ICML 2025 Papers

Estimating causal effects is crucial for decision-makers in many applications, but it is particularly challenging with observational network data due to peer interactions. Some algorithms have been proposed to estimate causal effects involving network data, particularly peer effects, but they often fail to tell apart diverse peer effects. To address this issue, we propose a general setting which considers both peer direct effects and peer indirect effects, and the effect of an individual's own treatment, and provide the identification conditions of these causal effects. To differentiate these effects, we leverage causal mediation analysis and tailor it specifically for network data. Furthermore, given the inherent challenges of accurately estimating effects in networked environments, we propose to incorporate attention mechanisms to capture the varying influences of different neighbors and to explore high-order neighbor effects using multi-layer graph neural networks (GNNs). Additionally, we employ the Hilbert-Schmidt Independence Criterion (HSIC) to further enhance the model’s robustness and accuracy. Extensive experiments on two semi-synthetic datasets derived from real-world networks and on a dataset from a recommendation system confirm the effectiveness of our approach. Our findings have the potential to improve intervention strategies in networked systems, particularly in social networks and public health.

Graph neural networks (GNNs) have been widely used in various domains such as social networks, molecular biology, or recommendation systems. Concurrently, different explanations methods of GNNs have arisen to complement its blackbox nature. Explanations of the GNNs’ predictions can be categorized into two types—factual and counterfactual. Given a GNN trained on binary classification into “accept” and “reject” classes, a global counterfactual explanation consists in generating a small set of “accept” graphs relevant to all of the input “reject” graphs. The transformation of a “reject” graph into an “accept” graph is called a recourse. A common recourse explanation is a small set of recourse, from which every “reject” graph can be turned into an “accept” graph. Although local counterfactual explanations have been studied extensively, the problem of finding common recourse for global counterfactual explanation remains unexplored, particularly for GNNs. In this paper, we formalize the common recourse explanation problem, and design an effective algorithm, COMRECGC, to solve it. We benchmark our algorithm against strong baselines on four different real-world graphs datasets and demonstrate the superior performance of COMRECGC against the competitors. We also compare the common recourse explanations to the graph counterfactual explanation, showing that common recourse explanations are either comparable or superior, making them worth considering for applications such as drug discovery or computational biology.

Although directed graphs (digraphs) offer strong modeling capabilities for complex topological systems, existing DiGraph Neural Networks (DiGNNs) struggle to fully capture the concealed rich structural information. This data-level limitation results in model-level sub-optimal predictive performance and underscores the necessity of further exploring the potential correlations between the directed edges (topology) and node profiles (features and labels) from a data-centric perspective, thereby empowering model-centric neural networks with stronger encoding capabilities. In this paper, we propose **E**ntropy-driven **D**igraph knowl**E**dge distillatio**N** (EDEN), which can serve as a data-centric digraph learning paradigm or a model-agnostic hot-and-plug data-centric Knowledge Distillation (KD) module. EDEN implements data-centric machine learning by constructing a coarse-grained Hierarchical Knowledge Tree (HKT) using proposed hierarchical encoding theory, and refining HKT through mutual information analysis of node profiles to guide knowledge distillation during training. As a general framework, EDEN naturally extends to undirected graphs and consistently delivers strong performance. Extensive experiments on 14 (di)graph datasets—spanning both homophily and heterophily settings—and across four downstream tasks show that EDEN achieves SOTA results and significantly enhances existing (Di)GNNs.

We present a novel, and effective, approach to achieve optimal mesh relocation in finite element methods (FEMs). The cost and accuracy of FEMs is critically dependent on the choice of mesh points. Mesh relocation (r-adaptivity) seeks to optimise the mesh geometry to obtain the best solution accuracy at given computational budget. Classical r-adaptivity relies on the solution of a separate nonlinear ``meshing'' PDE to determine mesh point locations. This incurs significant cost at remeshing, and relies on estimates that relate interpolation- and FEM-error. Recent machine learning approaches have focused on the construction of fast surrogates for such classical methods. Instead, our new approach trains a graph neural network (GNN) to determine mesh point locations by directly minimising the FE solution error from the PDE system Firedrake to achieve higher solution accuracy. Our GNN architecture closely aligns the mesh solution space to that of classical meshing methodologies, thus replacing classical estimates for optimality with a learnable strategy. This allows for rapid and robust training and results in an extremely efficient and effective GNN approach to online r-adaptivity. Our method outperforms both classical, and prior ML, approaches to r-adaptive meshing. In particular, it achieves lower FE solution error, whilst retaining the significant speed-up over classical methods observed in prior ML work.

