Understanding the high-order relationship between urban form and function is essential for modeling the underlying mechanisms of sustainable urban systems. Nevertheless, it is challenging to establish an accurate data representation for complex urban forms that are readily explicable in human terms. This study proposed the concept of core urban morphology representation and developed an explainable deep learning framework for explicably symbolizing complex urban forms into the novel representation, which we call CoMo. By interpretating the well-trained deep learning model with a stable weighted F1-score of 89.14%, CoMo presents a promising approach for revealing links between urban function and urban form in terms of core urban morphology representation. Using Boston as a study area, we analyzed the core urban forms at the individual-building, block, and neighborhood level that are important to corresponding urban functions. The residential core forms follow a gradual morphological pattern along the urban spine, which is consistent with a center-urban-suburban transition. Furthermore, we prove that urban morphology directly affects land use efficiency, which has a significantly strong correlation with the location (R2=0.721, p<0.001). Overall, CoMo can explicably symbolize urban forms, provide evidence for the classic urban location theory, and offer mechanistic insights for digital twins.
In computational structural biology, predicting metal-binding sites and their corresponding metal types is challenging due to the complexity of protein structures and interactions. Conventional sequence- and structure-based prediction approaches cannot capture the complex evolutionary relationships driving these interactions to facilitate understanding, while recent co-evolution-based approaches do not fully consider the entire structure of the co-evolved residue network. In this paper, we introduce MBGNN (Metal-Binding Graph Neural Network) that utilizes the entire co-evolved residue network and effectively captures the complex dependencies within protein structures via graph neural networks to enhance the prediction of co-evolved metal-binding residues and their associated metal types. Experimental results on a public dataset show that MBGNN outperforms existing co-evolution-based metal-binding prediction methods, and it is also competitive against recent sequence-based methods, showing the potential of integrating co-evolutionary insights with advanced machine learning to deepen our understanding of protein-metal interactions. The MBGNN code is publicly available at https://github.com/SRastegari/MBGNN.
Traditional Graph Neural Network (GNN) approaches for fake news detection (FND) often depend on auxiliary, non-textual data such as user interaction histories or content dissemination patterns. However, these data sources are not always accessible, limiting the effectiveness and applicability of such methods. Additionally, existing models frequently struggle to capture the detailed and intricate relationships within textual information, reducing their overall accuracy. In order to address these challenges Advanced Text Analysis Graph Neural Network (ATA-GNN) is proposed in this paper. The proposed model is designed to operate solely on textual data. ATA-GNN employs innovative topic modelling (clustering) techniques to identify typical words for each topic, leveraging multiple clustering dimensions to achieve a comprehensive semantic understanding of the text. This multi-layered design enables the model to uncover intricate textual patterns while contextualizing them within a broader semantic framework, significantly enhancing its interpretative capabilities. Extensive evaluations on widely used benchmark datasets demonstrate that ATA-GNN surpasses the performance of current GNN-based FND methods. These findings validate the potential of integrating advanced text clustering within GNN architectures to achieve more reliable and text-focused detection solutions.
Interpretability is crucial to enhance trust in machine learning models for medical diagnostics. However, most state-of-the-art image classifiers based on neural networks are not interpretable. As a result, clinicians often resort to known biomarkers for diagnosis, although biomarker-based classification typically performs worse than large neural networks. This work proposes a method that surpasses the performance of established machine learning models while simultaneously improving prediction interpretability for diabetic retinopathy staging from optical coherence tomography angiography (OCTA) images. Our method is based on a novel biology-informed heterogeneous graph representation that models retinal vessel segments, intercapillary areas, and the foveal avascular zone (FAZ) in a human-interpretable way. This graph representation allows us to frame diabetic retinopathy staging as a graph-level classification task, which we solve using an efficient graph neural network. We benchmark our method against well-established baselines, including classical biomarker-based classifiers, convolutional neural networks (CNNs), and vision transformers. Our model outperforms all baselines on two datasets. Crucially, we use our biology-informed graph to provide explanations of unprecedented detail. Our approach surpasses existing methods in precisely localizing and identifying critical vessels or intercapillary areas. In addition, we give informative and human-interpretable attributions to critical characteristics. Our work contributes to the development of clinical decision-support tools in ophthalmology.
