ICML 2026 论文列表

Relational deep learning (RDL) converts relational databases (RDBs) into heterogeneous graphs, but graphs derived directly from database schemas are often not well suited for how graph neural networks (GNNs) perform relational reasoning. We study what makes a relational graph suitable for deep learning and show that schema-derived graphs suffer from two systematic failures: information overload and semantic fragmentation. Through an empirical analysis on real-world databases, we find that effective graphs arise from a task-dependent balance between removing task-irrelevant structure and injecting task-aligned relational connectivity. Filtering exhibits a non-monotonic effect on performance, while structural injection is beneficial only when it reflects the logic of the downstream task. Based on these findings, we develop an end-to-end structural optimizer that applies both operations to adapt relational graphs automatically. Across 23 tasks spanning classification, regression, and recommendation, the optimized graphs consistently improve accuracy while often reducing inference cost.

This work proposes a framework LGKDE that learns kernel density estimation for graphs. The key challenge in graph density estimation lies in effectively capturing both structural patterns and semantic variations while maintaining theoretical guarantees. Combining graph kernels and kernel density estimation (KDE) is a standard approach to graph density estimation, but has unsatisfactory performance due to the handcrafted and fixed features of kernels. Our method LGKDE leverages graph neural networks to represent each graph as a discrete distribution and utilizes maximum mean discrepancy to learn the graph metric for multi-scale KDE, where all parameters are learned by maximizing the density of graphs relative to the density of their well-designed perturbed counterparts. The perturbations are conducted on both node features and graph spectra, which helps better characterize the boundary of normal density regions. Theoretically, we establish consistency and convergence guarantees for LGKDE, including bounds on the mean integrated squared error, robustness, and generalization. We validate LGKDE by demonstrating its effectiveness in recovering the underlying density of synthetic graph distributions and applying it to graph anomaly detection across diverse benchmark datasets. Extensive empirical evaluation shows that LGKDE demonstrates superior performance compared to state-of-the-art baselines on most benchmark datasets.

Three-dimensional (3D) shape classification plays a central role in computer vision and computer-aided design (CAD), underpinning applications in intelligent manufacturing, automated inspection, and digital engineering. Despite recent progress with 3D CNNs and graph-based approaches, existing methods often overlook the geometric-topological regularities and symmetry principles intrinsic to CAD boundary representations (B-reps). To address this challenge, we introduce EquiCAD, a symmetry-aware learning framework that integrates equivariant representations with graph-based reasoning. By leveraging group-theoretic decomposition of curve and surface descriptors, EquiCAD preserves symmetry-consistent feature transformations while retaining rich geometric details. The model further exploits hierarchical message passing to capture interactions between local features and global structure. Experimental results across multiple datasets, including SolidLetters, Parts, the Machining Feature benchmark, and our newly constructed Features dataset, demonstrate substantial improvements over prior state-of-the-art approaches, particularly on industrially relevant shapes with fine-grained attributes. These findings highlight the value of symmetry-aware modeling for robust and generalizable 3D shape analysis.

Can multi-task self-supervised learning on graphs be coordinated without the usual tug-of-war between objectives? Graph self-supervised learning (SSL) offers a growing toolbox of pretext objectives—mutual information, reconstruction, contrastive learning—yet combining them reliably remains a challenge due to objective interference and training instability. Most multi-pretext pipelines use per-update mixing, forcing every parameter update to be a compromise, leading to three failure modes: Disagreement (conflict-induced negative transfer), Drift (nonstationary objective utility), and Drought (hidden starvation of underserved objectives). We argue that coordination is fundamentally a temporal allocation problem: deciding when each objective receives optimization budget, not merely how to weigh them. We introduce ControlG, a control-theoretic framework that recasts multi-objective graph SSL as feedback-controlled temporal allocation by estimating per-objective difficulty and pairwise antagonism, planning target budgets via a Pareto-aware log-hypervolume planner, and scheduling with a Proportional–Integral–Derivative (PID) controller. Across 9 datasets, ControlG consistently outperforms state-of-the-art baselines, while producing an auditable schedule that reveals which objectives drove learning.

