NeurIPS 2025 Papers

GNNs have achieved remarkable performance across a range of tasks, but their reliability under distribution shifts remains a significant challenge. In particular, energy-based OOD detection methods—which compute energy scores from GNN logits—suffer from unstable performance due to a fundamental coupling between the norm and direction of node embeddings. Our analysis reveals that this coupling leads to systematic misclassification of high-norm OOD samples and hinders reliable ID–OOD separation. Interestingly, GNNs also exhibit a desirable inductive bias known as angular clustering, where embeddings of the same class align in direction. Motivated by these observations, we propose GeoEnergy (Geometric Logit Decoupling for Energy-Based OOD Detection), a plug-and-play framework that enforces hyperspherical logit geometry by normalizing class weights while preserving embedding norms. This decoupling yields more structured energy distributions, sharper intra-class alignment, and improved calibration. GeoEnergy can be integrated into existing energy-based GNNs without retraining or architectural modification. Extensive experiments demonstrate that GeoEnergy consistently improves OOD detection performance and confidence reliability across various benchmarks and distribution shifts.

Graph Convolutional Networks (GCNs) based on linear aggregation have been widely applied across various domains due to their exceptional performance. To enhance performance, these networks often utilize the graph Laplacian norm to suppress the propagation of information from first-order neighbors. However, this approach may dilute valuable interaction information and make the model slowly learn sparse interaction relationships from neighbors, which increases training time and negatively affects performance. To address these issues, we introduce BoostGCN, a novel linear GCN model that focuses on amplifying significant interactions with first-order neighbors, which enables the model to accurately and quickly capture significant relationships. BoostGCN has relatively fixed parameters, making it user-friendly. Experiments on four real-world datasets demonstrate that BoostGCN outperforms existing state-of-the-art GCN models in both performance and efficiency.

Graph coarsening aims to diminish the size of a graph to lighten its memory footprint, and has numerous applications in graph signal processing and machine learning. It is usually defined using a reduction matrix and a lifting matrix, which, respectively, allows to project a graph signal from the original graph to the coarsened one and back. This results in a loss of information measured by the so-called Restricted Spectral Approximation (RSA). Most coarsening frameworks impose a fixed relationship between the reduction and lifting matrices, generally as pseudo-inverses of each other, and seek to define a coarsening that minimizes the RSA. In this paper, we remark that the roles of these two matrices are not entirely symmetric: indeed, putting constraints on the *lifting matrix alone* ensures the existence of important objects such as the coarsened graph's adjacency matrix or Laplacian. In light of this, in this paper, we introduce a more general notion of reduction matrix, that is *not* necessarily the pseudo-inverse of the lifting matrix. We establish a taxonomy of ``admissible'' families of reduction matrices, discuss the different properties that they must satisfy and whether they admit a closed-form description or not. We show that, for a *fixed* coarsening represented by a fixed lifting matrix, the RSA can be *further* reduced simply by modifying the reduction matrix. We explore different examples, including some based on a constrained optimization process of the RSA. Since this criterion has also been linked to the performance of Graph Neural Networks, we also illustrate the impact of this choices on different node classification tasks on coarsened graphs.

We consider the graph alignment problem, wherein the objective is to find a vertex correspondence between two graphs that maximizes the edge overlap. The graph alignment problem is an instance of the quadratic assignment problem (QAP), known to be NP-hard in the worst case even to approximately solve. In this paper, we analyze Birkhoff relaxation, a tight convex relaxation of QAP, and present theoretical guarantees on its performance when the inputs follow the Gaussian Wigner Model. More specifically, the weighted adjacency matrices are correlated Gaussian Orthogonal Ensemble with correlation $1/\sqrt{1+\sigma^2}$. Denote the optimal solutions of the QAP and Birkhoff relaxation by $\Pi^\star$ and $X^\star$ respectively. We show that $\|X^\star-\Pi^\star\|_F^2 = o(n)$ when $\sigma = o(n^{-1})$ and $\|X^\star-\Pi^\star\|_F^2 = \Omega(n)$ when $\sigma = \Omega(n^{-0.5})$. Thus, the optimal solution $X^\star$ transitions from a small perturbation of $\Pi^\star$ for small $\sigma$ to being well separated from $\Pi^\star$ as $\sigma$ becomes larger than $n^{-0.5}$. This result allows us to guarantee that simple rounding procedures on $X^\star$ align $1-o(1)$ fraction of vertices correctly whenever $\sigma = o(n^{-1})$. This condition on $\sigma$ to ensure the success of the Birkhoff relaxation is state-of-the-art.