This paper introduces a novel multiscale object-based graph neural network called MOB-GCN for hyperspectral image (HSI) classification. The central aim of this study is to enhance feature extraction and classification performance by utilizing multiscale object-based image analysis (OBIA). Traditional pixel-based methods often suffer from low accuracy and speckle noise, while single-scale OBIA approaches may overlook crucial information of image objects at different levels of detail. MOB-GCN overcomes these challenges by extracting and integrating features from multiple segmentation scales, leveraging the Multiresolution Graph Network (MGN) architecture to capture both fine-grained and global spatial patterns. MOB-GCN addresses this issue by extracting and integrating features from multiple segmentation scales to improve classification results using the Multiresolution Graph Network (MGN) architecture that can model fine-grained and global spatial patterns. By constructing a dynamic multiscale graph hierarchy, MOB-GCN offers a more comprehensive understanding of the intricate details and global context of HSIs. Experimental results demonstrate that MOB-GCN consistently outperforms single-scale graph convolutional networks (GCNs) in terms of classification accuracy, computational efficiency, and noise reduction, particularly when labeled data is limited. The implementation of MOB-GCN is publicly available at https://github.com/HySonLab/MultiscaleHSI
Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.
Predicting seizure freedom is essential for tailoring epilepsy treatment. But accurate prediction remains challenging with traditional methods, especially with diverse patient populations. This study developed a deep learning-based graph neural network (GNN) model to predict seizure freedom from stereo electroencephalography (sEEG) data in patients with refractory epilepsy. We utilized high-quality sEEG data from 15 pediatric patients to train a deep learning model that can accurately predict seizure freedom outcomes and advance understanding of brain connectivity at the seizure onset zone. Our model integrates local and global connectivity using graph convolutions with multi-scale attention mechanisms to capture connections between difficult-to-study regions such as the thalamus and motor regions. The model achieved an accuracy of 92.4% in binary class analysis, 86.6% in patient-wise analysis, and 81.4% in multi-class analysis. Node and edge-level feature analysis highlighted the anterior cingulate and frontal pole regions as key contributors to seizure freedom outcomes. The nodes identified by our model were also more likely to coincide with seizure onset zones. Our findings underscore the potential of new connectivity-based deep learning models such as GNNs for enhancing the prediction of seizure freedom, predicting seizure onset zones, connectivity analysis of the brain during seizure, as well as informing AI-assisted personalized epilepsy treatment planning.
Wide deployment of machine learning models on edge devices has rendered the model intellectual property (IP) and data privacy vulnerable. We propose GNNVault, the first secure Graph Neural Network (GNN) deployment strategy based on Trusted Execution Environment (TEE). GNNVault follows the design of 'partition-before-training' and includes a private GNN rectifier to complement with a public backbone model. This way, both critical GNN model parameters and the private graph used during inference are protected within secure TEE compartments. Real-world implementations with Intel SGX demonstrate that GNNVault safeguards GNN inference against state-of-the-art link stealing attacks with negligible accuracy degradation (<2%).
