Although deep learning models have demonstrated remarkable potential in weather prediction, most of them overlook either the \textbf{physics} of the underlying weather evolution or the \textbf{topology} of the Earth's surface. In light of these disadvantages, we develop PASSAT, a novel Physics-ASSisted And Topology-informed deep learning model for weather prediction. PASSAT attributes the weather evolution to two key factors: (i) the advection process that can be characterized by the advection equation and the Navier-Stokes equation; (ii) the Earth-atmosphere interaction that is difficult to both model and calculate. PASSAT also takes the topology of the Earth's surface into consideration, other than simply treating it as a plane. With these considerations, PASSAT numerically solves the advection equation and the Navier-Stokes equation on the spherical manifold, utilizes a spherical graph neural network to capture the Earth-atmosphere interaction, and generates the initial velocity fields that are critical to solving the advection equation from the same spherical graph neural network. In the $5.625^\circ$-resolution ERA5 data set, PASSAT outperforms both the state-of-the-art deep learning-based weather prediction models and the operational numerical weather prediction model IFS T42. Code and checkpoint are available at https://github.com/Yumenomae/PASSAT_5p625.
Graph Neural Networks (GNNs) have achieved significant success across various domains by leveraging graph structures in data. Existing spectral GNNs, which use low-degree polynomial filters to capture graph spectral properties, may not fully identify the graph's spectral characteristics because of the polynomial's small degree. However, increasing the polynomial degree is computationally expensive and beyond certain thresholds leads to performance plateaus or degradation. In this paper, we introduce the Piecewise Constant Spectral Graph Neural Network(PieCoN) to address these challenges. PieCoN combines constant spectral filters with polynomial filters to provide a more flexible way to leverage the graph structure. By adaptively partitioning the spectrum into intervals, our approach increases the range of spectral properties that can be effectively learned. Experiments on nine benchmark datasets, including both homophilic and heterophilic graphs, demonstrate that PieCoN is particularly effective on heterophilic datasets, highlighting its potential for a wide range of applications.
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.
Node Anomaly Detection (NAD) has gained significant attention in the deep learning community due to its diverse applications in real-world scenarios. Existing NAD methods primarily embed graphs within a single Euclidean space, while overlooking the potential of non-Euclidean spaces. Besides, to address the prevalent issue of limited supervision in real NAD tasks, previous methods tend to leverage synthetic data to collect auxiliary information, which is not an effective solution as shown in our experiments. To overcome these challenges, we introduce a novel SpaceGNN model designed for NAD tasks with extremely limited labels. Specifically, we provide deeper insights into a task-relevant framework by empirically analyzing the benefits of different spaces for node representations, based on which, we design a Learnable Space Projection function that effectively encodes nodes into suitable spaces. Besides, we introduce the concept of weighted homogeneity, which we empirically and theoretically validate as an effective coefficient during information propagation. This concept inspires the design of the Distance Aware Propagation module. Furthermore, we propose the Multiple Space Ensemble module, which extracts comprehensive information for NAD under conditions of extremely limited supervision. Our findings indicate that this module is more beneficial than data augmentation techniques for NAD. Extensive experiments conducted on 9 real datasets confirm the superiority of SpaceGNN, which outperforms the best rival by an average of 8.55% in AUC and 4.31% in F1 scores. Our code is available at https://github.com/xydong127/SpaceGNN.
Within-frequency coupling (WFC) and cross-frequency coupling (CFC) in brain networks reflect neural synchronization within the same frequency band and cross-band oscillatory interactions, respectively. Their synergy provides a comprehensive understanding of neural mechanisms underlying cognitive states such as emotion. However, existing multi-channel EEG studies often analyze WFC or CFC separately, failing to fully leverage their complementary properties. This study proposes a dual-branch graph neural network (DB-GNN) to jointly identify within- and cross-frequency coupled brain networks. Firstly, DBGNN leverages its unique dual-branch learning architecture to efficiently mine global collaborative information and local cross-frequency and within-frequency coupling information. Secondly, to more fully perceive the global information of cross-frequency and within-frequency coupling, the global perception branch of DB-GNN adopts a Transformer architecture. To prevent overfitting of the Transformer architecture, this study integrates prior within- and cross-frequency coupling information into the Transformer inference process, thereby enhancing the generalization capability of DB-GNN. Finally, a multi-scale graph contrastive learning regularization term is introduced to constrain the global and local perception branches of DB-GNN at both graph-level and node-level, enhancing its joint perception ability and further improving its generalization performance. Experimental validation on the emotion recognition dataset shows that DB-GNN achieves a testing accuracy of 97.88% and an F1- score of 97.87%, reaching the state-of-the-art performance.