Graph Neural Networks (GNNs) are widely used for node classification, yet their opaque decision-making limits trust and adoption. While local explanations offer insights into individual predictions, global explanation methods—those that characterize an entire class—remain underdeveloped. Existing global explainers rely on motif discovery in small graphs, an approach that breaks down in large, real-world settings where subgraph repetition is rare, node attributes are high-dimensional, and predictions arise from complex structure-attribute interactions. We propose GnnXemplar, a novel global explainer inspired from Exemplar Theory from cognitive science. GnnXemplar identifies representative nodes in the GNN embedding space—exemplars—and explains predictions using natural language rules derived from their neighborhoods. Exemplar selection is framed as a coverage maximization problem over reverse $k$-nearest neighbors, for which we provide an efficient greedy approximation. To derive interpretable rules, we employ a self-refining prompt strategy using large language models (LLMs). Experiments across diverse benchmarks show that GnnXemplar significantly outperforms existing methods in fidelity, scalability, and human interpretability, as validated by a user study with 60 participants.

We consider the empirical distribution of the embeddings of a $k$-layer polynomial GNN on a semi-supervised node classification task and prove a central limit theorem for them. Assuming a community based model for the underlying graph, with growing average degree $\nu_n\to\infty$, we show that the empirical distribution of the centered features, when scaled by $\nu_{n}^{k-1/2}$ converge in 1-Wasserstein distance to a centered stable mixture of multivariate normal distributions. In addition, the joint empirical distribution of uncentered features and labels when normalized by $\nu_n^k$ approach that of mixture of multivariate normal distributions, with stable means and covariance matrices vanishing as $\nu_n^{-1}$. We explicitly identify the asymptotic means and covariances, showing that the mixture collapses towards a 1-D version as $k$ is increased. Our results provides a precise and nuanced lens on how oversmoothing presents itself in the large graph limit, in the sparse regime. In particular, we show that training with cross-entropy on these embeddings is asymptotically equivalent to training on these nearly collapsed Gaussian mixtures.

Graph attention has demonstrated superior performance in graph learning tasks. However, learning from global interactions can be challenging due to the large number of nodes. In this paper, we discover a new phenomenon termed over-aggregating. Over-aggregating arises when a large volume of messages is aggregated into a single node with less discrimination, leading to the dilution of the key messages and potential information loss. To address this, we propose Wideformer, a plug-and-play method for graph attention. Wideformer divides the aggregation of all nodes into parallel processes and guides the model to focus on specific subsets of these processes. The division can limit the input volume per aggregation, avoiding message dilution and reducing information loss. The guiding step sorts and weights the aggregation outputs, prioritizing the informative messages. Evaluations show that Wideformer can effectively mitigate over-aggregating. As a result, the backbone methods can focus on the informative messages, achieving superior performance compared to baseline methods.

Graph Neural Networks (GNNs) have shown significant success for graph-based tasks. Motivated by the prevalence of large datasets in real-world applications, pooling layers are crucial components of GNNs. By reducing the size of input graphs, pooling enables faster training and potentially better generalisation. However, existing pooling operations often optimise for the learning task at the expense of discarding fundamental graph structures, thus reducing interpretability. This leads to unreliable performance across dataset types, downstream tasks and pooling ratios. Addressing these concerns, we propose novel graph pooling layers for structure-aware pooling via edge collapses. Our methods leverage diffusion geometry and iteratively reduce a graph’s size while preserving both its metric structure and its structural diversity. We guide pooling using *magnitude*, an isometry-invariant diversity measure, which permits us to control the fidelity of the pooling process. Further, we use the *spread* of a metric space as a faster and more stable alternative ensuring computational efficiency. Empirical results demonstrate that our methods (i) achieve top performance compared to alternative pooling layers across a range of diverse graph classification tasks, (ii) preserve key spectral properties of the input graphs, and (iii) retain high accuracy across varying pooling ratios.

Explicit noise-level conditioning is widely regarded as essential for the effective operation of Graph Diffusion Models (GDMs). In this work, we challenge this assumption by investigating whether denoisers can implicitly infer noise levels directly from corrupted graph structures, potentially eliminating the need for explicit noise conditioning. To this end, we develop a theoretical framework centered on Bernoulli edge-flip corruptions and extend it to encompass more complex scenarios involving coupled structure-attribute noise. Extensive empirical evaluations on both synthetic and real-world graph datasets, using models such as GDSS and DiGress, provide strong support for our theoretical findings. Notably, unconditional GDMs achieve performance comparable or superior to their conditioned counterparts, while also offering reductions in parameters (4-6%) and computation time (8-10%). Our results suggest that the high-dimensional nature of graph data itself often encodes sufficient information for the denoising process, opening avenues for simpler, more efficient GDM architectures.

