of the adjacency matrix. However, the theoretical properties of these truncated PEs are unknown. In this work, we initiate the study of these truncated PEs. Theoretically, we show that, under truncation, several families of PEs are fundamentally different in expressive power. As a corollary, we show that truncated spectral PEs are no longer stronger than the 1-WL test. We also study a family of spectral PEs, the

k

-harmonic distances, to highlight the differences in expressive power of even closely related truncated PEs. Finally, we experimentally show that a mix of truncated PEs is preferable to any single family on real-world datasets.

James Flora, Mitchell Black, Weng-Keen Wong +1

School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, USA · Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, California, USA.

GNN Expressivity Positional Encoding

Jun 2, 2026cs.LG

Are Common Substructures Transferable? Riemannian Graph Foundation Model with Neural Vector Bundles

Foundation models have sparked a revolution via a pretraining-adaptation paradigm, with recent efforts extending this success to graphs. Unlike other modalities, graphs contain rich structural patterns, yet their structural transferability remains poorly understood. Prior studies consider common substructures in the discrete realm, and we are motivated by a fundamental question: Are common substructures transferable? The underlying theory is largely underexplored. In this work, we shift toward learning transferable structures through the lens of functional behavior. Theoretically, we connect transferable substructures to intrinsic geometry of the representation space. However, characterizing such intrinsic geometry has rarely been touched. Grounded in Riemannian geometry, we develop a graph intrinsic geometry learning framework called Neural Vector Bundle, which enables parsing intrinsic geometry with local coordinates. Building on this, we design GAUGE, a pretrainable neural architecture that constructs the vector bundle, flattening geometrically compatible local coordinates, and a new Dirichlet loss, which also measures the transfer effort. We empirically validate its superior expressiveness in challenging tasks including zero-shot link prediction and graph isomorphism.

Li Sun, Zhenhao Huang, Yiding Wang +3

Beijing University of Posts and Telecommunications, Beijing, China · North China Electric Power University, Beijing, China · University of Cambridge, Cambridge, UK +1

GNN Expressivity Geometric Representation Learning Transfer Learning Graph Foundation Models Riemannian Geometry

May 31, 2026cs.LG

Temporal Motif Signatures for Temporal Graph Neural Networks

Real temporal interaction streams carry predictive structure in short-horizon motif patterns -- repetition, reciprocity, star diversity, triadic flow -- that vanilla temporal graph neural networks (TGNNs) often fail to expose to their edge scorers. We show this concretely on MOOC interaction prediction, where a small four-feature family of past-window star counts already delivers most of the lift over a strong static GNN. Across a wide set of real and synthetic temporal datasets we find that motif activity organizes consistently along three scale-stable axes (dyadic recency/reciprocity, star diversity, triadic flow), and we use this empirical structure to design a compact 13-coordinate, leakage-safe, candidate-local motif feature map h(u, v, t) that linearly embeds into any static or temporal encoder without architectural changes. A temporal Weisfeiler-Leman (WL) analysis places the augmentation relative to the first level of an anchored temporal-WL hierarchy and exhibits a candidate-anchored pair on which motif features distinguish. We demonstrate empirically that the same augmentation consistently lifts performance across heterogeneous tasks: TGB link-property prediction across all five baselines, edge classification on Bitcoin Alpha/OTC and MOOC, and graph-level classification of synthetic temporal generators.

Dylan Sandfelder, Mihai Cucuringu, Xiaowen Dong

University of Oxford · University of California, Los Angeles

Temporal GNNs GNN Expressivity Temporal Link Prediction

May 25, 2026cs.LG

Invariant-Based Weight Sharing for Message Passing

Message-passing neural networks (MPNNs) are a powerful framework for learning representations of graph-structured domains. However, weights in MPNNs act on features only, limiting their ability to capture structural patterns. We introduce a novel structure-aware weight sharing principle that explicitly incorporates information inherent to the graph structure. Weights are indexed directly by user-chosen graph invariants, i.e., functions preserved under node permutations, enabling systematic reuse across structurally equivalent subgraphs. We present ShareGNNs, which instantiate this principle within a simple encoder-decoder architecture, resulting in an MPNN with learnable adjacency and transformer-like connectivity. We show that their expressivity is at least as strong as the discriminative power of the chosen invariants, providing explicit control over the model complexity. Experiments on synthetic and real-world data, as well as subgraph counting tasks, demonstrate consistent improvements over standard MPNNs, competitive expressivity beyond the 1-WL test, and scalability to large datasets.