Drug-target interaction (DTI) prediction is a core task in drug development and precision medicine in the biomedical field. However, traditional machine learning methods generally have the black box problem, which makes it difficult to reveal the deep correlation between the model decision mechanism and the interaction pattern between biological molecules. This study proposes a heterogeneous network drug target interaction prediction framework, integrating graph neural network and multi scale signal processing technology to construct a model with both efficient prediction and multi level interpretability. Its technical breakthroughs are mainly reflected in the following three dimensions:Local global feature collaborative perception module. Based on heterogeneous graph convolutional neural network (HGCN), a multi order neighbor aggregation strategy is designed.Multi scale graph signal decomposition and biological interpretation module. A deep hierarchical node feature transform (GWT) architecture is proposed.Contrastive learning combining multi dimensional perspectives and hierarchical representations. By comparing the learning models, the node representations from the two perspectives of HGCN and GWT are aligned and fused, so that the model can integrate multi dimensional information and improve the prediction robustness. Experimental results show that our framework shows excellent prediction performance on all datasets. This study provides a complete solution for drug target discovery from black box prediction to mechanism decoding, and its methodology has important reference value for modeling complex biomolecular interaction systems.
Protein-protein interactions (PPIs) are fundamental for deciphering cellular functions,disease pathways,and drug discovery.Although existing neural networks and machine learning methods have achieved high accuracy in PPI prediction,their black-box nature leads to a lack of causal interpretation of the prediction results and difficulty in capturing hierarchical geometries and multi-scale dynamic interaction patterns among proteins.To address these challenges, we propose HyboWaveNet,a novel deep learning framework that collaborates with hyperbolic graphical neural networks (HGNNs) and multiscale graphical wavelet transform for robust PPI prediction. Mapping protein features to Lorentz space simulates hierarchical topological relationships among biomolecules via a hyperbolic distance metric,enabling node feature representations that better fit biological a priori.HyboWaveNet inherently simulates hierarchical and scale-free biological relationships, while the integration of wavelet transforms enables adaptive extraction of local and global interaction features across different resolutions. Our framework generates node feature representations via a graph neural network under the Lorenz model and generates pairs of positive samples under multiple different views for comparative learning, followed by further feature extraction via multi-scale graph wavelet transforms to predict potential PPIs. Experiments on public datasets show that HyboWaveNet improves over both existing state-of-the-art methods. We also demonstrate through ablation experimental studies that the multi-scale graph wavelet transform module improves the predictive performance and generalization ability of HyboWaveNet. This work links geometric deep learning and signal processing to advance PPI prediction, providing a principled approach for analyzing complex biological systems
Reconfigurable intelligent surface (RIS) is emerging as a promising technology for next-generation wireless communication networks, offering a variety of merits such as the ability to tailor the communication environment. Moreover, deploying multiple RISs helps mitigate severe signal blocking between the base station (BS) and users, providing a practical and efficient solution to enhance the service coverage. However, fully reaping the potential of a multi-RIS aided communication system requires solving a non-convex optimization problem. This challenge motivates the adoption of learning-based methods for determining the optimal policy. In this paper, we introduce a novel heterogeneous graph neural network (GNN) to effectively leverage the graph topology of a wireless communication environment. Specifically, we design an association scheme that selects a suitable RIS for each user. Then, we maximize the weighted sum rate (WSR) of all the users by iteratively optimizing the RIS association scheme, and beamforming designs until the considered heterogeneous GNN converges. Based on the proposed approach, each user is associated with the best RIS, which is shown to significantly improve the system capacity in multi-RIS multi-user millimeter wave (mmWave) communications. Specifically, simulation results demonstrate that the proposed heterogeneous GNN closely approaches the performance of the high-complexity alternating optimization (AO) algorithm in the considered multi-RIS aided communication system, and it outperforms other benchmark schemes. Moreover, the performance improvement achieved through the RIS association scheme is shown to be of the order of 30%.
