Cooperative localization leverages noisy inter-node distance measurements and exchanged wireless messages to estimate node positions in a wireless network. In communication-constrained environments, however, transmitting large messages becomes problematic. In this paper, we propose an approach for communication-efficient cooperative localization that addresses two main challenges. First, cooperative localization often needs to be performed over wireless networks with loopy graph topologies. Second is the need for designing an algorithm that has low localization error while simultaneously requiring a much lower communication overhead. Existing methods fall short of addressing these two challenges concurrently. To achieve this, we propose a vector quantized message passing neural network (VQ-MPNN) for cooperative localization. Through end-to-end neural network training, VQ-MPNN enables the co-design of node localization and message compression. Specifically, VQ-MPNN treats prior node positions and distance measurements as node and edge features, respectively, which are encoded as node and edge states using a graph neural network. To find an efficient representation for the node state, we construct a vector quantized codebook for all node states such that instead of sending long messages, each node only needs to transmit a codeword index. Numerical evaluations demonstrates that our proposed VQ-MPNN approach can deliver localization errors that are similar to existing approaches while reducing the overall communication overhead by an order of magnitude.
This study proposes a credit card fraud detection method based on Heterogeneous Graph Neural Network (HGNN) to address fraud in complex transaction networks. Unlike traditional machine learning methods that rely solely on numerical features of transaction records, this approach constructs heterogeneous transaction graphs. These graphs incorporate multiple node types, including users, merchants, and transactions. By leveraging graph neural networks, the model captures higher-order transaction relationships. A Graph Attention Mechanism is employed to dynamically assign weights to different transaction relationships. Additionally, a Temporal Decay Mechanism is integrated to enhance the model's sensitivity to time-related fraud patterns. To address the scarcity of fraudulent transaction samples, this study applies SMOTE oversampling and Cost-sensitive Learning. These techniques strengthen the model's ability to identify fraudulent transactions. Experimental results demonstrate that the proposed method outperforms existing GNN models, including GCN, GAT, and GraphSAGE, on the IEEE-CIS Fraud Detection dataset. The model achieves notable improvements in both accuracy and OC-ROC. Future research may explore the integration of dynamic graph neural networks and reinforcement learning. Such advancements could enhance the real-time adaptability of fraud detection systems and provide more intelligent solutions for financial risk control.
We present a method based on graph neural network (GNN) for prediction of probabilities of usage of shopping-mall corridors. The heterogeneous graph network of shops and corridor paths are obtained from floorplans of the malls by creating vector layers for corridors, shops and entrances. These are subsequently assimilated into nodes and edges of graphs. The prediction of the usage probability is based on the shop features, namely, the area and usage categories they fall into, and on the graph connecting these shops, corridor junctions and entrances by corridor paths. Though the presented method is applicable for training on datasets obtained from a field survey or from pedestrian-detecting sensors, the target data of the supervised deep-learning work flow in this work are obtained from a probability method. We also include a context-specific representation learning of latent features. The usage-probability prediction is made on each edge, which is a connection by a section of corridor path between the adjacent nodes representing the shops or corridor points. To create a feature for each edge, the hidden-layer feature vectors acquired in the message-passing GNN layers at the nodes of each edge are averaged and concatenated with the vector obtained by their multiplication. These edge-features are then passed to multilayer perceptrons (MLP) to make the final prediction of usage probability on each edge. The samples of synthetic learning dataset for each shopping mall are obtained by changing the shops' usage and area categories, and by subsequently feeding the graph into the probability model. When including different shopping malls in a single dataset, we also propose to consider graph-level features to inform the model with specific identifying features of each mall.
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation, specialized assays are typically used. However, these assays are often costly and have lengthy processing times, which limits their widespread availability in routine clinical practice. In contrast, whole slide images (WSIs) for the majority of cancer patients can be more readily available. As such, given the ready availability of WSIs, there is a compelling need to explore the potential relationship between WSIs and DNA methylation patterns. To address this, we propose an end-to-end graph neural network based weakly supervised learning framework to predict the methylation state of gene groups exhibiting coherent patterns across samples. Using data from three cohorts from The Cancer Genome Atlas (TCGA) - TCGA-LGG (Brain Lower Grade Glioma), TCGA-GBM (Glioblastoma Multiforme) ($n$=729) and TCGA-KIRC (Kidney Renal Clear Cell Carcinoma) ($n$=511) - we demonstrate that the proposed approach achieves significantly higher AUROC scores than the state-of-the-art (SOTA) methods, by more than $20\%$. We conduct gene set enrichment analyses on the gene groups and show that majority of the gene groups are significantly enriched in important hallmarks and pathways. We also generate spatially enriched heatmaps to further investigate links between histological patterns and DNA methylation states. To the best of our knowledge, this is the first study that explores association of spatially resolved histological patterns with gene group methylation states across multiple cancer types using weakly supervised deep learning.