Florian Seiffarth

University of Bonn, Bonn, Germany · Lamarr Institute for Machine Learning and Artificial Intelligence, Bonn, Germany

Graph Neural Networks GNN Expressivity Message Passing Neural Networks

May 25, 2026stat.ME

Different Statistical Perspectives for Understanding Generalisation in Graph Neural Networks

Graph Neural Networks (GNN) are currently the most popular approach for learning and prediction on graph-structured data and are deployed in various fields, from social network analysis to drug discovery. However, there is limited mathematical understanding of the performance of GNNs. We discuss the various perspectives used to study statistical generalisation in GNNs. We identify three broad frameworks. The first approach, rooted in learning theory, relies on uniform convergence bounds and the complexity of the hypothesis class of specific GNN architectures. This approach also builds on the expressivity of GNNs, typically studied through the lens of graph isomorphism tests. The second principle is to simplify the neural architecture by analysing GNNs under the asymptotics of infinitely many parameters or infinite graph size. This approach approximates GNNs using Gaussian processes, neural tangent kernels or graphon neural network operators, which allow studying the generalisation or stability of trained GNNs. The third framework studies GNNs under random graph models, often the contextual stochastic block model, and derives non-asymptotic error rates using tools from high-dimensional statistics. We highlight some key theoretical results and discuss a few limitations and open research questions for each perspective.

Nil Ayday, Mahalakshmi Sabanayagam, Debarghya Ghoshdastidar

Technical University of Munich, School of Computation, Information and Technology, Boltzmannstr. 3, Garching, 85748, Germany. · Australian Institute for Machine Learning, Adelaide University,2026 Adelaide, SA 5000, Australia.

Neural Network Generalization Graph Neural Networks GNN Expressivity Statistical Learning Theory

May 22, 2026cs.LG

Weisfeiler-Leman Is Incomplete on Simple Spectrum Graphs, so Canonicalize Them

Graphs with a simple spectrum admit cubic-time isomorphism testing, yet we prove that for every natural number

k

, the

k

-Weisfeiler-Leman (

k

-WL) test cannot distinguish all non-isomorphic graphs with a simple spectrum. As the WL hierarchy upper-bounds the distinguishing power of widely-used Graph Neural Networks (GNNs), this incompleteness applies to all such GNNs, ruling out completeness for every

k

-WL-aligned GNN family. To close this gap, we introduce PRiSM (Partition, Refine, Solve, Match), the first provably complete canonicalization of simple-spectrum eigendecompositions. PRiSM obtains the completeness guarantee that prior canonicalizations provably lack, and resolves the open problem of achieving complete expressivity on simple-spectrum graphs. When composed with DeepSets or a Transformer, PRiSM achieves universal approximation on simple-spectrum graphs, justifying the use of canonicalized Laplacian positional encodings. Empirically, PRiSM performs comparably to or outperforms existing spectral canonicalizations on graph regression, classification, and expressivity

Snir Hordan, Nadav Dym, Tim Seppelt

Faculty of Mathematics Technion - Israel Institute of Technology · IT University of Copenhagen

Graph Neural Networks GNN Expressivity

May 18, 2026cs.DB

Expressive Power of Deep Homomorphism Networks over Relational Databases

The expressive limitations of message-passing Graph Neural Networks (GNNs) have motivated a wide range of more powerful graph learning architectures. We advocate Deep Homomorphism Networks (DHNs) as a model particularly well-suited for learning over relational databases, due to their close connection to important fragments of SQL such as conjunctive queries. We study the precise expressive power of DHNs by relating them to various natural fragments and extensions of first-order logic (FO). For DHNs with max, sum, and mean aggregations, we establish connections to the unary negation fragment (UNFO) and to the extensions of UNFO with counting quantifiers and with ratio quantifiers. We further relate sum-aggregation DHNs to the unary quantifier alternation fragment of FO and to an extension of FO with expressive counting. Through the classical correspondence between FO and SQL, these results also illuminate the relation between DHNs and SQL. They also enable us to study the decidability of two fundamental static analysis problems for DHNs, the emptiness problem and the subsumption problem. Finally, we confirm through experiments that the established differences in expressive power are reflected in the performance on suitable prediction tasks.