This paper proposes a supervised training algorithm for learning stochastic resource allocation policies with generative diffusion models (GDMs). We formulate the allocation problem as the maximization of an ergodic utility function subject to ergodic Quality of Service (QoS) constraints. Given samples from a stochastic expert policy that yields a near-optimal solution to the problem, we train a GDM policy to imitate the expert and generate new samples from the optimal distribution. We achieve near-optimal performance through sequential execution of the generated samples. To enable generalization to a family of network configurations, we parameterize the backward diffusion process with a graph neural network (GNN) architecture. We present numerical results in a case study of power control in multi-user interference networks.
The growing luminosity frontier at the Large Hadron Collider is challenging the reconstruction and analysis of particle collision events. Increased particle multiplicities are straining latency and storage requirements at the data acquisition stage, while new complications are emerging, including higher background levels and more frequent particle vertex misassociations. This in turn necessitates the development of more holistic and scalable reconstruction methods that take advantage of recent advances in machine learning. We propose a novel Heterogeneous Graph Neural Network (HGNN) architecture featuring unique representations for diverse particle collision relationships and integrated graph pruning layers for scalability. Trained with a multi-task paradigm in an environment mimicking the LHCb experiment, this HGNN significantly improves beauty hadron reconstruction performance. Notably, it concurrently performs particle vertex association and graph pruning within a single framework. We quantify reconstruction and pruning performance, demonstrate enhanced inference time scaling with event complexity, and mitigate potential performance loss using a weighted message passing scheme.
Nonlinear optical (NLO) materials for generating lasers via second harmonic generation (SHG) are highly sought in today's technology. However, discovering novel materials with considerable SHG is challenging due to the time-consuming and costly nature of both experimental methods and first-principles calculations. In this study, we present a deep learning approach using the Atomistic Line Graph Neural Network (ALIGNN) to predict NLO properties. Sourcing data from the Novel Opto-Electronic Materials Discovery (NOEMD) database and using the Kurtz-Perry (KP) coefficient as the key target, we developed a robust model capable of accurately estimating nonlinear optical responses. Our results demonstrate that the model achieves 82.5% accuracy at a tolerated absolute error up to 1 pm/V and relative error not exceeding 0.5. This work highlights the potential of deep learning in accelerating the discovery and design of advanced optical materials with desired properties.
In this paper, we present LBM-GNN, a novel approach that enhances the traditional Lattice Boltzmann Method (LBM) with Graph Neural Networks (GNNs). We apply this method to fluid dynamics simulations, demonstrating improved stability and accuracy compared to standard LBM implementations. The method is validated using benchmark problems such as the Taylor-Green vortex, focusing on accuracy, conservation properties, and performance across different Reynolds numbers and grid resolutions. Our results indicate that GNN-enhanced LBM can maintain better conservation properties while improving numerical stability at higher Reynolds numbers.
Recent research on graph neural networks (GNNs) has explored mechanisms for capturing local uncertainty and exploiting graph hierarchies to mitigate data sparsity and leverage structural properties. However, the synergistic integration of these two approaches remains underexplored. This work introduces a novel architecture, the Hierarchical Uncertainty-Aware Graph Neural Network (HU-GNN), which unifies multi-scale representation learning, principled uncertainty estimation, and self-supervised embedding diversity within a single end-to-end framework. Specifically, HU-GNN adaptively forms node clusters and estimates uncertainty at multiple structural scales from individual nodes to higher levels. These uncertainty estimates guide a robust message-passing mechanism and attention weighting, effectively mitigating noise and adversarial perturbations while preserving predictive accuracy on semi-supervised classification tasks. We also offer key theoretical contributions, including a probabilistic formulation, rigorous uncertainty-calibration guarantees, and formal robustness bounds. Extensive experiments on standard benchmarks demonstrate that our model achieves state-of-the-art robustness and interpretability.