Fingerprint-based indoor localization is often labor-intensive due to the need for dense grids and repeated measurements across time and space. Maintaining high localization accuracy with extremely sparse fingerprints remains a persistent challenge. Existing benchmark methods primarily rely on the measured fingerprints, while neglecting valuable spatial and environmental characteristics. In this paper, we propose a systematic integration of an Attentional Graph Neural Network (AGNN) model, capable of learning spatial adjacency relationships and aggregating information from neighboring fingerprints, and a meta-learning framework that utilizes datasets with similar environmental characteristics to enhance model training. To minimize the labor required for fingerprint collection, we introduce two novel data augmentation strategies: 1) unlabeled fingerprint augmentation using moving platforms, which enables the semi-supervised AGNN model to incorporate information from unlabeled fingerprints, and 2) synthetic labeled fingerprint augmentation through environmental digital twins, which enhances the meta-learning framework through a practical distribution alignment, which can minimize the feature discrepancy between synthetic and real-world fingerprints effectively. By integrating these novel modules, we propose the Attentional Graph Meta-Learning (AGML) model. This novel model combines the strengths of the AGNN model and the meta-learning framework to address the challenges posed by extremely sparse fingerprints. To validate our approach, we collected multiple datasets from both consumer-grade WiFi devices and professional equipment across diverse environments. Extensive experiments conducted on both synthetic and real-world datasets demonstrate that the AGML model-based localization method consistently outperforms all baseline methods using sparse fingerprints across all evaluated metrics.
This paper proposes a new algorithm -- Trading Graph Neural Network (TGNN) that can structurally estimate the impact of asset features, dealer features and relationship features on asset prices in trading networks. It combines the strength of the traditional simulated method of moments (SMM) and recent machine learning techniques -- Graph Neural Network (GNN). It outperforms existing reduced-form methods with network centrality measures in prediction accuracy. The method can be used on networks with any structure, allowing for heterogeneity among both traders and assets.
Accurate epidemic forecasting is crucial for effective disease control and prevention. Traditional compartmental models often struggle to estimate temporally and spatially varying epidemiological parameters, while deep learning models typically overlook disease transmission dynamics and lack interpretability in the epidemiological context. To address these limitations, we propose a novel Causal Spatiotemporal Graph Neural Network (CSTGNN), a hybrid framework that integrates a Spatio-Contact SIR model with Graph Neural Networks (GNNs) to capture the spatiotemporal propagation of epidemics. Inter-regional human mobility exhibits continuous and smooth spatiotemporal patterns, leading to adjacent graph structures that share underlying mobility dynamics. To model these dynamics, we employ an adaptive static connectivity graph to represent the stable components of human mobility and utilize a temporal dynamics model to capture fluctuations within these patterns. By integrating the adaptive static connectivity graph with the temporal dynamics graph, we construct a dynamic graph that encapsulates the comprehensive properties of human mobility networks. Additionally, to capture temporal trends and variations in infectious disease spread, we introduce a temporal decomposition model to handle temporal dependence. This model is then integrated with a dynamic graph convolutional network for epidemic forecasting. We validate our model using real-world datasets at the provincial level in China and the state level in Germany. Extensive studies demonstrate that our method effectively models the spatiotemporal dynamics of infectious diseases, providing a valuable tool for forecasting and intervention strategies. Furthermore, analysis of the learned parameters offers insights into disease transmission mechanisms, enhancing the interpretability and practical applicability of our model.