By synergizing graph topology with the global expressive power of attention, Graph Transformers (GTs) have emerged as a powerful architecture for node classification. Existing GTs mainly focus on diverse topology injection paradigms, which fundamentally construct different propagation operators. However, a unified theoretical understanding of what constitutes a desirable propagation operator remains largely unexplored. To bridge this gap, this paper rethinks GTs from a graph signal denoising perspective, revealing that a block-diagonal structure is a desirable structural prior for graph denoising. To efficiently instantiate this prior, this paper introduces BDFormer, which imposes spectral block regularization on the affinity of a compact set of latent anchors. Furthermore, by introducing hard assignments between nodes and anchors, BDFormer establishes sparse, structured propagation that suppresses noisy cross-class propagation in linear time. Meanwhile, the learned global affinity guides the pruning of inter-class edges in the graph topology, enabling both global and local propagation to jointly adhere to the target block-diagonal structure. Extensive experiments on benchmark datasets demonstrate the superiority and scalability of BDFormer.

scRNA-seq clustering is a critical task for analyzing single-cell RNA sequencing (scRNA-seq) data, as it groups cells with similar gene expression profiles. Transformers, as powerful foundational models, have been applied to scRNA-seq clustering. Their self-attention mechanism automatically assigns higher attention weights to cells within the same cluster, enhancing the distinction between clusters. Existing methods for scRNA-seq clustering, such as graph transformer-based models, treat each cell as a token in a sequence. Their computational and space complexities are $\mathcal{O}(n^2)$ with respect to the number of cells, limiting their applicability to large-scale scRNA-seq datasets. To address this challenge, we propose a Bipartite Graph Transformer-based clustering model (BGFormer) for scRNA-seq data. We introduce a set of learnable anchor tokens as shared reference points to represent the entire dataset. A bipartite graph attention mechanism is introduced to learn the similarity between cells and anchor tokens, bringing cells of the same class closer together in the embedding space. BGFormer achieves linear computational complexity with respect to the number of cells, making it scalable to large datasets. Experimental results on multiple large-scale scRNA-seq datasets demonstrate the effectiveness and scalability of BGFormer.

Regular expressions (regexes) frequently exhibit super-linear worst-case behavior in regex engines, exposing software to Regex Denial-of-Service (ReDoS) attacks. Detecting such vulnerabilities is challenging, especially for extended features such as lookarounds and backreferences: existing static approaches are efficient but often lack support for extended features, whereas dynamic and hybrid approaches reduce false positives by executing regex matching on real engines, but incur high runtime overhead. To address this trade-off, we propose ReDoS-MotifGNN (RMGNN), a motif-based graph learning framework for ReDoS detection that leverages the low inference latency of graph neural networks (GNNs). RMGNN converts regexes into Heterogeneous Regex Graphs (HRGs) and encodes three ReDoS-related motifs into HRGs to incorporate domain priors, while preserving the syntactic structure and extended features of the input regex. Furthermore, it applies heterogeneous propagation with kernel-guided motif learning to capture multi-scale semantics, which are fused via residual cross-attention for robust prediction. Comprehensive evaluation on four real-world datasets (over 317k regexes) demonstrates that RMGNN outperforms six state-of-the-art baselines in F1-score and achieves an average 244$\times$ speedup over the top F1-performing baseline.

Handling missing node features is a key challenge for deploying Graph Neural Networks (GNNs) in real-world domains such as healthcare and sensor networks. Existing studies mostly address relatively benign scenarios, namely benchmark datasets with (a) high-dimensional but sparse node features and (b) incomplete data generated under Missing Completely At Random (MCAR) mechanisms. For (a), we theoretically prove that high sparsity substantially limits the information loss caused by missingness, making all models appear robust and preventing a meaningful comparison of their performance. To overcome this limitation, we introduce one synthetic and three real-world datasets with dense, semantically meaningful features. For (b), we move beyond MCAR and design evaluation protocols with more realistic missingness mechanisms. Moreover, we provide a theoretical background to state explicit assumptions on the missingness process and analyze their implications for different methods. Building on this analysis, we show that a simple baseline adapted to the graph domain is competitive with respect to specialized architectures across diverse datasets and missingness regimes.