Effectively modeling time information and incorporating it into applications or models involving chronologically occurring events is crucial. Real-world scenarios often involve diverse and complex time patterns, which pose significant challenges for time encoding methods. While previous methods focus on capturing time patterns, many rely on specific inductive biases, such as using trigonometric functions to model periodicity. This narrow focus on single-pattern modeling makes them less effective in handling the diversity and complexities of real-world time patterns. In this paper, we investigate to improve the existing commonly used time encoding methods and introduce **Learnable Transformation-based Generalized Time Encoding (LeTE)**. We propose using deep function learning techniques to parameterize nonlinear transformations in time encoding, making them learnable and capable of modeling generalized time patterns, including diverse and complex temporal dynamics. By enabling learnable transformations, LeTE encompasses previous methods as specific cases and allows seamless integration into a wide range of tasks. Through extensive experiments across diverse domains, we demonstrate the versatility and effectiveness of LeTE.

The isomorphism problem is a key challenge in both graph and hypergraph domains, crucial for applications like protein design, chemical pathways, and community detection. Hypergraph isomorphism, which models high-order relationships in real-world scenarios, remains underexplored compared to the graph isomorphism. Current algorithms for hypergraphs, like the 1-dimensional generalized Weisfeiler-Lehman test (1-GWL), lag behind advancements in graph isomorphism tests, limiting most hypergraph neural networks to 1-GWL's expressive power. To address this, we propose the high-dimensional GWL (k-GWL), generalizing k-WL from graphs to hypergraphs. We prove that k-GWL reduces to k-WL for simple graphs, and thus develop a unified isomorphism method for both graphs and hypergraphs. We also successfully establish a clear and complete understanding of the GWL hierarchy of expressivity, showing that (k+1)-GWL is more expressive than k-GWL with illustrative examples. Based on k-GWL, we develop a hypergraph neural network model named k-HNN with improved expressive power of k-GWL, which achieves superior performance on real-world datasets, including a 6\% accuracy improvement on the Steam-Player dataset over the runner-up. Our code is available at https://github.com/talence-zcq/KGWL.

Group fairness based on adversarial training has gained significant attention on graph data, which was implemented by masking sensitive attributes to generate fair feature views. However, existing models suffer from training instability due to uncertainty of the generated masks and the trade-off between fairness and utility. In this work, we propose a stable fair Graph Neural Network (SFG) to maintain training stability while preserving accuracy and fairness performance. Specifically, we first theoretically derive a tight upper Lipschitz bound to control the stability of existing adversarial-based models and employ a stochastic projected subgradient algorithm to constrain the bound, which operates in a block-coordinate manner. Additionally, we construct the uncertainty set to train the model, which can prevent unstable training by dropping some overfitting nodes caused by chasing fairness. Extensive experiments conducted on three real-world datasets demonstrate that SFG is stable and outperforms other state-of-the-art adversarial-based methods in terms of both fairness and utility performance. Codes are available at https://github.com/sh-qiangchen/SFG.

Self-Explainable Graph Neural Networks (SE-GNNs) are popular explainable-by-design GNNs, but their explanations' properties and limitations are not well understood. Our first contribution fills this gap by formalizing the explanations extracted by some popular SE-GNNs, referred to as Minimal Explanations (MEs), and comparing them to established notions of explanations, namely Prime Implicant (PI) and faithful explanations. Our analysis reveals that MEs match PI explanations for a restricted but significant family of tasks. In general, however, they can be less informative than PI explanations and are surprisingly misaligned with widely accepted notions of faithfulness. Although faithful and PI explanations are informative, they are intractable to find and we show that they can be prohibitively large. Given these observations, a natural choice is to augment SE-GNNs with alternative modalities of explanations taking care of SE-GNNs’ limitations. To this end, we propose Dual-Channel GNNs that integrate a white-box rule extractor and a standard SE-GNN, adaptively combining both channels. Our experiments show that even a simple instantiation of Dual-Channel GNNs can recover succinct rules and perform on par or better than widely used SE-GNNs.

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the *motifs* that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are *binary*, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

Graph Convolutional Neural Networks (GCNs) have gained widespread popularity in various fields like personal healthcare and financial systems, due to their remarkable performance. Despite the growing demand for cloud-based GCN services, privacy concerns over sensitive graph data remain significant. Homomorphic Encryption (HE) facilitates Privacy-Preserving Machine Learning (PPML) by allowing computations to be performed on encrypted data. However, HE introduces substantial computational overhead, particularly for GCN operations that require rotations and multiplications in matrix products. The sparsity of GCNs offers significant performance potential, but their irregularity introduces additional operations that reduce practical gains. In this paper, we propose FicGCN, a HE-based framework specifically designed to harness the sparse characteristics of GCNs and strike a globally optimal balance between aggregation and combination operations. FicGCN employs a latency-aware packing scheme, a Sparse Intra-Ciphertext Aggregation (SpIntra-CA) method to minimize rotation overhead, and a region-based data reordering driven by local adjacency structure. We evaluated FicGCN on several popular datasets, and the results show that FicGCN achieved the best performance across all tested datasets, with up to a $4.10\times$ improvement over the latest design.