In this paper, we consider the distributed optimal control problem for linear networked systems. In particular, we are interested in learning distributed optimal controllers using graph recurrent neural networks (GRNNs). Most of the existing approaches result in centralized optimal controllers with offline training processes. However, as the increasing demand of network resilience, the optimal controllers are further expected to be distributed, and are desirable to be trained in an online distributed fashion, which are also the main contributions of our work. To solve this problem, we first propose a GRNN-based distributed optimal control method, and we cast the problem as a self-supervised learning problem. Then, the distributed online training is achieved via distributed gradient computation, and inspired by the (consensus-based) distributed optimization idea, a distributed online training optimizer is designed. Furthermore, the local closed-loop stability of the linear networked system under our proposed GRNN-based controller is provided by assuming that the nonlinear activation function of the GRNN-based controller is both local sector-bounded and slope-restricted. The effectiveness of our proposed method is illustrated by numerical simulations using a specifically developed simulator.
Dyadic social relationships, which refer to relationships between two individuals who know each other through repeated interactions (or not), are shaped by shared spatial and temporal experiences. Current computational methods for modeling these relationships face three major challenges: (1) the failure to model asymmetric relationships, e.g., one individual may perceive the other as a friend while the other perceives them as an acquaintance, (2) the disruption of continuous interactions by discrete frame sampling, which segments the temporal continuity of interaction in real-world scenarios, and (3) the limitation to consider periodic behavioral cues, such as rhythmic vocalizations or recurrent gestures, which are crucial for inferring the evolution of dyadic relationships. To address these challenges, we propose AsyReC, a multimodal graph-based framework for asymmetric dyadic relationship classification, with three core innovations: (i) a triplet graph neural network with node-edge dual attention that dynamically weights multimodal cues to capture interaction asymmetries (addressing challenge 1); (ii) a clip-level relationship learning architecture that preserves temporal continuity, enabling fine-grained modeling of real-world interaction dynamics (addressing challenge 2); and (iii) a periodic temporal encoder that projects time indices onto sine/cosine waveforms to model recurrent behavioral patterns (addressing challenge 3). Extensive experiments on two public datasets demonstrate state-of-the-art performance, while ablation studies validate the critical role of asymmetric interaction modeling and periodic temporal encoding in improving the robustness of dyadic relationship classification in real-world scenarios. Our code is publicly available at: https://github.com/tw-repository/AsyReC.
Understanding how urban socio-demographic and environmental factors relate with health is essential for public health and urban planning. However, traditional statistical methods struggle with nonlinear effects, while machine learning models often fail to capture geographical (nearby areas being more similar) and topological (unequal connectivity between places) effects in an interpretable way. To address this, we propose MedGNN, a spatio-topologically explicit framework that constructs a 2-hop spatial graph, integrating positional and locational node embeddings with urban characteristics in a graph neural network. Applied to MEDSAT, a comprehensive dataset covering over 150 environmental and socio-demographic factors and six prescription outcomes (depression, anxiety, diabetes, hypertension, asthma, and opioids) across 4,835 Greater London neighborhoods, MedGNN improved predictions by over 25% on average compared to baseline methods. Using depression prescriptions as a case study, we analyzed graph embeddings via geographical principal component analysis, identifying findings that: align with prior research (e.g., higher antidepressant prescriptions among older and White populations), contribute to ongoing debates (e.g., greenery linked to higher and NO2 to lower prescriptions), and warrant further study (e.g., canopy evaporation correlated with fewer prescriptions). These results demonstrate MedGNN's potential, and more broadly, of carefully applied machine learning, to advance transdisciplinary public health research.
Aerodynamic optimization is crucial for developing eco-friendly, aerodynamic, and stylish cars, which requires close collaboration between aerodynamicists and stylists, a collaboration impaired by the time-consuming nature of aerodynamic simulations. Surrogate models offer a viable solution to reduce this overhead, but they are untested in real-world aerodynamic datasets. We present a comparative evaluation of two surrogate modeling approaches for predicting drag on a real-world dataset: a Convolutional Neural Network (CNN) model that uses a signed distance field as input and a commercial tool based on Graph Neural Networks (GNN) that directly processes a surface mesh. In contrast to previous studies based on datasets created from parameterized geometries, our dataset comprises 343 geometries derived from 32 baseline vehicle geometries across five distinct car projects, reflecting the diverse, free-form modifications encountered in the typical vehicle development process. Our results show that the CNN-based method achieves a mean absolute error of 2.3 drag counts, while the GNN-based method achieves 3.8. Both methods achieve approximately 77% accuracy in predicting the direction of drag change relative to the baseline geometry. While both methods effectively capture the broader trends between baseline groups (set of samples derived from a single baseline geometry), they struggle to varying extents in capturing the finer intra-baseline group variations. In summary, our findings suggest that aerodynamicists can effectively use both methods to predict drag in under two minutes, which is at least 600 times faster than performing a simulation. However, there remains room for improvement in capturing the finer details of the geometry.
