ICML 2026 Papers

Chain-of-Thought (CoT) prompting has shown promise in enhancing the reasoning capabilities of large language models (LLMs) on text-attributed graphs (TAGs). This work reframes CoT-based graph learning through the principle of clustering as reasoning, offering a $k$-means interpretation of how iterative reasoning operates over graph-structured data. We observe that existing graph CoT methods rely on disjoint architectures and fixed graph representations, limiting step-by-step semantic-topological interaction and interpretability. To overcome this limitation, we propose a unified framework named KCoT that integrates CoT reasoning with graph representation learning. Our key theoretical result reveals a formal mathematical correspondence between a Transformer block and the $k$-means algorithm, allowing reasoning to be interpreted as iterative assignment and update steps. Based on this insight, we introduce a Semantic Discriminating Prompt that explicitly formulates these steps as structured CoT reasoning, together with a structure-grounded alignment strategy to fuse topological priors with evolving thought-conditioned representations. Experiments on standard benchmarks demonstrate consistent improvements over state-of-the-art methods, validating clustering as a principled mechanism for CoT-based graph learning.

Approximate Nearest Neighbor Search (ANNS) is fundamental to modern AI applications. Most existing solutions optimize query efficiency but fail to align with the practical requirements of modern workloads. In this paper, we outline six critical demands of modern AI applications: high query efficiency, fast indexing, low memory footprint, scalability to high dimensionality, robustness across varying retrieval sizes, and support for online insertions. To satisfy all these demands, we introduce Projection-Augmented Graph (PAG), a new ANNS framework that integrates projection techniques into a graph index. PAG reduces unnecessary exact distance computations through asymmetric comparisons between exact and approximate distances as guided by projection-based statistical tests. Three key components are designed and integrated into the graph index to optimize indexing and searching. Experiments on six modern datasets demonstrate that PAG consistently achieves superior queries per second (QPS)-recall performance---up to 5$\times$ faster than HNSW---while offering fast indexing speed and moderate memory footprint. PAG remains robust as dimensionality and retrieval size increase and naturally supports online insertions. Our source code is available at: https://github.com/KejingLu-810/PAG/.

Graph Neural Networks (GNNs) have achieved remarkable success in graph analysis due to the Message-Passing (MP) mechanism, yet they struggle with heterophilic graphs where connected nodes often have distinct labels or dissimilar attributes. Graph Contrastive Learning (GCL) serves as a promising approach to extract the information beyond neighboring nodes, effectively mitigating the limitations of the MP mechanism in handling heterophilic graphs. Nevertheless, GCL faces two critical challenges when applied to heterophilic graphs, i.e., the potential distribution shift from data augmentation and the loss of robustness caused by high-frequency signals. To address these problems, we propose a novel model, namely the Spectral Fusion Contrastive Learning with Topology-Adaptive Graph Augmentation (SFCLTA) for unsupervised graph representation learning. Our method dynamically adjusts graph structures via a heterophily-aware augmentation strategy, and constrains high-frequency distortions by spectral regularization. We utilize the confidence-weighted fusion to enhance the robustness. Additionally, we introduce a feature reconstruction task as a prerequisite to explicitly mitigate feature-level distribution shifts. Experiments on multiple real-world datasets demonstrate that the proposed SFCLTA consistently outperforms baseline models in multiple tasks. Our code is released on https://github.com/JonathanGXu/SFCLTA.

Graph foundation models (GFMs), pretrained on massive graph data, have transformed graph machine learning by supporting general-purpose reasoning across diverse graph tasks and domains. Existing GFMs pretrained with fixed-hop subgraph sampling impose a fixed receptive field, causing scale mismatch on diverse tasks, which often require heterogeneous and unknown structural contexts beyond a fixed sampling scale. We propose **R-GFM**, a Riemannian Graph-of-Graphs (GoG) based foundation model, that treats *structural scale* as a first-class citizen in modeling. R-GFM constructs a multi-scale GoG over-sampled subgraphs at different hop distances and learns geometry-adaptive representations from Riemannian manifolds. Theoretical analysis shows that R-GFM reduces structural domain generalization error compared to fixed-scale GFMs. Experiments on various datasets demonstrate that R-GFM achieves state-of-the-art performance, with up to a **49\%** relative improvement on downstream tasks.