We propose a novel Graph Neural Network (GNN) model, named DeepStateGNN, for analyzing traffic data, demonstrating its efficacy in two critical tasks: forecasting and reconstruction. Unlike typical GNN methods that treat each traffic sensor as an individual graph node, DeepStateGNN clusters sensors into higher-level graph nodes, dubbed Deep State Nodes, based on various similarity criteria, resulting in a fixed number of nodes in a Deep State graph. The term "Deep State" nodes is a play on words, referencing hidden networks of power that, like these nodes, secretly govern traffic independently of visible sensors. These Deep State Nodes are defined by several similarity factors, including spatial proximity (e.g., sensors located nearby in the road network), functional similarity (e.g., sensors on similar types of freeways), and behavioral similarity under specific conditions (e.g., traffic behavior during rain). This clustering approach allows for dynamic and adaptive node grouping, as sensors can belong to multiple clusters and clusters may evolve over time. Our experimental results show that DeepStateGNN offers superior scalability and faster training, while also delivering more accurate results than competitors. It effectively handles large-scale sensor networks, outperforming other methods in both traffic forecasting and reconstruction accuracy.
Since heterogeneity presents a fundamental challenge in graph federated learning, many existing methods are proposed to deal with node feature heterogeneity and structure heterogeneity. However, they overlook the critical homophily heterogeneity, which refers to the substantial variation in homophily levels across graph data from different clients. The homophily level represents the proportion of edges connecting nodes that belong to the same class. Due to adapting to their local homophily, local models capture inconsistent spectral properties across different clients, significantly reducing the effectiveness of collaboration. Specifically, local models trained on graphs with high homophily tend to capture low-frequency information, whereas local models trained on graphs with low homophily tend to capture high-frequency information. To effectively deal with homophily heterophily, we introduce the spectral Graph Neural Network (GNN) and propose a novel Federated learning method by mining Graph Spectral Properties (FedGSP). On one hand, our proposed FedGSP enables clients to share generic spectral properties (i.e., low-frequency information), allowing all clients to benefit through collaboration. On the other hand, inspired by our theoretical findings, our proposed FedGSP allows clients to complement non-generic spectral properties by acquiring the spectral properties they lack (i.e., high-frequency information), thereby obtaining additional information gain. Extensive experiments conducted on six homophilic and five heterophilic graph datasets, across both non-overlapping and overlapping settings, validate the superiority of our method over eleven state-of-the-art methods. Notably, our FedGSP outperforms the second-best method by an average margin of 3.28% on all heterophilic datasets.
In-band network telemetry (INT) is essential to network management due to its real-time visibility. However, because of the rapid increase in network devices and services, it has become crucial to have targeted access to detailed network information in a dynamic network environment. This paper proposes an intelligent network telemetry system called NTP-INT to obtain more fine-grained network information on high-load switches. Specifically, NTP-INT consists of three modules: network traffic prediction module, network pruning module, and probe path planning module. Firstly, the network traffic prediction module adopts a Multi-Temporal Graph Neural Network (MTGNN) to predict future network traffic and identify high-load switches. Then, we design the network pruning algorithm to generate a subnetwork covering all high-load switches to reduce the complexity of probe path planning. Finally, the probe path planning module uses an attention-mechanism-based deep reinforcement learning (DEL) model to plan efficient probe paths in the network slice. The experimental results demonstrate that NTP-INT can acquire more precise network information on high-load switches while decreasing the control overhead by 50\%.
Water distribution systems (WDSs) are an important part of critical infrastructure becoming increasingly significant in the face of climate change and urban population growth. We propose a robust and scalable surrogate deep learning (DL) model to enable efficient planning, expansion, and rehabilitation of WDSs. Our approach incorporates an improved graph neural network architecture, an adapted physics-informed algorithm, an innovative training scheme, and a physics-preserving data normalization method. Evaluation results on a number of WDSs demonstrate that our model outperforms the current state-of-the-art DL model. Moreover, our method allows us to scale the model to bigger and more realistic WDSs. Furthermore, our approach makes the model more robust to out-of-distribution input features (demands, pipe diameters). Hence, our proposed method constitutes a significant step towards bridging the simulation-to-real gap in the use of artificial intelligence for WDSs.