Graph neural networks (GNNs) are widely used in graph learning and most architectures propagate information by passing messages between vertices. In this work, we shift our attention to GNNs that perform message passing on *edges* and introduce EB-1WL, an edge-based color-refinement test, and a corresponding architecture, EB-GNN. Our EB-GNN architecture is inspired by the classic triangle-counting algorithm of Chiba and Nishizeki and passes messages along edges and triangles. Our contributions are as follows: 1. Theoretically, we show that EB-1WL is significantly more expressive than 1WL. We provide a complete logical characterization of EB-1WL in first-order logic, along with distinguishability results via homomorphism counting. To the best of our knowledge, EB-GNN has the strongest theoretical expressivity guarantees among edge-based message-passing GNNs in the literature. 2. Unlike many GNN architectures that are more expressive than 1WL, we prove that EB-1WL and EB-GNN admit near-linear time and memory usage on practical graph learning workloads. 3. We show in experiments that EB-GNN is a highly efficient general-purpose architecture: it substantially outperforms simple MPNNs and remains competitive with task-specialized state-of-the-art GNNs at substantially lower computational cost.

Graph Neural Networks (GNNs) suffer from overfitting and over-squashing of long-range information. Stochastic graph augmentations (e.g., edge deletion) regularize training against overfitting but can introduce train-inference misalignment and do not improve over-squashing. In contrast, rewiring methods improve connectivity to mitigate over-squashing, but are not designed to regularize training. We propose *Random Add-Drop Edge (RADE)*, a stochastic graph augmentation method that jointly drops and adds edges to address both overfitting and over-squashing simultaneously. RADE is provably designed to align training and inference so that random augmentations regularize training without distribution shift, while supporting long-range communication at inference. We further propose and study a mini-batch gradient-norm balancing algorithm that adapts deletion and addition rates during training, rendering RADE hyperparameter-free in practice. Experiments on node- and graph-classification benchmarks show that RADE is a strong regularizer and mitigates over-squashing. Ablations support the roles of train-inference alignment, adaptive rate selection, and the complementary effects of random edge deletion and edge addition.

Graph foundation models (GFMs) aim to reuse a single backbone across diverse graph domains, yet their transfer is often uneven and can exhibit negative transfer. While most prior work improves transfer through architectural or adaptation choices, we ask a data-centric question: *which properties of two graph domains determine how much a fixed representation model changes its outputs?* Using a graphon-based continuous limit for dense graphs, we show that for both set-based and message-passing tokenizations, any Lipschitz backbone admits an explicit decomposition of cross-domain output shift into (i) graph-specific finite-sample approximation terms and (ii) an intrinsic, relabeling-invariant domain discrepancy capturing structural mismatch. A key ingredient is positional-encoding (PE) stability: we establish stability guarantees for spectral PEs and highlight contrasting behaviors of eigenvector- versus subspace-based PEs. Experiments on synthetic and real graphs validate the theory and translate the decomposition into guidance for data curation in GFM transfer.

Graph Neural Networks (GNNs) are increasingly adopting the "pre-training, adaptation" paradigm, which first pre-train GNNs on large-scale unlabeled graph data and then adapt them to specific downstream tasks. As a common pattern, graph prompting adapts to the frozen encoder by modifying the input graph structure, rather than fine-tuning the model parameters. However, most existing graph prompting approaches optimize the continuous and weighted adjacency structure in the adaptation phase, while requiring a hard discretization at inference time. This difference causes a train-test mismatch which is particularly harmful in few-shot regimes. To address the issue, we propose **Di**screte **P**rompting for **G**raphs, a discrete prompting framework that directly learns task-specific topology prompts in the combinatorial space. DiP-G operates on multi-hop local candidate subgraphs to ensure scalability, generates hard (k)-sparse prompts through a perturbed Top-(k) solver, and optimizes the discrete structures using an I-MLE gradient estimator. To improve the efficiency of backward pass, we further introduce an adaptive active-set screening rule that accelerates the target solve and can provably maintain the accuracy of the solution. Extensive experiments conducted on multiple benchmark datasets have validated the effectiveness of our proposed method.

