Data synthesis is gaining momentum as a privacy-enhancing technology. While single-table tabular data generation has seen considerable progress, current methods for multi-table data often lack the flexibility and expressiveness needed to capture complex relational structures. In particular, they struggle with long-range dependencies and complex foreign-key relationships, such as tables with multiple parent tables or multiple types of links between the same pair of tables. We propose a generative model for relational data that generates the content of a relational dataset given the graph formed by the foreign-key relationships. We do this by learning a deep generative model of the content of the whole relational database by flow matching, where the neural network trained to denoise records leverages a graph neural network to obtain information from connected records. Our method is flexible, as it can support relational datasets with complex structures, and expressive, as the generation of each record can be influenced by any other record within the same connected component. We evaluate our method on several benchmark datasets and show that it achieves state-of-the-art performance in terms of synthetic data fidelity.
Clinical studies reveal disruptions in brain structural connectivity (SC) and functional connectivity (FC) in neuropsychiatric disorders such as schizophrenia (SZ). Traditional approaches might rely solely on SC due to limited functional data availability, hindering comprehension of cognitive and behavioral impairments in individuals with SZ by neglecting the intricate SC-FC interrelationship. To tackle the challenge, we propose a novel physics-guided deep learning framework that leverages a neural oscillation model to describe the dynamics of a collection of interconnected neural oscillators, which operate via nerve fibers dispersed across the brain's structure. Our proposed framework utilizes SC to simultaneously generate FC by learning SC-FC coupling from a system dynamics perspective. Additionally, it employs a novel multi-view graph neural network (GNN) with a joint loss to perform correlation-based SC-FC fusion and classification of individuals with SZ. Experiments conducted on a clinical dataset exhibited improved performance, demonstrating the robustness of our proposed approach.
Temporal Graph Neural Networks (TGNNs) have gained growing attention for modeling and predicting structures in temporal graphs. However, existing TGNNs primarily focus on pairwise interactions while overlooking higher-order structures that are integral to link formation and evolution in real-world temporal graphs. Meanwhile, these models often suffer from efficiency bottlenecks, further limiting their expressive power. To tackle these challenges, we propose a Higher-order structure Temporal Graph Neural Network, which incorporates hypergraph representations into temporal graph learning. In particular, we develop an algorithm to identify the underlying higher-order structures, enhancing the model's ability to capture the group interactions. Furthermore, by aggregating multiple edge features into hyperedge representations, HTGN effectively reduces memory cost during training. We theoretically demonstrate the enhanced expressiveness of our approach and validate its effectiveness and efficiency through extensive experiments on various real-world temporal graphs. Experimental results show that HTGN achieves superior performance on dynamic link prediction while reducing memory costs by up to 50\% compared to existing methods.
Graph structure learning is a core problem in graph-based machine learning, essential for uncovering latent relationships and ensuring model interpretability. However, most existing approaches are ill-suited for large-scale and dynamically evolving graphs, as they often require complete re-learning of the structure upon the arrival of new nodes and incur substantial computational and memory costs. In this work, we propose GraphFLEx: a unified and scalable framework for Graph Structure Learning in Large and Expanding Graphs. GraphFLEx mitigates the scalability bottlenecks by restricting edge formation to structurally relevant subsets of nodes identified through a combination of clustering and coarsening techniques. This dramatically reduces the search space and enables efficient, incremental graph updates. The framework supports 48 flexible configurations by integrating diverse choices of learning paradigms, coarsening strategies, and clustering methods, making it adaptable to a wide range of graph settings and learning objectives. Extensive experiments across 26 diverse datasets and Graph Neural Network architectures demonstrate that GraphFLEx achieves state-of-the-art performance with significantly improved scalability.
Conformal symmetries, i.e.\ coordinate transformations that preserve angles, play a key role in many fields, including physics, mathematics, computer vision and (geometric) machine learning. Here we build a neural network that is equivariant under general conformal transformations. To achieve this, we lift data from flat Euclidean space to Anti de Sitter (AdS) space. This allows us to exploit a known correspondence between conformal transformations of flat space and isometric transformations on the AdS space. We then build upon the fact that such isometric transformations have been extensively studied on general geometries in the geometric deep learning literature. We employ message-passing layers conditioned on the proper distance, yielding a computationally efficient framework. We validate our model on tasks from computer vision and statistical physics, demonstrating strong performance, improved generalization capacities, and the ability to extract conformal data such as scaling dimensions from the trained network.