Discrete Flow Matching (DFM) presents a promising approach for graph generation; however, existing adaptations often introduce substantial complexity by incorporating task-specific heuristics, compromising the continuity equation and significantly expanding the hyperparameter space. Moreover, their sampling efficiency remains limited, as the required number of steps is often comparable to diffusion models, diminishing DFM’s practical advantages. To address these limitations, we propose SimGFM, a simplified graph DFM for graph generation. Leveraging characteristic patterns in graph-generation trajectories, SimGFM relies only on the scheduler and rate matrix, eliminating heavy heuristics and hyperparameter tuning, and achieves large step reductions while preserving SOTA results. SimGFM achieves strong empirical results: on QM9, it matches prior models requiring 500–1000 steps with only 10 steps, and on most datasets, its performance at 50 steps matches or surpasses these baselines, demonstrating both efficiency and competitiveness. Our source code is available at https://github.com/LUOyk1999/SimGFM.

Graph Contrastive Learning (GCL), which trains graph encoders by maximizing similarity between positive samples and minimizing it between negative ones, has emerged as a mainstream graph pre-training paradigm. It is widely recognized that positive samples are essential in GCLs. Ideally, maximizing the similarity of positive samples enables graph encoders to capture intrinsic semantic and patterns of graph data. However, we discover an interesting phenomenon: GCLs can achieve competitive performance even without positive samples. This motivates us to revisit the fundamental mechanism of positive samples in GCLs. From the perspective of Dirichlet energy, we theoretically finds that message passing, a key mechanism in graph encoders, trivializes the maximization of positive samples, preventing GCLs from effectively learning from positive samples. To address this, we propose SPGCL to mitigate the trivialization caused by message passing and restore the learning efficacy of positive samples. Specifically, we find that high Dirichlet energy features help positive samples provide effective learning signals while low Dirichlet energy features contribute little to positive learning signal but is useful for positive sampling. Based on this, SPGCL propagates only high Dirichlet energy features and uses low energy features to construct a probability matrix for reliable positive sampling. Extensive experiments demonstrate the effectiveness of SPGCL.

Understanding what graph neural networks can learn, especially their ability to learn to execute algorithms, remains a central theoretical challenge. In this work, we prove exact learnability results for graph algorithms under bounded-degree and finite-precision constraints. Our approach follows a two-step process. First, we train an ensemble of multi-layer perceptrons (MLPs) to execute the local instructions of a single node. Second, during inference, we use the trained MLP ensemble as the update function within a graph neural network (GNN). Leveraging Neural Tangent Kernel (NTK) theory, we show that local instructions can be learned from a small training set, enabling the complete graph algorithm to be executed during inference without error and with high probability. To illustrate the learning power of our setting, we establish a rigorous learnability result for the LOCAL model of distributed computation. We further demonstrate positive learnability results for widely studied algorithms such as message flooding, breadth-first and depth-first search, and Bellman-Ford.

Graph neural networks (GNNs) excel in graph analyzing tasks but often suffer from poor generalization under Out-of-Distribution (OOD) scenarios. Although this problem has attracted increasing attention, most solutions primarily rely on empirical designs, lacking effective mechanisms to characterize and quantify invariance for graph representation learning. To address these limitations, we propose DIGL, a novel graph learning method that improves the OOD generalization of GNNs. Our work makes an initial attempt to geometrize invariance for graphs by introducing computational optimal transport (OT) theory to characterize invariance principle. Specifically, we formulate the underlying invariant prototype shared by graphs across different environments as a distribution barycenter, and consider graph representations in each specific environment as distortions of the prototype. Building on this idea, we establish an invariant learning framework to promote the model to learn purely invariant graph representations for downstream tasks. Moreover, we derive a unified optimization objective for model implementation and provide theoretical analysis to justify our method. Extensive experiments on a broad range of benchmark datasets demonstrate the superior generalization ability of our method compared with baseline methods under various OOD settings.

Graphs with heterophily, where adjacent nodes carry different labels, are prevalent in real-world applications, from social networks to molecular interactions. However, existing spectral Graph Neural Network (GNN) approaches tailored for heterophilous graph classification suffer from hub-dominated (node with large degree) aggregation and oversmoothing, as their suboptimal polynomial filters introduce approximation errors and blend distant signals. To address the degree-biased aggregation and suboptimal polynomial filtering, we introduce a Hierarchical Multi‐view HAAR (HMH), a novel spectral graph‐learning framework that scales in near‑linear time. HMH first learns feature- and structure-aware \emph{signed} affinities via a heterophily-aware encoder, then constructs a soft graph hierarchy guided by these embeddings. At each hierarchical level, HMH constructs a sparse, orthonormal, and locality-aware Haar basis to apply learnable spectral filters in the frequency domain. Finally, skip-connection unpooling layers combine outputs from all hierarchical levels back into the original graph, effectively preventing hub domination and long-range signal bottleneck (over-squashing). Experimentation shows that HMH outperforms state‑of‑the‑art spectral baselines, achieving up to a 3 \% improvement on node classification and 7 \% on graph classification datasets, all while maintaining linear scalability. Our code is available at https://github.com/sazzad1008/Scalable-HMH101