Hypergraph contrastive learning has shown strong potential for modeling high-order relations, but most existing methods implicitly assume that nodes within the same hyperedge are semantically homogeneous. In real-world hypergraphs, this assumption often breaks down: heterogeneous node--hyperedge interactions may introduce noisy signals during augmentation and message passing, leading to feature contamination and false-positive contrastive alignment. To address this issue, we propose H$^2$CL, a heterogeneity-aware hypergraph contrastive learning framework for robust representation learning. H$^2$CL first estimates node--hyperedge heterogeneity from input features and uses it to guide a Heterogeneity-Aware View Generator, which selectively masks high-heterogeneity incidences and constructs cleaner contrastive views. It further introduces a Heterogeneity-Aware Hypergraph Encoder that dynamically reweights information propagation in both node-to-hyperedge and hyperedge-to-node aggregation, enabling hyperedges to aggregate more homogeneous signals while suppressing heterogeneous noise. We also provide theoretical analysis showing that the encoder corresponds to a coordinate descent step for minimizing a heterogeneity-weighted Dirichlet energy. Extensive experiments on standard benchmarks and larger-scale hypergraphs demonstrate that H$^2$CL achieves competitive or superior performance compared with recent baselines, remains robust under structural noise, and learns reweighting patterns that effectively reduce heterogeneity during message passing. Our code is available at: https://github.com/sxu-yaokx/HHCL

Recommendation systems seek to accurately model user preferences from a large set of candidate items. Graph neural networks (GNNs) have emerged as a dominant approach in this domain due to their ability to capture high-order user–item interactions. Recent efforts have aimed to enhance GNN-based representation learning by incorporating the semantic reasoning capabilities of large language models (LLMs). However, existing methods often process graph structural information and LLM-derived semantic knowledge separately, creating a supervisory gap between structural proximity and semantic relevance. To bridge this gap, we propose CCLRec, a consensus-driven contrastive learning framework for recommendation. CCLRec deeply integrates structural and semantic information by identifying consistent signals. Specifically, we first use an LLM to extract semantic representations of items and to sample candidate positive/negative sets in the semantic space. We then introduce a structural–semantic consensus mining strategy that computes the intersection between a node’s structural neighbors in the graph and its semantically similar items. This allows us to identify high-confidence positive pairs endorsed by both collaborative filtering patterns and LLM-based reasoning. By centering contrastive learning on these consensus pairs and applying a weight-aware reinforcement mechanism during training, CCLRec significantly amplifies the contribution of high-quality consensus features during training. Experiments across multiple public benchmarks show that CCLRec consistently outperforms state-of-the-art methods on key metrics, demonstrating the effectiveness of our consensus-aware design.

Graph neural networks (GNNs) tightly couple their input-output parameters to dataset-specific feature spaces and target sets, exhibiting limited transferability across different datasets. In contrast, language models (LMs) generalize flexibly via a unified input-output interface, motivating recent attempts to adapt LMs to graph tasks. However, existing methods struggle to encode whole-graph information, leading to potential information loss and suboptimal graph understanding. In this work, we propose a novel weight-level information injection paradigm for adapting LMs to graph tasks. This paradigm injects whole-graph information by generating task-specific weight updates that interact directly with hidden representations. Instantiating this paradigm following low-rank adaptation (LoRA), we introduce GaRA, a Graph-aware LoRA generation model. GaRA constructs low-rank weight updates conditioned on the original graph structures and constrains the norm of the generated updates, thus injecting whole-graph information and avoiding the optimization bias in the weight generation. Empirical studies demonstrate that GaRA consistently outperforms baselines on zero-shot graph learning tasks.