Relational Deep Learning (RDL) is a promising approach for building state-of-the-art predictive models on multi-table relational data by representing it as a heterogeneous temporal graph. However, commonly used Graph Neural Network models suffer from fundamental limitations in capturing complex structural patterns and long-range dependencies that are inherent in relational data. While Graph Transformers have emerged as powerful alternatives to GNNs on general graphs, applying them to relational entity graphs presents unique challenges: (i) Traditional positional encodings fail to generalize to massive, heterogeneous graphs; (ii) existing architectures cannot model the temporal dynamics and schema constraints of relational data; (iii) existing tokenization schemes lose critical structural information. Here we introduce the Relational Graph Transformer (RelGT), the first graph transformer architecture designed specifically for relational tables. RelGT employs a novel multi-element tokenization strategy that decomposes each node into five components (features, type, hop distance, time, and local structure), enabling efficient encoding of heterogeneity, temporality, and topology without expensive precomputation. Our architecture combines local attention over sampled subgraphs with global attention to learnable centroids, incorporating both local and database-wide representations. Across 21 tasks from the RelBench benchmark, RelGT consistently matches or outperforms GNN baselines by up to 18%, establishing Graph Transformers as a powerful architecture for Relational Deep Learning.
Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods, though effective for small molecules, only model the single unit of polymers and fail to produce consistent vector representations for the true polymer structure with varying numbers of units. To address this challenge, we introduce Graph Repetition Invariance (GRIN), a novel method to learn polymer representations that are invariant to the number of repeating units in their graph representations. GRIN integrates a graph-based maximum spanning tree alignment with repeat-unit augmentation to ensure structural consistency. We provide theoretical guarantees for repetition-invariance from both model and data perspectives, demonstrating that three repeating units are the minimal augmentation required for optimal invariant representation learning. GRIN outperforms state-of-the-art baselines on both homopolymer and copolymer benchmarks, learning stable, repetition-invariant representations that generalize effectively to polymer chains of unseen sizes.
We present GNN-Suite, a robust modular framework for constructing and benchmarking Graph Neural Network (GNN) architectures in computational biology. GNN-Suite standardises experimentation and reproducibility using the Nextflow workflow to evaluate GNN performance. We demonstrate its utility in identifying cancer-driver genes by constructing molecular networks from protein-protein interaction (PPI) data from STRING and BioGRID and annotating nodes with features from the PCAWG, PID, and COSMIC-CGC repositories. Our design enables fair comparisons among diverse GNN architectures including GAT, GAT3H, GCN, GCN2, GIN, GTN, HGCN, PHGCN, and GraphSAGE and a baseline Logistic Regression (LR) model. All GNNs were configured as standardised two-layer models and trained with uniform hyperparameters (dropout = 0.2; Adam optimiser with learning rate = 0.01; and an adjusted binary cross-entropy loss to address class imbalance) over an 80/20 train-test split for 300 epochs. Each model was evaluated over 10 independent runs with different random seeds to yield statistically robust performance metrics, with balanced accuracy (BACC) as the primary measure. Notably, GCN2 achieved the highest BACC (0.807 +/- 0.035) on a STRING-based network, although all GNN types outperformed the LR baseline, highlighting the advantage of network-based learning over feature-only approaches. Our results show that a common framework for implementing and evaluating GNN architectures aids in identifying not only the best model but also the most effective means of incorporating complementary data. By making GNN-Suite publicly available, we aim to foster reproducible research and promote improved benchmarking standards in computational biology. Future work will explore additional omics datasets and further refine network architectures to enhance predictive accuracy and interpretability in biomedical applications.