Graph coarsening reduces the size of a graph while preserving certain properties. Most existing methods preserve either spectral or spatial characteristics. Recent research shows that topology-preserving coarsening methods maintain GNN performance on coarsened graphs but suffer from exponential time complexity. To address these problems, we propose Scalable Topology-Preserving Graph Coarsening (STPGC) by introducing the concepts of graph strong collapse and graph edge collapse extended from algebraic topology. STPGC comprises three new algorithms, GStrongCollapse, GEdgeCollapse, and NeighborhoodConing, based on these two concepts, which eliminate dominated nodes and edges while rigorously preserving topological features. We further prove that STPGC preserves the GNN receptive field and develop approximate algorithms to accelerate GNN training. Experiments on node classification with GNNs demonstrate the efficiency and effectiveness of STPGC.

Graph neural networks (GNNs) have been demonstrated to be powerful tools for analyzing structural graph data. However, most existing methods usually rely on fixed adjacency structures for information propagation, lacking strong adaptability to the latent semantic relationships that exist but are not explicitly connected in graph, especially in complementary high-pass and low-pass filtering views. To this end, this paper proposes a novel Dual-channel Dynamic Graph Neural Network (DCD-GNN), mainly consisting of parallel representation learning channels: a static structure-preserving channel and a dynamic adjacency-enhancing channel. The dynamic channel exploits both low-pass structural filtering and high-pass personalized detail via the self-attention adjacency learning and then integrates them for comprehensive semantic modeling, while the static channel maintains structural stability. Both channels employ a multi-scale representation fusion mechanism and a unified and discriminative node embedding representation is obtained by integrating them. Extensive experiments on various benchmark datasets verify the superiority of DCD-GNN in discriminative graph representation learning.

High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce. While self-supervised pretraining on molecular graphs has shown promise, many existing approaches either depend on hand-crafted augmentations or complex generative objectives, and often rely solely on 2D topology, leaving valuable 3D structural information underutilized. To address this gap, we introduce C-FREE (**C**ontrast-**F**ree **R**epresentation learning on **E**go-n**e**ts), a simple framework that integrates 2D graphs with ensembles of 3D conformers. C-FREE learns molecular representations by predicting subgraph embeddings from their complementary neighborhoods in the latent space, using fixed-radius ego-nets as modeling units across different conformers. This design allows us to integrate both geometric and topological information within a hybrid Graph Neural Network (GNN)-Transformer backbone, without negatives, positional encodings, or expensive pre-processing. Pretraining on the GEOM dataset, which provides rich 3D conformational diversity, C-FREE achieves state-of-the-art results on MoleculeNet, surpassing contrastive, generative, and other multimodal self-supervised methods. Fine-tuning across datasets with diverse sizes and molecule types further demonstrates that pretraining transfers effectively to new chemical domains, highlighting the importance of 3D-informed molecular representations.

Hypergraphs are graph generalizations with key applications in domains such as healthcare, where strict data privacy requirements apply, or bioinformatics, where testing new compounds is costly. However, due to their combinatorial nature, hypergraph representations are often either intractable or lead to significant information loss. For this reason, research into hypergraph synthesis is limited, and state-of-the-art approaches yield poor generation quality in terms of overall structural patterns and graph-level validity. To address such shortcomings, we introduce SuperHype, an exact and tractable hypergraph diffusion model. The core of SuperHype is the graph-superposition decomposition, a novel representation that embeds a hypergraph into a multi-layer graph, enabling a tractable representation with no loss of generalization. To generate new samples from such representations, we introduce a Graph-Superposition Transformer that treats the superposition as an interconnected sequence of layers. Moreover, we enhance the model's performance by incorporating hypergraph-specific auxiliary features and aggregating indirect node interactions via triplet pooling. Our evaluation across five datasets shows that SuperHype generally reproduces local and global connectivity patterns with superior fidelity compared to state-of-the-art baselines.