Moritz Schönherr, Balder ten Cate, Maurice Funk +3

Leipzig University · University of Amsterdam · Technion & RelationalAI

Logical Reasoning Graph Neural Networks GNN Expressivity Relational Reasoning Relational Databases

May 13, 2026cs.LG

The WidthWall: A Strict Expressivity Hierarchy for Hypergraph Neural Networks

Hypergraphs provide a natural framework to model higher-order interactions in scientific, social, and biological systems. Hypergraph neural networks (HGNNs) aim to learn from such data, yet it remains unclear which higher-order structures these models can represent. We show that hypergraph expressivity is governed by which small patterns an architecture can detect and count. We formalize this via homomorphism densities, which measure how often a structural motif appears in a hypergraph. Combining classical homomorphism-count completeness with invariant approximation, we show that homomorphism densities generate all continuous hypergraph invariants and organize them into a strict hierarchy indexed by hypertree width. This yields a Width Wall: a fundamental architectural limit beyond which no hidden dimension, training procedure or fixed-depth HGNN can represent invariants requiring wider patterns. Our framework provides a unified characterization of 15 HGNN architectures, precisely identifies information lost by clique expansion, and motivates density-aware models that extend expressivity beyond bounded-width message passing. We experimentally validate this finding on an APPLICATION NODE CLASSIFICATION SUITE of real-world hypergraphs, where the Width Wall predicts when graph-reduction baselines fail and when density features help.

Fengqing Jiang, Yuetai Li, Yichen Feng +6

University of Washington · Western Washington University · King Abdulaziz City for Science and Technology +1

GNN Expressivity Hypergraph Neural Networks Neural Network Expressivity

May 13, 2026cs.LG

MLGIB: Multi-Label Graph Information Bottleneck for Expressive and Robust Message Passing

Graph Neural Networks (GNNs) suffer from over-squashing in deep message passing, where information from exponentially growing neighborhoods is compressed into fixed-dimensional representations. We show that this issue becomes a distinct failure mode in multi-label graphs: neighboring nodes often share only limited labels while differing across many irrelevant ones, causing predictive signals to be diluted by noisy label information. To address this challenge, we propose the Multi-Label Graph Information Bottleneck (MLGIB), which formulates multi-label message passing as constrained information transmission under irrelevant label noise. MLGIB balances expressiveness and robustness by preserving predictive label signals while suppressing irrelevant noise. Specifically, it constructs a Markovian dependence space and derives tractable variational bounds, where the lower bound maximizes mutual information with target labels and the upper bound constrains redundant source information. These bounds lead to an end-to-end label-aware message-passing architecture. Extensive experiments on multiple benchmarks demonstrate consistent improvements over existing methods, validating the effectiveness and generality of the proposed framework.

Chaokai Wu, Haofu Shi, Ningxuan Ma +2

Multi-Label Classification Graph Neural Networks Information Bottleneck GNN Expressivity Message Passing Neural Networks

May 7, 2026cs.LG

Full-Spectrum Graph Neural Networks: Expressive and Scalable

It is well established that spectral graph neural networks (GNNs) can universally approximate node signals; however, their expressive power remains bounded by the 1-dimensional Weisfeiler-Lehman test, which is mirrored in their lack of universality for higher-order signals. To go beyond this bound, we propose the Full-Spectrum GNNs (FSpecGNNs), a second-order generalization of classical spectral GNNs. FSpecGNN advances spectral filtering from two perspectives: (1) it lifts signals from the node domain to the node-pair domain; and (2) it extends the univariate spectral filter over eigenvalues to a bivariate filter over eigenvalue pairs. We show that classical spectral GNNs arise as a diagonal special case of FSpecGNNs, and prove that FSpecGNNs can be at most as expressive as Local 2-GNN while universally approximating node-pair signals, the latter being particularly beneficial for heterophilic graph learning. Moreover, FSpecGNN admits scalable implementations that avoid explicit node-pair-level computations; combined with a low-rank approximation that reduces full-spectrum convolution to a combination of polynomial spectral filters, it enables learning on large graphs. Empirically, FSpecGNN validates the predicted expressivity and delivers strong performance on heterophilic benchmarks.

Xiaohan Wang, Deyu Bo, Longlong Li +1

Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

Graph Neural Networks GNN Expressivity Spectral Methods Spectral Graph Convolution