Many real-world graphs exhibit diverse and complex topological structures that are not well captured by geometric manifolds with uniform global curvature, such as hyperbolic or spherical spaces. Recently, there has been growing interest in embedding graphs into pseudo-Riemannian manifolds, which generalize both hyperbolic and spherical geometries. However, existing approaches face three significant limitations, including the ineffective pseudo-Riemannain framework, the shallow architectures, and the absence of clear guideline for selecting suitable pseudo-Riemannian manifolds. To address these issues, we introduce a novel diffeomorphic framework for graph embedding that aligns with the nature of pseudo-Riemannian manifolds. Subsequently, we propose the pseudo-Riemannian Graph Transformer for learning representations of complex graph structures. Our diffeomorphic framework in pseudo-Riemannian geometry enables the principled definitions of core transformer components, including linear attention, residual connection, and layer normalization. Finally, we develop a lightweight space searching algorithm to automatically identify the most suitable pseudo-Riemannian manifold for an input graph. Extensive experiments on diverse real-world graphs demonstrate that our model consistently outperforms other baselines in both node classification and link prediction tasks.

Recent advances have demonstrated the effectiveness of graph-based machine learning on relational databases (RDBs) for predictive tasks. Such approaches require transforming RDBs into graphs, a process we refer to as RDB-to-graph modeling, where rows of tables are represented as nodes and foreign-key relationships as edges. Yet, effective modeling of RDBs into graphs remains challenging. Specifically, there exist numerous ways to model RDBs into graphs, and performance on predictive tasks varies significantly depending on the chosen graph model of RDBs. In our analysis, we find that the best-performing graph model can yield up to a 10\% higher performance compared to the common heuristic rule for graph modeling, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph model–performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 10 automatic RDB-to-graph modeling methods on the $12$ tasks about 380$\times$ faster than on-the-fly evaluation, which requires repeated GNN training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling. Our datasets and code are available at https://github.com/chlehdwon/RDB2G-Bench.

In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field.

In typical graph neural networks (GNNs), feature representation learning naturally evolves through iteratively updating node features and exchanging information based on graph topology. In this context, we conceptualize that the learning process in GNNs is a mean-field game (MFG), where each graph node is an agent, interacting with its topologically connected neighbors. However, current GNNs often employ the identical MFG strategy across different graph datasets, regardless of whether the graph exhibits homophilic or heterophilic characteristics. To address this challenge, we propose to formulate the learning mechanism into a variational framework of the MFG inverse problem, introducing an in-context selective message passing paradigm for each agent, which promotes the best overall outcome for the graph. Specifically, we seek for the application-adaptive transportation function (controlling information exchange throughout the graph) and reaction function (controlling feature representation learning on each agent), *on the fly*, which allows us to uncover the most suitable selective mechanism of message passing by solving an MFG variational problem through the lens of Hamiltonian flows. Taken together, our variational framework unifies existing GNN models into various mean-field games with distinct equilibrium states, each characterized by the learned in-context message passing operators. Furthermore, we present an agnostic end-to-end deep model, coined *Game-of-GNN*, to jointly identify the message passing mechanism and fine-tune the GNN hyper-parameters on top of the elucidated message passing operators. *Game-of-GNN* has achieved SOTA performance on diverse graph data, including popular benchmark datasets and human connectomes. More importantly, the mathematical insight of MFG framework provides a new window to understand the foundational principles of graph learning as an interactive dynamical system, which allows us to reshape the idea of designing next-generation GNN models.

Graph Neural Networks (GNNs) are widely used to compute representations of node pairs for downstream tasks such as link prediction. Yet, theoretical understanding of their expressive power has focused almost entirely on graph-level representations. In this work, we shift the focus to links and provide the first comprehensive study of GNN expressiveness in link representation. We introduce a unifying framework, the $k_\phi$-$k_\rho$-$m$ framework, that subsumes existing message-passing link models and enables formal expressiveness comparisons. Using this framework, we derive a hierarchy of state-of-the-art methods and offer theoretical tools to analyze future architectures. To complement our analysis, we propose a synthetic evaluation protocol comprising the first benchmark specifically designed to assess link-level expressiveness. Finally, we ask: does expressiveness matter in practice? We use a graph symmetry metric that quantifies the difficulty of distinguishing links and show that while expressive models may underperform on standard benchmarks, they significantly outperform simpler ones as symmetry increases, highlighting the need for dataset-aware model selection.