Explainability is necessary for many tasks in biomedical research. Recent explainability methods have focused on attention, gradient, and Shapley value. These do not handle data with strong associated prior knowledge and fail to constrain explainability results based on known relationships between predictive features. We propose GraphPINE, a graph neural network (GNN) architecture leveraging domain-specific prior knowledge to initialize node importance optimized during training for drug response prediction. Typically, a manual post-prediction step examines literature (i.e., prior knowledge) to understand returned predictive features. While node importance can be obtained for gradient and attention after prediction, node importance from these methods lacks complementary prior knowledge; GraphPINE seeks to overcome this limitation. GraphPINE differs from other GNN gating methods by utilizing an LSTM-like sequential format. We introduce an importance propagation layer that unifies 1) updates for feature matrix and node importance and 2) uses GNN-based graph propagation of feature values. This initialization and updating mechanism allows for informed feature learning and improved graph representation. We apply GraphPINE to cancer drug response prediction using drug screening and gene data collected for over 5,000 gene nodes included in a gene-gene graph with a drug-target interaction (DTI) graph for initial importance. The gene-gene graph and DTIs were obtained from curated sources and weighted by article count discussing relationships between drugs and genes. GraphPINE achieves a PR-AUC of 0.894 and ROC-AUC of 0.796 across 952 drugs. Code is available at https://anonymous.4open.science/r/GraphPINE-40DE.
TGraphX presents a novel paradigm in deep learning by unifying convolutional neural networks (CNNs) with graph neural networks (GNNs) to enhance visual reasoning tasks. Traditional CNNs excel at extracting rich spatial features from images but lack the inherent capability to model inter-object relationships. Conversely, conventional GNNs typically rely on flattened node features, thereby discarding vital spatial details. TGraphX overcomes these limitations by employing CNNs to generate multi-dimensional node features (e.g., (3*128*128) tensors) that preserve local spatial semantics. These spatially aware nodes participate in a graph where message passing is performed using 1*1 convolutions, which fuse adjacent features while maintaining their structure. Furthermore, a deep CNN aggregator with residual connections is used to robustly refine the fused messages, ensuring stable gradient flow and end-to-end trainability. Our approach not only bridges the gap between spatial feature extraction and relational reasoning but also demonstrates significant improvements in object detection refinement and ensemble reasoning.
Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank, PETIMOT shows superior performance in time and accuracy, capturing protein dynamics, particularly large/slow conformational changes, compared to state-of-the-art flow-matching approaches and traditional physics-based models.
Recommender systems increasingly aim to combine signals from both user reviews and purchase (or other interaction) behaviors. While user-written comments provide explicit insights about preferences, merging these textual representations from large language models (LLMs) with graph-based embeddings of user actions remains a challenging task. In this work, we propose a framework that employs both a Graph Neural Network (GNN)-based model and an LLM to produce review-aware representations, preserving review semantics while mitigating textual noise. Our approach utilizes a hybrid objective that balances user-item interactions against text-derived features, ensuring that user's both behavioral and linguistic signals are effectively captured. We evaluate this method on multiple datasets from diverse application domains, demonstrating consistent improvements over a baseline GNN-based recommender model. Notably, our model achieves significant gains in recommendation accuracy when review data is sparse or unevenly distributed. These findings highlight the importance of integrating LLM-driven textual feedback with GNN-derived user behavioral patterns to develop robust, context-aware recommender systems.
In this contribution, we demonstrate that Graph Neural Networks and Transformers can learn to reason about geometric constraints. We train them to predict spatial position of points in a discrete 2D grid from a set of constraints that uniquely describe hidden figures containing these points. Both models are able to predict the position of points and interestingly, they form the hidden figures described by the input constraints in the embedding space during the reasoning process. Our analysis shows that both models recover the grid structure during training so that the embeddings corresponding to the points within the grid organize themselves in a 2D subspace and reflect the neighborhood structure of the grid. We also show that the Graph Neural Network we design for the task performs significantly better than the Transformer and is also easier to scale.