Language Modeling is a prevalent task in Natural Language Processing. The currently existing most recent and most successful language models often tend to build a massive model with billions of parameters, feed in a tremendous amount of text data, and train with enormous computation resources which require millions of dollars. In this project, we aim to address an important sub-task in language modeling, i.e., context embedding. We propose an approach to exploit the Graph Convolution operation in GNNs to encode the context and use it in coalition with LSTMs to predict the next word given a local context of preceding words. We test this on the custom Wikipedia text corpus using a very limited amount of resources and show that this approach works fairly well to predict the next word.
Cell-free massive MIMO (CF-mMIMO) has emerged as a promising paradigm for delivering uniformly high-quality coverage in future wireless networks. To address the inherent challenges of precoding in such distributed systems, recent studies have explored the use of graph neural network (GNN)-based methods, using their powerful representation capabilities. However, these approaches have predominantly been trained and validated on synthetic datasets, leaving their generalizability to real-world propagation environments largely unverified. In this work, we initially pre-train the GNN using simulated channel state information (CSI) data, which incorporates standard propagation models and small-scale Rayleigh fading. Subsequently, we finetune the model on real-world CSI measurements collected from a physical testbed equipped with distributed access points (APs). To balance the retention of pre-trained features with adaptation to real-world conditions, we adopt a layer-freezing strategy during fine-tuning, wherein several GNN layers are frozen and only the later layers remain trainable. Numerical results demonstrate that the fine-tuned GNN significantly outperforms the pre-trained model, achieving an approximate 8.2 bits per channel use gain at 20 dB signal-to-noise ratio (SNR), corresponding to a 15.7 % improvement. These findings highlight the critical role of transfer learning and underscore the potential of GNN-based precoding techniques to effectively generalize from synthetic to real-world wireless environments.
We consider the problem of optimal link scheduling in large-scale wireless ad hoc networks. We specifically aim for the maximum long-term average performance, subject to a minimum transmission requirement for each link to ensure fairness. With a graph structure utilized to represent the conflicts of links, we formulate a constrained optimization problem to learn the scheduling policy, which is parameterized with a graph neural network (GNN). To address the challenge of long-term performance, we use the state-augmentation technique. In particular, by augmenting the Lagrangian dual variables as dynamic inputs to the scheduling policy, the GNN can be trained to gradually adapt the scheduling decisions to achieve the minimum transmission requirements. We verify the efficacy of our proposed policy through numerical simulations and compare its performance with several baselines in various network settings.
Purpose: Recently, there has been a revived interest in system neuroscience causation models, driven by their unique capability to unravel complex relationships in multi-scale brain networks. In this paper, we present a novel method that leverages causal dynamics to achieve effective fMRI-based subject and task fingerprinting. Methods: By applying an implicit-explicit discretization scheme, we develop a two-timescale linear state-space model. Through data-driven identification of its parameters, the model captures causal signatures, including directed interactions among brain regions from a spatial perspective, and disentangled fast and slow dynamic modes of brain activity from a temporal perspective. These causal signatures are then integrated with: (i) a modal decomposition and projection method for model-based subject identification, and (ii) a Graph Neural Network (GNN) framework for learning-based task classification. Furthermore, we introduce the concept of the brain reachability landscape as a novel visualization tool, which quantitatively characterizes the maximum possible activation levels of brain regions under various fMRI tasks. Results: We evaluate the proposed approach using the Human Connectome Project dataset and demonstrate its advantage over non-causality-based methods. The obtained causal signatures are visualized and demonstrate clear biological relevance with established understandings of brain function. Conclusion: We verified the feasibility and effectiveness of utilizing brain causal signatures for subject and task fingerprinting. Additionally, our work paves the way for further studies on causal fingerprints with potential applications in both healthy controls and neurodegenerative diseases.
Cross-user variability in Human Activity Recognition (HAR) remains a critical challenge due to differences in sensor placement, body dynamics, and behavioral patterns. Traditional methods often fail to capture biomechanical invariants that persist across users, limiting their generalization capability. We propose an Edge-Enhanced Graph-Based Adversarial Domain Generalization (EEG-ADG) framework that integrates anatomical correlation knowledge into a unified graph neural network (GNN) architecture. By modeling three biomechanically motivated relationships together-Interconnected Units, Analogous Units, and Lateral Units-our method encodes domain-invariant features while addressing user-specific variability through Variational Edge Feature Extractor. A Gradient Reversal Layer (GRL) enforces adversarial domain generalization, ensuring robustness to unseen users. Extensive experiments on OPPORTUNITY and DSADS datasets demonstrate state-of-the-art performance. Our work bridges biomechanical principles with graph-based adversarial learning by integrating information fusion techniques. This fusion of information underpins our unified and generalized model for cross-user HAR.