Learning on large graphs presents significant challenges, with traditional Message Passing Neural Networks suffering from computational and memory costs scaling linearly with the number of edges. We introduce the Intersecting Block Graph (IBG), a low-rank factorization of large directed graphs based on combinations of intersecting bipartite components, each consisting of a pair of communities, for source and target nodes. By giving less weight to non-edges, we show how to efficiently approximate any graph, sparse or dense, by a dense IBG. Specifically, we prove a constructive version of the weak regularity lemma, showing that for any chosen accuracy, every graph, regardless of its size or sparsity, can be approximated by a dense IBG whose rank depends only on the accuracy. This dependence of the rank solely on the accuracy, and not on the sparsity level, is in contrast to previous forms of the weak regularity lemma. We present a graph neural network architecture operating on the IBG representation of the graph and demonstrating competitive performance on node classification, spatio-temporal graph analysis, and knowledge graph completion, while having memory and computational complexity linear in the number of nodes rather than edges.
Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language Models (LLMs) can generate code from natural language queries, runtime code generation is severely limited due to unverified code, security risks, longer response times, and higher computational costs. To bridge the gap, we propose an offline simulation framework to curate a software-specific skillset, a collection of verified scripts, by exploiting LLMs and publicly available scripting guides. Our framework comprises two components: (1) task creation, using top-down functionality guidance and bottom-up API synergy exploration to generate helpful tasks; and (2) skill generation with trials, refining and validating scripts based on execution feedback. To efficiently navigate the extensive API landscape, we introduce a Graph Neural Network (GNN)-based link prediction model to capture API synergy, enabling the generation of skills involving underutilized APIs and expanding the skillset's diversity. Experiments with Adobe Illustrator demonstrate that our framework significantly improves automation success rates, reduces response time, and saves runtime token costs compared to traditional runtime code generation. This is the first attempt to use software scripting interfaces as a testbed for LLM-based systems, highlighting the advantages of leveraging execution feedback in a controlled environment and offering valuable insights into aligning AI capabilities with user needs in specialized software domains.
The high degrees of freedom and complex structure of garments present significant challenges for clothing manipulation. In this paper, we propose a general topological dynamics model to fold complex clothing. By utilizing the visible folding structure as the topological skeleton, we design a novel topological graph to represent the clothing state. This topological graph is low-dimensional and applied for complex clothing in various folding states. It indicates the constraints of clothing and enables predictions regarding clothing movement. To extract graphs from self-occlusion, we apply semantic segmentation to analyze the occlusion relationships and decompose the clothing structure. The decomposed structure is then combined with keypoint detection to generate the topological graph. To analyze the behavior of the topological graph, we employ an improved Graph Neural Network (GNN) to learn the general dynamics. The GNN model can predict the deformation of clothing and is employed to calculate the deformation Jacobi matrix for control. Experiments using jackets validate the algorithm's effectiveness to recognize and fold complex clothing with self-occlusion.
Effective and efficient graph representation learning is essential for enabling critical downstream tasks, such as node classification, link prediction, and subgraph search. However, existing graph neural network (GNN) architectures often struggle to adapt to diverse and complex graph structures, limiting their ability to produce structure-aware and task-discriminative representations. To address this challenge, we propose ABG-NAS, a novel framework for automated graph neural network architecture search tailored for efficient graph representation learning. ABG-NAS encompasses three key components: a Comprehensive Architecture Search Space (CASS), an Adaptive Genetic Optimization Strategy (AGOS), and a Bayesian-Guided Tuning Module (BGTM). CASS systematically explores diverse propagation (P) and transformation (T) operations, enabling the discovery of GNN architectures capable of capturing intricate graph characteristics. AGOS dynamically balances exploration and exploitation, ensuring search efficiency and preserving solution diversity. BGTM further optimizes hyperparameters periodically, enhancing the scalability and robustness of the resulting architectures. Empirical evaluations on benchmark datasets (Cora, PubMed, Citeseer, and CoraFull) demonstrate that ABG-NAS consistently outperforms both manually designed GNNs and state-of-the-art neural architecture search (NAS) methods. These results highlight the potential of ABG-NAS to advance graph representation learning by providing scalable and adaptive solutions for diverse graph structures. Our code is publicly available at https://github.com/sserranw/ABG-NAS.