The integration of Large Language Models (LLMs) with Graph Neural Networks (GNNs) has recently been explored to enhance the capabilities of Text Attribute Graphs (TAGs). Most existing methods feed textual descriptions of the graph structure or neighbouring nodes' text directly into LLMs. However, these approaches often cause LLMs to treat structural information simply as general contextual text, thus limiting their effectiveness in graph-related tasks. In this paper, we introduce LanSAGNN (Language Semantic Anisotropic Graph Neural Network), a framework that extends the concept of anisotropic GNNs to the natural language level. This model leverages LLMs to extract tailor-made semantic information for node pairs, effectively capturing the unique interactions within node relationships. In addition, we propose an efficient dual-layer LLMs finetuning architecture to better align LLMs' outputs with graph tasks. Experimental results demonstrate that LanSAGNN significantly enhances existing LLM-based methods without increasing complexity while also exhibiting strong robustness against interference.
In this contribution, we provide a comprehensive evaluation of graph neural networks applied to Boolean satisfiability problems, accompanied by an intuitive explanation of the mechanisms enabling the model to generalize to different instances. We introduce several training improvements, particularly a novel closest assignment supervision method that dynamically adapts to the model's current state, significantly enhancing performance on problems with larger solution spaces. Our experiments demonstrate the suitability of variable-clause graph representations with recurrent neural network updates, which achieve good accuracy on SAT assignment prediction while reducing computational demands. We extend the base graph neural network into a diffusion model that facilitates incremental sampling and can be effectively combined with classical techniques like unit propagation. Through analysis of embedding space patterns and optimization trajectories, we show how these networks implicitly perform a process very similar to continuous relaxations of MaxSAT, offering an interpretable view of their reasoning process. This understanding guides our design choices and explains the ability of recurrent architectures to scale effectively at inference time beyond their training distribution, which we demonstrate with test-time scaling experiments.
While unmanned aerial vehicles (UAVs) with flexible mobility are envisioned to enhance physical layer security in wireless communications, the efficient security design that adapts to such high network dynamics is rather challenging. The conventional approaches extended from optimization perspectives are usually quite involved, especially when jointly considering factors in different scales such as deployment and transmission in UAV-related scenarios. In this paper, we address the UAV-enabled multi-user secure communications by proposing a deep graph reinforcement learning framework. Specifically, we reinterpret the security beamforming as a graph neural network (GNN) learning task, where mutual interference among users is managed through the message-passing mechanism. Then, the UAV deployment is obtained through soft actor-critic reinforcement learning, where the GNN-based security beamforming is exploited to guide the deployment strategy update. Simulation results demonstrate that the proposed approach achieves near-optimal security performance and significantly enhances the efficiency of strategy determination. Moreover, the deep graph reinforcement learning framework offers a scalable solution, adaptable to various network scenarios and configurations, establishing a robust basis for information security in UAV-enabled communications.
While graph neural networks (GNNs) operating in hyperbolic spaces have shown promise for modeling hierarchical and complex relational data, a critical limitation often overlooked is their potentially limited discriminative power compared to their Euclidean counterparts or fundamental graph isomorphism tests like the Weisfeiler-Lehman (WL) hierarchy. Existing hyperbolic aggregation schemes, while curvature-aware, may not sufficiently capture the intricate structural differences required to robustly distinguish non-isomorphic graphs owing to non-injective aggregation functions. To address this expressiveness gap in hyperbolic graph learning, we introduce the Lorentzian Graph Isomorphic Network (LGIN), a novel GNN designed to achieve enhanced discriminative capabilities within the Lorentzian model of hyperbolic space. LGIN proposes a new update rule that effectively combines local neighborhood information with a richer representation of graph structure designed to preserve the Lorentzian metric tensor. This represents a significant step towards building more expressive GNNs in non-Euclidean geometries, overcoming a common bottleneck in current hyperbolic methods. We conduct extensive evaluations across nine diverse benchmark datasets, including molecular and protein structures. LGIN consistently outperforms or matches state-of-the-art hyperbolic and Euclidean GNNs, showcasing its practical efficacy and validating its superior ability to capture complex graph structures and distinguish between different graphs. To the best of our knowledge, LGIN is the first work to study the framework behind a powerful GNN on the hyperbolic space. The code for our paper can be found at https://github.com/Deceptrax123/LGIN