Reliable street-level traffic volume data, covering multiple modes of transportation, helps urban planning by informing decisions on infrastructure improvements, traffic management, and public transportation. Yet, traffic sensors measuring traffic volume are typically scarcely located, due to their high deployment and maintenance costs. To address this, interpolation methods can estimate traffic volumes at unobserved locations using available data. Graph Neural Networks have shown strong performance in traffic volume forecasting, particularly on highways and major arterial networks. Applying them to urban settings, however, presents unique challenges: urban networks exhibit greater structural diversity, traffic volumes are highly overdispersed with many zeros, the best way to account for spatial dependencies remains unclear, and sensor coverage is often very sparse. We introduce the Graph Neural Network for Urban Interpolation (GNNUI), a novel urban traffic volume estimation approach. GNNUI employs a masking algorithm to learn interpolation, integrates node features to capture functional roles, and uses a loss function tailored to zero-inflated traffic distributions. In addition to the model, we introduce two new open, large-scale urban traffic volume benchmarks, covering different transportation modes: Strava cycling data from Berlin and New York City taxi data. GNNUI outperforms recent, some graph-based, interpolation methods across metrics (MAE, RMSE, true-zero rate, Kullback-Leibler divergence) and remains robust from 90% to 1% sensor coverage. On Strava, for instance, MAE rises only from 7.1 to 10.5, on Taxi from 23.0 to 40.4, demonstrating strong performance under extreme data scarcity, common in real-world urban settings. We also examine how graph connectivity choices influence model accuracy.
Nowadays, numerous online platforms can be described as multi-modal heterogeneous networks (MMHNs), such as Douban's movie networks and Amazon's product review networks. Accurately categorizing nodes within these networks is crucial for analyzing the corresponding entities, which requires effective representation learning on nodes. However, existing multi-modal fusion methods often adopt either early fusion strategies which may lose the unique characteristics of individual modalities, or late fusion approaches overlooking the cross-modal guidance in GNN-based information propagation. In this paper, we propose a novel model for node classification in MMHNs, named Heterogeneous Graph Neural Network with Inter-Modal Attention (HGNN-IMA). It learns node representations by capturing the mutual influence of multiple modalities during the information propagation process, within the framework of heterogeneous graph transformer. Specifically, a nested inter-modal attention mechanism is integrated into the inter-node attention to achieve adaptive multi-modal fusion, and modality alignment is also taken into account to encourage the propagation among nodes with consistent similarities across all modalities. Moreover, an attention loss is augmented to mitigate the impact of missing modalities. Extensive experiments validate the superiority of the model in the node classification task, providing an innovative view to handle multi-modal data, especially when accompanied with network structures.
Deepfake technology poses increasing risks such as privacy invasion and identity theft. To address these threats, we propose WaveGuard, a proactive watermarking framework that enhances robustness and imperceptibility via frequency-domain embedding and graph-based structural consistency. Specifically, we embed watermarks into high-frequency sub-bands using Dual-Tree Complex Wavelet Transform (DT-CWT) and employ a Structural Consistency Graph Neural Network (SC-GNN) to preserve visual quality. We also design an attention module to refine embedding precision. Experimental results on face swap and reenactment tasks demonstrate that WaveGuard outperforms state-of-the-art methods in both robustness and visual quality. Code is available at https://github.com/vpsg-research/WaveGuard.