This paper establishes the theoretical limits of graph clustering under the Popularity-Adjusted Block Model (PABM), addressing limitations of existing models. In contrast to the Stochastic Block Model (SBM), which assumes uniform vertex degrees, and to the Degree-Corrected Block Model (DCBM), which applies uniform degree corrections across clusters, PABM introduces separate popularity parameters for intra- and inter-cluster connections. Our main contribution is the characterization of the optimal error rate for clustering under PABM, which provides novel insights on clustering hardness: we demonstrate that unlike SBM and DCBM, cluster recovery remains possible in PABM even when traditional edge-density signals vanish, provided intra- and inter-cluster popularity coefficients differ. This highlights a dimension of degree heterogeneity captured by PABM but overlooked by DCBM: local differences in connectivity patterns can enhance cluster separability independently of global edge densities. Finally, because PABM exhibits a richer structure, its expected adjacency matrix has rank between $k$ and $k^2$, where $k$ is the number of clusters. As a result, spectral embeddings based on the top $k$ eigenvectors may fail to capture important structural information. Our numerical experiments on both synthetic and real datasets confirm that spectral clustering algorithms incorporating $k^2$ eigenvectors outperform traditional spectral approaches.

We investigate optimal transport (OT) for measures on graph metric spaces with different total masses. To mitigate the limitations of traditional $L^p$ geometry, Orlicz-Wasserstein (OW) and generalized Sobolev transport (GST) employ \emph{Orlicz geometric structure}, leveraging convex functions to capture nuanced geometric relationships and remarkably contribute to advance certain machine learning approaches. However, both OW and GST are restricted to measures with equal total mass, limiting their applicability to real-world scenarios where mass variation is common, and input measures may have noisy supports, or outliers. To address unbalanced measures, OW can either incorporate mass constraints or marginal discrepancy penalization, but this leads to a more complex two-level optimization problem. Additionally, GST provides a scalable yet rigid framework, which poses significant challenges to extend GST to accommodate nonnegative measures. To tackle these challenges, in this work we revisit the entropy partial transport (EPT) problem. By exploiting Caffarelli \& McCann's insights, we develop a novel variant of EPT endowed with Orlicz geometric structure, called \emph{Orlicz-EPT}. We establish theoretical background to solve Orlicz-EPT using a binary search algorithmic approach. Especially, by leveraging the dual EPT and the underlying graph structure, we formulate a novel regularization approach that leads to the proposed \emph{Orlicz-Sobolev transport} (OST). Notably, we demonstrate that OST can be efficiently computed by simply solving a univariate optimization problem, in stark contrast to the intensive computation needed for Orlicz-EPT. Building on this, we derive geometric structures for OST and draw its connections to other transport distances. We empirically illustrate that OST is several-order faster than Orlicz-EPT. Furthermore, we show preliminary evidence on the advantages of OST for measures on a graph in document classification and topological data analysis.

Combinatorial optimization (CO) problems, central to operation research and theoretical computer science, present significant computational challenges due to their $\mathcal{NP}$-hard nature. While large language models (LLMs) have emerged as promising tools for CO—either by directly generating solutions or synthesizing solver-specific codes—existing approaches often $\textit{neglect critical structural priors inherent to CO problems}$, leading to suboptimality and iterative inefficiency. Inspired by human experts’ success in leveraging CO structures for algorithm design, we propose $\texttt{STRCMP}$, a novel structure-aware LLM-based algorithm discovery framework that systematically integrates structure priors to enhance solution quality and solving efficiency. Our framework combines a graph neural network (GNN) for extracting structural embeddings from CO instances with an LLM conditioned on these embeddings to identify high-performed algorithms in the form of solver-specific codes. This composite architecture ensures syntactic correctness, preserves problem topology, and aligns with natural language objectives, while an evolutionary refinement process iteratively optimizes generated algorithm. Extensive evaluations across Mixed Integer Linear Programming and Boolean Satisfiability problems, using nine benchmark datasets, demonstrate that our proposed $\texttt{STRCMP}$ outperforms five strong neural and LLM-based methods by a large margin, in terms of both solution optimality and computational efficiency. The code is publicly available in the repository: https://github.com/Y-Palver/L2O-STRCMP.

Topological descriptors have been increasingly utilized for capturing multiscale structural information in relational data. In this work, we consider various filtrations on the (box) product of graphs and the effect on their outputs on the topological descriptors - the Euler characteristic (EC) and persistent homology (PH). In particular, we establish a complete characterization of the expressive power of EC on general color-based filtrations. We also show that the PH descriptors of (virtual) graph products contain strictly more information than the computation on individual graphs, whereas EC does not. Additionally, we provide algorithms to compute the PH diagrams of the product of vertex- and edge-level filtrations on the graph product. We also substantiate our theoretical analysis with empirical investigations on runtime analysis, expressivity, and graph classification performance. Overall, this work paves way for powerful graph persistent descriptors via product filtrations. Code is available at https://github.com/Aalto-QuML/tda_graph_product.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the source and reconstructed graphs and leverages a differentiable matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.