Satisfiability (SAT) solvers based on techniques such as conflict driven clause learning (CDCL) have produced excellent performance on both synthetic and real world industrial problems. While these CDCL solvers only operate on a per-problem basis, graph neural network (GNN) based solvers bring new benefits to the field by allowing practitioners to exploit knowledge gained from solved problems to expedite solving of new SAT problems. However, one specific area that is often studied in the context of CDCL solvers, but largely overlooked in GNN solvers, is the relationship between graph theoretic measure of structure in SAT problems and the generalisation ability of GNN solvers. To bridge the gap between structural graph properties (e.g., modularity, self-similarity) and the generalisability (or lack thereof) of GNN based SAT solvers, we present StructureSAT: a curated dataset, along with code to further generate novel examples, containing a diverse set of SAT problems from well known problem domains. Furthermore, we utilise a novel splitting method that focuses on deconstructing the families into more detailed hierarchies based on their structural properties. With the new dataset, we aim to help explain problematic generalisation in existing GNN SAT solvers by exploiting knowledge of structural graph properties. We conclude with multiple future directions that can help researchers in GNN based SAT solving develop more effective and generalisable SAT solvers.
Graph Neural Networks (GNNs) are models that leverage the graph structure to transmit information between nodes, typically through the message-passing operation. While widely successful, this approach is well known to suffer from the over-smoothing and over-squashing phenomena, which result in representational collapse as the number of layers increases and insensitivity to the information contained at distant and poorly connected nodes, respectively. In this paper, we present a unified view of these problems through the lens of vanishing gradients, using ideas from linear control theory for our analysis. We propose an interpretation of GNNs as recurrent models and empirically demonstrate that a simple state-space formulation of a GNN effectively alleviates over-smoothing and over-squashing at no extra trainable parameter cost. Further, we show theoretically and empirically that (i) GNNs are by design prone to extreme gradient vanishing even after a few layers; (ii) Over-smoothing is directly related to the mechanism causing vanishing gradients; (iii) Over-squashing is most easily alleviated by a combination of graph rewiring and vanishing gradient mitigation. We believe our work will help bridge the gap between the recurrent and graph neural network literature and will unlock the design of new deep and performant GNNs.
Stock trend prediction involves forecasting the future price movements by analyzing historical data and various market indicators. With the advancement of machine learning, graph neural networks (GNNs) have been extensively employed in stock prediction due to their powerful capability to capture spatiotemporal dependencies of stocks. However, despite the efforts of various GNN stock predictors to enhance predictive performance, the improvements remain limited, as they focus solely on analyzing historical spatiotemporal dependencies, overlooking the correlation between historical and future patterns. In this study, we propose a novel distillation-based future-aware GNN framework (DishFT-GNN) for stock trend prediction. Specifically, DishFT-GNN trains a teacher model and a student model, iteratively. The teacher model learns to capture the correlation between distribution shifts of historical and future data, which is then utilized as intermediate supervision to guide the student model to learn future-aware spatiotemporal embeddings for accurate prediction. Through extensive experiments on two real-world datasets, we verify the state-of-the-art performance of DishFT-GNN.
Polarization and fragmentation in social media amplify user biases, making it increasingly important to understand the evolution of opinions. Opinion dynamics provide interpretability for studying opinion evolution, yet incorporating these insights into predictive models remains challenging. This challenge arises due to the inherent complexity of the diversity of opinion fusion rules and the difficulty in capturing equilibrium states while avoiding over-smoothing. This paper constructs a unified opinion dynamics model to integrate different opinion fusion rules and generates corresponding synthetic datasets. To fully leverage the advantages of unified opinion dynamics, we introduces UniGO, a framework for modeling opinion evolution on graphs. Using a coarsen-refine mechanism, UniGO efficiently models opinion dynamics through a graph neural network, mitigating over-smoothing while preserving equilibrium phenomena. UniGO leverages pretraining on synthetic datasets, which enhances its ability to generalize to real-world scenarios, providing a viable paradigm for applications of opinion dynamics. Experimental results on both synthetic and real-world datasets demonstrate UniGO's effectiveness in capturing complex opinion formation processes and predicting future evolution. The pretrained model also shows strong generalization capability, validating the benefits of using synthetic data to boost real-world performance.