Diffusion-based generative models have significantly advanced text-to-image synthesis, demonstrating impressive text comprehension and zero-shot generalization. These models refine images from random noise based on textual prompts, with initial reliance on text input shifting towards enhanced visual fidelity over time. This transition suggests that static model parameters might not optimally address the distinct phases of generation. We introduce LGR-AD (Learning Graph Representation of Agent Diffusers), a novel multi-agent system designed to improve adaptability in dynamic computer vision tasks. LGR-AD models the generation process as a distributed system of interacting agents, each representing an expert sub-model. These agents dynamically adapt to varying conditions and collaborate through a graph neural network that encodes their relationships and performance metrics. Our approach employs a coordination mechanism based on top-$k$ maximum spanning trees, optimizing the generation process. Each agent's decision-making is guided by a meta-model that minimizes a novel loss function, balancing accuracy and diversity. Theoretical analysis and extensive empirical evaluations show that LGR-AD outperforms traditional diffusion models across various benchmarks, highlighting its potential for scalable and flexible solutions in complex image generation tasks. Code is available at: https://github.com/YousIA/LGR_AD
Following up on our earlier study in [J. Bardhan et al., Machine learning-enhanced search for a vectorlike singlet B quark decaying to a singlet scalar or pseudoscalar, Phys. Rev. D 107 (2023) 115001; arXiv:2212.02442], we investigate the LHC prospects of pair-produced vectorlike $B$ quarks decaying exotically to a new gauge-singlet (pseudo)scalar field $\Phi$ and a $b$ quark. After the electroweak symmetry breaking, the $\Phi$ decays predominantly to $gg/bb$ final states, leading to a fully hadronic $2b+4j$ or $6b$ signature. Because of the large Standard Model background and the lack of leptonic handles, it is a difficult channel to probe. To overcome the challenge, we employ a hybrid deep learning model containing a graph neural network followed by a deep neural network. We estimate that such a state-of-the-art deep learning analysis pipeline can lead to a performance comparable to that in the semi-leptonic mode, taking the discovery (exclusion) reach up to about $M_B=1.8\:(2.4)$~TeV at HL-LHC when $B$ decays fully exotically, i.e., BR$(B \to b\Phi) = 100\%$.
Large Language Models (LLMs) have achieved remarkable success across various domains. However, they still face significant challenges, including high computational costs for training and limitations in solving complex reasoning problems. Although existing methods have extended the reasoning capabilities of LLMs through structured paradigms, these approaches often rely on task-specific prompts and predefined reasoning processes, which constrain their flexibility and generalizability. To address these limitations, we propose a novel framework that leverages graph learning to enable more flexible and adaptive reasoning capabilities for LLMs. Specifically, this approach models the reasoning process of a problem as a graph and employs LLM-based graph learning to guide the adaptive generation of each reasoning step. To further enhance the adaptability of the model, we introduce a Graph Neural Network (GNN) module to perform representation learning on the generated reasoning process, enabling real-time adjustments to both the model and the prompt. Experimental results demonstrate that this method significantly improves reasoning performance across multiple tasks without requiring additional training or task-specific prompt design. Code can be found in https://github.com/zch65458525/L2T.
Terahertz (THz) unmanned aerial vehicle (UAV) networks with flexible topologies and ultra-high data rates are expected to empower numerous applications in security surveillance, disaster response, and environmental monitoring, among others. However, the dynamic topologies hinder the efficient long-term joint power and antenna array resource allocation for THz links among UAVs. Furthermore, the continuous nature of power and the discrete nature of antennas cause this joint resource allocation problem to be a mixed-integer nonlinear programming (MINLP) problem with non-convexity and NP-hardness. Inspired by recent rapid advancements in deep reinforcement learning (DRL), a graph neural network (GNN) aided DRL algorithm for resource allocation in the dynamic THz UAV network with an emphasis on self-node features (GLOVE) is proposed in this paper, with the aim of resource efficiency (RE) maximization. When training the allocation policy for each UAV, GLOVE learns the relationship between this UAV and its neighboring UAVs via GNN, while also emphasizing the important self-node features of this UAV. In addition, a multi-task structure is leveraged by GLOVE to cooperatively train resource allocation decisions for the power and sub-arrays of all UAVs. Experimental results illustrate that GLOVE outperforms benchmark schemes in terms of the highest RE and the lowest latency. Moreover, unlike the benchmark methods with severe packet loss, GLOVE maintains zero packet loss during the entire training process, demonstrating its better robustness under the highly dynamic THz UAV network.