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
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.
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.
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.
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
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.
Cellular reprogramming, the artificial transformation of one cell type into another, has been attracting increasing research attention due to its therapeutic potential for complex diseases. However, discovering reprogramming strategies through classical wet-lab experiments is hindered by lengthy time commitments and high costs. In this study, we explore the use of deep reinforcement learning (DRL) to control Boolean network models of complex biological systems, such as gene regulatory networks and signalling pathway networks. We formulate a novel control problem for Boolean network models under the asynchronous update mode in the context of cellular reprogramming. To facilitate scalability, we consider our previously introduced concept of a pseudo-attractor and we improve our procedure for effective identification of pseudo-attractor states. Finally, we devise a computational framework to solve the control problem. To leverage the structure of biological systems, we incorporate graph neural networks with graph convolutions into the artificial neural network approximator for the action-value function learned by the DRL agent. Experiments on a number of large real-world biological networks from literature demonstrate the scalability and effectiveness of our approach.
The growing need for Trusted AI (TAI) highlights the importance of interpretability and robustness in machine learning models. However, many existing tools overlook graph data and rarely combine these two aspects into a single solution. Graph Neural Networks (GNNs) have become a popular approach, achieving top results across various tasks. We introduce GNN-AID (Graph Neural Network Analysis, Interpretation, and Defense), an open-source framework designed for graph data to address this gap. Built as a Python library, GNN-AID supports advanced trust methods and architectural layers, allowing users to analyze graph datasets and GNN behavior using attacks, defenses, and interpretability methods. GNN-AID is built on PyTorch-Geometric, offering preloaded datasets, models, and support for any GNNs through customizable interfaces. It also includes a web interface with tools for graph visualization and no-code features like an interactive model builder, simplifying the exploration and analysis of GNNs. The framework also supports MLOps techniques, ensuring reproducibility and result versioning to track and revisit analyses efficiently. GNN-AID is a flexible tool for developers and researchers. It helps developers create, analyze, and customize graph models, while also providing access to prebuilt datasets and models for quick experimentation. Researchers can use the framework to explore advanced topics on the relationship between interpretability and robustness, test defense strategies, and combine methods to protect against different types of attacks. We also show how defenses against evasion and poisoning attacks can conflict when applied to graph data, highlighting the complex connections between defense strategies. GNN-AID is available at \href{https://github.com/ispras/GNN-AID}{github.com/ispras/GNN-AID}
Classifying potentially hazardous asteroids (PHAs) is crucial for planetary defense and deep space navigation, yet traditional methods often overlook the dynamical relationships among asteroids. We introduce a Graph Neural Network (GNN) approach that models asteroids as nodes with orbital and physical features, connected by edges representing their similarities, using a NASA dataset of 958,524 records. Despite an extreme class imbalance with only 0.22% of the dataset with the hazardous label, our model achieves an overall accuracy of 99% and an AUC of 0.99, with a recall of 78% and an F1-score of 37% for hazardous asteroids after applying the Synthetic Minority Oversampling Technique. Feature importance analysis highlights albedo, perihelion distance, and semi-major axis as main predictors. This framework supports planetary defense missions and confirms AI's potential in enabling autonomous navigation for future missions such as NASA's NEO Surveyor and ESA's Ramses, offering an interpretable and scalable solution for asteroid hazard assessment.
Graph Neural Network (GNN) research is rapidly advancing due to GNNs' capacity to learn distributed representations from graph-structured data. However, centralizing large volumes of real-world graph data for GNN training is often impractical due to privacy concerns, regulatory restrictions, and commercial competition. Federated learning (FL), a distributed learning paradigm, offers a solution by preserving data privacy with collaborative model training. Despite progress in training huge vision and language models, federated learning for GNNs remains underexplored. To address this challenge, we present a novel method for federated learning on GNNs based on spectral GNNs equipped with neural ordinary differential equations (ODE) for better information capture, showing promising results across both homophilic and heterophilic graphs. Our approach effectively handles non-Independent and Identically Distributed (non-IID) data, while also achieving performance comparable to existing methods that only operate on IID data. It is designed to be privacy-preserving and bandwidth-optimized, making it suitable for real-world applications such as social network analysis, recommendation systems, and fraud detection, which often involve complex, non-IID, and heterophilic graph structures. Our results in the area of federated learning on non-IID heterophilic graphs demonstrate significant improvements, while also achieving better performance on homophilic graphs. This work highlights the potential of federated learning in diverse and challenging graph settings. Open-source code available on GitHub (https://github.com/SpringWiz11/Fed-GNODEFormer).
The standard approach for visual place recognition is to use global image descriptors to retrieve the most similar database images for a given query image. The results can then be further improved with re-ranking methods that re-order the top scoring images. However, existing methods focus on re-ranking based on the same image descriptors that were used for the initial retrieval, which we argue provides limited additional signal. In this work we propose Generalized Contextual Similarity Aggregation (GCSA), which is a graph neural network-based re-ranking method that, in addition to the visual descriptors, can leverage other types of available side information. This can for example be other sensor data (such as signal strength of nearby WiFi or BlueTooth endpoints) or geometric properties such as camera poses for database images. In many applications this information is already present or can be acquired with low effort. Our architecture leverages the concept of affinity vectors to allow for a shared encoding of the heterogeneous multi-modal input. Two large-scale datasets, covering both outdoor and indoor localization scenarios, are utilized for training and evaluation. In experiments we show significant improvement not only on image retrieval metrics, but also for the downstream visual localization task.
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.
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.
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
Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities. On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.