Low Earth Orbit (LEO) satellite communication is a critical component in the development of sixth generation (6G) networks. The integration of massive multiple-input multiple-output (MIMO) technology is being actively explored to enhance the performance of LEO satellite communications. However, the limited power of LEO satellites poses a significant challenge in improving communication energy efficiency (EE) under constrained power conditions. Artificial intelligence (AI) methods are increasingly recognized as promising solutions for optimizing energy consumption while enhancing system performance, thus enabling more efficient and sustainable communications. This paper proposes approaches to address the challenges associated with precoding in massive MIMO LEO satellite communications. First, we introduce an end-to-end graph neural network (GNN) framework that effectively reduces the computational complexity of traditional precoding methods. Next, we introduce a deep unfolding of the Dinkelbach algorithm and the weighted minimum mean square error (WMMSE) approach to achieve enhanced EE, transforming iterative optimization processes into a structured neural network, thereby improving convergence speed and computational efficiency. Furthermore, we incorporate the Taylor expansion method to approximate matrix inversion within the GNN, enhancing both the interpretability and performance of the proposed method. Numerical experiments demonstrate the validity of our proposed method in terms of complexity and robustness, achieving significant improvements over state-of-the-art methods.
Next-generation wireless cellular networks are expected to provide unparalleled Quality-of-Service (QoS) for emerging wireless applications, necessitating strict performance guarantees, e.g., in terms of link-level data rates. A critical challenge in meeting these QoS requirements is the prevention of cell congestion, which involves balancing the load to ensure sufficient radio resources are available for each cell to serve its designated User Equipments (UEs). In this work, a novel QoS-aware Load Balancing (LB) approach is developed to optimize the performance of Guaranteed Bit Rate (GBR) and Best Effort (BE) traffic in a multi-band Open Radio Access Network (O-RAN) under QoS and resource constraints. The proposed solution builds on Graph Reinforcement Learning (GRL), a powerful framework at the intersection of Graph Neural Network (GNN) and RL. The QoS-aware LB is modeled as a Markov Decision Process, with states represented as graphs. QoS consideration are integrated into both state representations and reward signal design. The LB agent is then trained using an off-policy dueling Deep Q Network (DQN) that leverages a GNN-based architecture. This design ensures the LB policy is invariant to the ordering of nodes (UE or cell), flexible in handling various network sizes, and capable of accounting for spatial node dependencies in LB decisions. Performance of the GRL-based solution is compared with two baseline methods. Results show substantial performance gains, including a $53\%$ reduction in QoS violations and a fourfold increase in the 5th percentile rate for BE traffic.
We propose a multimodal spatiotemporal graph neural network (STG) framework to predict colorectal cancer liver metastasis (CRLM) progression. Current clinical models do not effectively integrate the tumor's spatial heterogeneity, dynamic evolution, and complex multimodal data relationships, limiting their predictive accuracy. Our STG framework combines preoperative CT imaging and clinical data into a heterogeneous graph structure, enabling joint modeling of tumor distribution and temporal evolution through spatial topology and cross-modal edges. The framework uses GraphSAGE to aggregate spatiotemporal neighborhood information and leverages supervised and contrastive learning strategies to enhance the model's ability to capture temporal features and improve robustness. A lightweight version of the model reduces parameter count by 78.55%, maintaining near-state-of-the-art performance. The model jointly optimizes recurrence risk regression and survival analysis tasks, with contrastive loss improving feature representational discriminability and cross-modal consistency. Experimental results on the MSKCC CRLM dataset show a time-adjacent accuracy of 85% and a mean absolute error of 1.1005, significantly outperforming existing methods. The innovative heterogeneous graph construction and spatiotemporal decoupling mechanism effectively uncover the associations between dynamic tumor microenvironment changes and prognosis, providing reliable quantitative support for personalized treatment decisions.