The construction of the brain functional network often follows the hand-crafted Correlation Coefficients without any learnable components. Meanwhile, most efforts are made to the models, such as graph neural networks, that make predictions with the constructed brain network as input. Unfortunately, the fixed brain network may lose critical information during construction and lead to difficulty in performance improvement, even with deliberately designed graph models. From this perspective, the current situation is similar to the machine learning community, i.e., hand-crafted features and learnable predictors, before the advent of representation learning. In fact, the brain network can be regarded as a graph-structured learnable representation of the brain. By drawing on representation learning, this paper presents the Brain Representation (BRep) learning problem. To this end, the widely used linear and nonlinear correlations are enhanced to be high-order, parametric, and learnable. The expressive brain representation shifts the heavy computational burden away from downstream architectures, enabling a simple yet accurate predictor. Theoretical analysis guarantees the model's universal approximation to any U/V-statistics. Extensive evaluations demonstrate that BRep possesses superior performance, high efficiency, and interpretability. The code is available at https://github.com/Kevin-916/BRep-demo/.

Size transfer scales Graph Convolutional Networks (GCNs) by applying models trained on sampled subgraphs to larger target graphs. However, existing theoretical guarantees are typically confined to dense graphs or restricted sparsity regimes, failing to cover the arbitrary sparsity of real-world networks. To bridge this gap, we introduce the Generalized Graphon Convolutional Network (GWCN) based on the generalized graphon theory. Unlike the classical graphon limit which vanishes in sparse settings, GWCN employs stretching to construct a non-trivial limit that preserves topological structure. We derive an explicit transfer error bound that decomposes into size-dependent and density-dependent components, providing a unified guarantee across arbitrary sparsity levels. Empirical results on real-world networks corroborate our findings, demonstrating that transfer error vanishes as graph size increases and edge density decreases.

Modern neural networks have shown promise for solving partial differential equations over surfaces, often by discretizing the surface as a mesh and learning with a mesh-aware graph neural network. However, graph neural networks suffer from oversmoothing, where a node's features become increasingly similar to those of its neighbors. Unitary graph convolutions, which are mathematically constrained to preserve smoothness, have been proposed to address this issue. Despite this, in many physical systems, such as diffusion processes, smoothness naturally increases and unitarity may be overconstraining. In this paper, we systematically study the smoothing effects of different GNNs for dynamics modeling and prove that unitary convolutions hurt performance for such tasks. We propose relaxed unitary convolutions that balance smoothness preservation with the natural smoothing required for physical systems. We also generalize unitary and relaxed unitary convolutions from graphs to meshes. In experiments on PDEs such as the heat and wave equations over complex meshes and on weather forecasting, we find that our method outperforms several strong baselines, including mesh-aware transformers and equivariant neural networks. Our code is available at github.com/EdwardBerman/rayleigh_analysis

Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction.

Graph Convolutional Networks (GCNs) are defined based on aggregating the information of adjacent nodes, that are usually treated as equally important and may limit the representational power of existing GCNs. To address this shortcoming, we propose a novel Global Interacted Graph Convolutional Network (GI-GCN), that leverages the solution vectors maintained during the iterative updates of the Dominant Set to adaptively characterize the global importance distribution over all nodes. Specifically, at each convolution layer, this distribution is adopted to adaptively modulate the importance weights of node features before performing the local message passing. We show that this convolution strategy can effectively capture the highly correlated information between nonadjacent nodes through the Dominant Set algorithm, not only emphasizing the critical graph-level information but also enhancing the discriminative power of graph representations. Furthermore, we optimize the memory complexity of the framework, significantly reducing the memory overhead associated with the global interaction modeling. Experiments demonstrate the effectiveness of the proposed GI-GCN model.

We propose an adaptive node feature selection approach for graph neural networks (GNNs) that identifies and removes unnecessary features during training. The ability to measure how features contribute to model output is key for interpreting decisions and reducing dimensionality by eliminating unhelpful variables. However, graph-structured data introduces complex dependencies that may be unsuited to classical feature importance metrics. Inspired by this, we present a data-, model-, and task-agnostic method that determines relevant features during training based on changes in validation performance upon permuting feature values. We theoretically motivate our approach by characterizing how the relationships between node data and graph structure influences GNN performance. Empirically, we show that (i) our highly general approach rivals the performance of tailored feature selection approaches that exploit prior assumptions; (ii) we return meaningful feature importance scores well before the GNN is fully trained; and (iii) our scores demonstrably extract relevant properties that inform feature importance for various graph learning settings.