Mass spectrometry, especially so-called tandem mass spectrometry, is commonly used to assess the chemical diversity of samples. The resulting mass fragmentation spectra are representations of molecules of which the structure may have not been determined. This poses the challenge of experimentally determining or computationally predicting molecular structures from mass spectra. An alternative option is to predict molecular properties or molecular similarity directly from spectra. Various methodologies have been proposed to embed mass spectra for further use in machine learning tasks. However, these methodologies require preprocessing of the spectra, which often includes binning or sub-sampling peaks with the main reasoning of creating uniform vector sizes and removing noise. Here, we investigate two alternatives to the binning of mass spectra before down-stream machine learning tasks, namely, set-based and graph-based representations. Comparing the two proposed representations to train a set transformer and a graph neural network on a regression task, respectively, we show that they both perform substantially better than a multilayer perceptron trained on binned data.
Community detection is a cornerstone problem in social network analysis (SNA), aimed at identifying cohesive communities with minimal external links. However, the rise of generative AI and Metaverse introduce complexities by creating hybrid human-AI social networks (denoted by HASNs), where traditional methods fall short, especially in human-centric settings. This paper introduces a novel community detection problem in HASNs (denoted by MetaCD), which seeks to enhance human connectivity within communities while reducing the presence of AI nodes. Effective processing of MetaCD poses challenges due to the delicate trade-off between excluding certain AI nodes and maintaining community structure. To address this, we propose CUSA, an innovative framework incorporating AI-aware clustering techniques that navigate this trade-off by selectively retaining AI nodes that contribute to community integrity. Furthermore, given the scarcity of real-world HASNs, we devise four strategies for synthesizing these networks under various hypothetical scenarios. Empirical evaluations on real social networks, reconfigured as HASNs, demonstrate the effectiveness and practicality of our approach compared to traditional non-deep learning and graph neural network (GNN)-based methods.
Graph neural networks are gaining attention in fifth-generation (5G) core network digital twins, which are data-driven complex systems with numerous components. Analyzing these data can be challenging due to rare failure types, leading to imbalanced classification in multiclass settings. Digital twins of 5G networks increasingly employ graph classification as the main method for identifying failure types. However, the skewed distribution of failure occurrences is a significant class-imbalance problem that prevents practical graph data mining. Previous studies have not sufficiently addressed this complex problem. This paper, proposes class-Fourier GNN (CF-GNN) that introduces a class-oriented spectral filtering mechanism to ensure precise classification by estimating a unique spectral filter for each class. This work employs eigenvalue and eigenvector spectral filtering to capture and adapt to variations in minority classes, ensuring accurate class-specific feature discrimination, and adept at graph representation learning for complex local structures among neighbors in an end-to-end setting. The extensive experiments demonstrate that the proposed CF-GNN could help create new techniques for enhancing classifiers and investigate the characteristics of the multiclass imbalanced data in a network digital twin system.
Graph Neural Networks (GNNs) have recently become the predominant tools for studying graph data. Despite state-of-the-art performance on graph classification tasks, GNNs are overwhelmingly trained in a single domain under supervision, thus necessitating a prohibitively high demand for labels and resulting in poorly transferable representations. To address this challenge, we propose the Label-Propagation Tensor Graph Neural Network (LP-TGNN) framework to bridge the gap between graph data and traditional domain adaptation methods. It extracts graph topological information holistically with a tensor architecture and then reduces domain discrepancy through label propagation. It is readily compatible with general GNNs and domain adaptation techniques with minimal adjustment through pseudo-labeling. Experiments on various real-world benchmarks show that our LP-TGNN outperforms baselines by a notable margin. We also validate and analyze each component of the proposed framework in the ablation study.