Representation learning on text-attributed graphs (TAGs) is crucial for real-world applications, as it enables effective modeling of both rich node semantics and complex graph structure. Nevertheless, this task is intrinsically challenging due to structural–semantic mismatch stemming from divergent modality distributions, as well as dual-source noise inherent in node textual content and graph structure. Existing approaches often enforce a rigid fusion of distinct modalities while overlooking their inherent noise, which inevitably results in persistent distribution gaps and amplifies mixed interference during information propagation. To address these issues, we propose UDPD, an Uncertainty-modulated Dual-Path Diffusion model for robust text-attributed graph learning. Specifically, we first employ a dual-perspective node encoding strategy to separately learn semantic and structural embeddings. We then introduce a cooperative diffusion paradigm with parallel semantic and structural branches, where mutual guidance enables progressive alignment of different distributions while effectively suppressing modality inherent noise. Crucially, the reverse process is guided by node uncertainty, which is used to adaptively modulate cross-branch interaction strength, ensuring robust coupling and maximizing denoising effectiveness. Extensive experiments on five public benchmarks demonstrate the effectiveness and superiority of our UDPD over state-of-the-art baselines.

Graph Neural Networks (GNNs) on meshes have emerged as promising surrogates for computational mechanics, but standard local message passing struggles to propagate information across unstructured meshes, leading to large errors in regions with complex physics (e.g., shocks, wakes, boundary layers). Existing approaches enlarge connectivity with long-range edges chosen *a priori* via geometric heuristics or random sampling, which lack a mechanism to prioritize high-error regions and often introduce redundant communication. We propose **MiSe-GNN**, a dual-head architecture that adaptively augments graph connectivity using model-predicted *a posteriori* errors. MiSe-GNN jointly predicts physical fields and a node-wise error indicator; the predicted error is periodically converted into a hierarchy of additional edges via an adaptive tree that links high-error nodes to spatial pivots at multiple scales. This error-guided connectivity concentrates message passing where the surrogate is uncertain while keeping the graph sparse elsewhere, yielding a transparent and physically interpretable graph-space analogue of adaptive mesh refinement. Across industrial CFD and CSD benchmarks, MiSe-GNN consistently improves accuracy and accuracy–compute trade-offs over strong baselines, and qualitative analyses show that it routes communication toward physically challenging regions. These results establish *error-guided edge augmentation* as a robust and general design principle for long-range message passing in physics-aware GNNs.

This paper studies fairness-aware graph adaptation, aiming to transfer knowledge from a labeled source graph to an unlabeled target graph while addressing fairness. Most prior methods require target-domain attributes to learn invariant graph representations of sensitive attributes, which are often unavailable in practice. To address this limitation, we introduce \underline{C}ausality-attended Repres\underline{e}ntation Dientang\underline{l}ement with Structural A\underline{l}ignment (CELL) for fairness-aware graph adaptation without requiring target sensitive labels. CELL constructs a causal graph to model the graph-generation mechanism and guide fair representation disentanglement. Specifically, CELL uses sensitive and causal encoders to extract sensitive and causal factors, respectively, and promotes disentanglement by minimizing their conditional mutual information. To leverage unlabeled target data, we further generate pseudo-labels for both target task labels and sensitive attributes, and use similarity relations to derive unbiased node representations. Finally, to further mitigate domain shift, we build a fairness-aware bipartite graph that provides additional structural supervision for cross-domain alignment. Experiments on benchmarks show that CELL consistently outperforms strong baselines in both predictive performance and fairness.

Transformers often fail to learn generalizable algorithms, instead relying on brittle heuristics. Using graph connectivity as a testbed, we explain this phenomenon both theoretically and empirically. We consider a simplified Transformer architecture, the Disentangled Transformer, and prove that an $L$-layer model can compute connectivity in graphs with diameters up to $3^L$, implementing an algorithm equivalent to computing powers of the adjacency matrix. By analyzing training dynamics, we prove that whether the model learns this strategy hinges on whether most training instances are within this model capacity. Within-capacity graphs (diameter $\leq 3^L$) drive the learning of the algorithmic solution while beyond-capacity graphs drive the learning of a simple heuristic based on node degrees. Finally, we empirically show that our insights transfer to standard Transformers: restricting training data to stay within a model's capacity makes both standard and Disentangled Transformers learn the exact algorithm.