We investigate the distance function learned by message passing neural networks (MPNNs) in specific tasks, aiming to capture the _functional_ distance between prediction targets that MPNNs implicitly learn. This contrasts with previous work, which links MPNN distances on arbitrary tasks to _structural_ distances on graphs that ignore task-specific information. To address this gap, we distill the distance between MPNN embeddings into an interpretable graph distance. Our method uses optimal transport on the Weisfeiler Leman Labeling Tree (WILT), where the edge weights reveal subgraphs that strongly influence the distance between embeddings. This approach generalizes two well-known graph kernels and can be computed in linear time. Through extensive experiments, we demonstrate that MPNNs define the relative position of embeddings by focusing on a small set of subgraphs that are known to be functionally important in the domain.

Directed acyclic graphs (DAGs) are a class of graphs commonly used in practice, with examples that include electronic circuits, Bayesian networks, and neural architectures. While many effective encoders exist for DAGs, it remains challenging to decode them in a principled manner, because the nodes of a DAG can have many different topological orders. In this work, we propose a grammar-based approach to constructing a principled, compact and equivalent sequential representation of a DAG. Specifically, we view a graph as derivations over an unambiguous grammar, where the DAG corresponds to a unique sequence of production rules. Equivalently, the procedure to construct such a description can be viewed as a lossless compression of the data. Such a representation has many uses, including building a generative model for graph generation, learning a latent space for property prediction, and leveraging the sequence representational continuity for Bayesian Optimization over structured data.

Fusing heterogeneous information remains a persistent challenge in modern data analysis. While significant progress has been made, existing approaches often fail to account for the inherent heterogeneity of object patterns across different semantic spaces. To address this limitation, we propose the **Cooperation of Experts (CoE)** framework, which encodes multi-typed information into unified heterogeneous multiplex networks. By transcending modality and connection differences, CoE provides a powerful and flexible model for capturing the intricate structures of real-world complex data. In our framework, dedicated encoders act as domain-specific experts, each specializing in learning distinct relational patterns in specific semantic spaces. To enhance robustness and extract complementary knowledge, these experts collaborate through a novel **large margin** mechanism supported by a tailored optimization strategy. Rigorous theoretical analyses guarantee the framework’s feasibility and stability, while extensive experiments across diverse benchmarks demonstrate its superior performance and broad applicability.

Graph Neural Networks (GNNs) have proven effective for learning from graph-structured data through their neighborhood-based message passing framework. Many hierarchical graph clustering pooling methods modify this framework by introducing clustering-based strategies, enabling the construction of more expressive and powerful models. However, all of these message passing framework heavily rely on the connectivity structure of graphs, limiting their ability to capture the rich geometric features inherent in geometric graphs. To address this, we propose Rhomboid Tiling (RT) clustering, a novel clustering method based on the rhomboid tiling structure, which performs clustering by leveraging the complex geometric information of the data and effectively extracts its higher-order geometric structures. Moreover, we design RTPool, a hierarchical graph clustering pooling model based on RT clustering for graph classification tasks. The proposed model demonstrates superior performance, outperforming 21 state-of-the-art competitors on all the 7 benchmark datasets.

Recommender systems are increasingly spreading to different areas like e-commerce or video streaming to alleviate information overload. One of the most fundamental methods for recommendation is Collaborative Filtering (CF), which leverages historical user-item interactions to infer user preferences. In recent years, Graph Neural Networks (GNNs) have been extensively studied to capture graph structures in CF tasks. Despite this remarkable progress, local structure modeling and embedding distortion still remain two notable limitations in the majority of GNN-based CF methods. Therefore, in this paper, we propose a novel Hyperbolic Graph Transformer architecture, to tackle the long-tail problems in CF tasks. Specifically, the proposed framework is comprised of two essential modules: 1) Local Hyperbolic Graph Convolutional Network (LHGCN), which performs graph convolution entirely in the hyperbolic manifold and captures the local structure of each node; 2) Hyperbolic Transformer, which is comprised of hyperbolic cross-attention mechanisms to capture global information. Furthermore, to enable its feasibility on large-scale data, we introduce an unbiased approximation of the cross-attention for linear computational complexity, with a theoretical guarantee in approximation errors. Empirical experiments demonstrate that our proposed model outperforms the leading collaborative filtering methods and significantly mitigates the long-tail issue in CF tasks. Our implementations are available in \url{https://github.com/EnkiXin/Hgformer}.

Heterogeneous Graph Neural Networks (HGNNs), have demonstrated excellent capabilities in processing heterogeneous information networks. Self-supervised learning on heterogeneous graphs, especially contrastive self-supervised strategy, shows great potential when there are no labels. However, this approach requires the use of carefully designed graph augmentation strategies and the selection of positive and negative samples. Determining the exact level of similarity between sample pairs is non-trivial.To solve this problem, we propose a novel self-supervised Heterogeneous graph neural network with Optimal Transport (HGOT) method which is designed to facilitate self-supervised learning for heterogeneous graphs without graph augmentation strategies. Different from traditional contrastive self-supervised learning, HGOT employs the optimal transport mechanism to relieve the laborious sampling process of positive and negative samples. Specifically, we design an aggregating view (central view) to integrate the semantic information contained in the views represented by different meta-paths (branch views). Then, we introduce an optimal transport plan to identify the transport relationship between the semantics contained in the branch view and the central view. This allows the optimal transport plan between graphs to align with the representations, forcing the encoder to learn node representations that are more similar to the graph space and of higher quality. Extensive experiments on four real-world datasets demonstrate that our proposed HGOT model can achieve state-of-the-art performance on various downstream tasks. In particular, in the node classification task, HGOT achieves an average of more than 6\% improvement in accuracy compared with state-of-the-art methods.

Processing global geometric context while preserving equivariance is crucial when modeling biological, chemical, and physical systems. Yet, this is challenging due to the computational demands of equivariance and global context at scale. Standard methods such as equivariant self-attention suffer from quadratic complexity, while local methods such as distance-based message passing sacrifice global information. Inspired by the recent success of state-space and long-convolutional models, we introduce Geometric Hyena, the first equivariant long-convolutional model for geometric systems. Geometric Hyena captures global geometric context at sub-quadratic complexity while maintaining equivariance to rotations and translations. Evaluated on all-atom property prediction of large RNA molecules and full protein molecular dynamics, Geometric Hyena outperforms existing equivariant models while requiring significantly less memory and compute that equivariant self-attention. Notably, our model processes the geometric context of $30k$ tokens $20 \times$ faster than the equivariant transformer and allows $72 \times$ longer context within the same budget.

Graph contrastive learning has attracted great interest as a dominant and promising self-supervised representation learning approach in recent years. While existing works follow the basic principle of pulling positive pairs closer and pushing negative pairs far away, they still suffer from several critical problems, such as the underlying semantic disturbance brought by augmentation strategies, the failure of GCN in capturing long-range dependence, rigidness and inefficiency of node sampling techniques. To address these issues, we propose Manifold Learning Inspired Lightweight Graph Contrastive Learning (ML$^2$-GCL), which inherits the merits of both manifold learning and GCN. ML$^2$-GCL avoids the potential risks of semantic disturbance with only one single view. It achieves global nonlinear structure recovery from locally linear fits, which can make up for the defects of GCN. The most amazing advantage is about the lightweight due to its closed-form solution of positive pairs weights and removal of pairwise distances calculation. Theoretical analysis proves the existence of the optimal closed-form solution. Extensive empirical results on various benchmarks and evaluation protocols demonstrate effectiveness and lightweight of ML$^2$-GCL. We release the code at https://github.com/a-hou/ML2-GCL.

Although graph contrastive learning (GCL) has been widely investigated, it is still a challenge to generate effective and stable graph augmentations. Existing methods often apply heuristic augmentation like random edge dropping, which may disrupt important graph structures and result in unstable GCL performance. In this paper, we propose **P**ositive-**i**ncentive **N**oise driven **G**raph **D**ata **A**ugmentation (PiNGDA), where positive-incentive noise (pi-noise) scientifically analyzes the beneficial effect of noise under the information theory. To bridge the standard GCL and pi-noise framework, we design a Gaussian auxiliary variable to convert the loss function to information entropy. We prove that the standard GCL with pre-defined augmentations is equivalent to estimate the beneficial noise via the point estimation. Following our analysis, PiNGDA is derived from learning the beneficial noise on both topology and attributes through a trainable noise generator for graph augmentations, instead of the simple estimation. Since the generator learns how to produce beneficial perturbations on graph topology and node attributes, PiNGDA is more reliable compared with the existing methods. Extensive experimental results validate the effectiveness and stability of PiNGDA.