Skin diseases affect millions worldwide.Early detection is key to preventing disfigurement,lifelong disability,or death.Dermoscopic images acquired in primary-care settings show high intra-class visual similarity and ...Skin diseases affect millions worldwide.Early detection is key to preventing disfigurement,lifelong disability,or death.Dermoscopic images acquired in primary-care settings show high intra-class visual similarity and severe class imbalance,and occasional imaging artifacts can create ambiguity for state-of-the-art convolutional neural networks(CNNs).We frame skin lesion recognition as graph-based reasoning and,to ensure fair evaluation and avoid data leakage,adopt a strict lesion-level partitioning strategy.Each image is first over-segmented using SLIC(Simple Linear Iterative Clustering)to produce perceptually homogeneous superpixels.These superpixels form the nodes of a region-adjacency graph whose edges encode spatial continuity.Node attributes are 1280-dimensional embeddings extracted with a lightweight yet expressive EfficientNet-B0 backbone,providing strong representational power at modest computational cost.The resulting graphs are processed by a five-layer Graph Attention Network(GAT)that learns to weight inter-node relationships dynamically and aggregates multi-hop context before classifying lesions into seven classes with a log-softmax output.Extensive experiments on the DermaMNIST benchmark show the proposed pipeline achieves 88.35%accuracy and 98.04%AUC,outperforming contemporary CNNs,AutoML approaches,and alternative graph neural networks.An ablation study indicates EfficientNet-B0 produces superior node descriptors compared with ResNet-18 and DenseNet,and that roughly five GAT layers strike a good balance between being too shallow and over-deep while avoiding oversmoothing.The method requires no data augmentation or external metadata,making it a drop-in upgrade for clinical computer-aided diagnosis systems.展开更多
Traditional Chinese medicine(TCM)features complex compatibility mechanisms involving multicomponent,multi-target,and multi-pathway interactions.This study presents an interpretable graph artificial intelligence(GraphA...Traditional Chinese medicine(TCM)features complex compatibility mechanisms involving multicomponent,multi-target,and multi-pathway interactions.This study presents an interpretable graph artificial intelligence(GraphAI)framework to quantify such mechanisms in Chinese herbal formulas(CHFs).A multidimensional TCM knowledge graph(TCM-MKG;https://zenodo.org/records/13763953)was constructed,integrating seven standardized modules:TCM terminology,Chinese patent medicines(CPMs),Chinese herbal pieces(CHPs),pharmacognostic origins(POs),chemical compounds,biological targets,and diseases.A neighbor-diffusion strategy was used to address the sparsity of compound-target associations,increasing target coverage from 12.0%to 98.7%.Graph neural networks(GNNs)with attention mechanisms were applied to 6,080 CHFs,modeled as graphs with CHPs as nodes.To embed domain-specific semantics,virtual nodes medicinal properties,i.e.,therapeutic nature,flavor,and meridian tropism,were introduced,enabling interpretable modeling of inter-CHP relationships.The model quantitatively captured classical compatibility roles such as“monarch-minister-assistant-guide”,and uncovered TCM etiological types derived from diagnostic and efficacy patterns.Model validation using 215 CHFs used for coronavirus disease 2019(COVID-19)management highlighted Radix Astragali-Rhizoma Phragmitis as a high-attention herb pair.Mass spectrometry(MS)and target prediction identified three active compounds,i.e.,methylinissolin-3-O-glucoside,corydalin,and pingbeinine,which converge on pathways such as neuroactive ligand-receptor interaction,xenobiotic response,and neuronal function,supporting their neuroimmune and detoxification potential.Given their high safety and dietary compatibility,this herb pair may offer therapeutic value for managing long COVID-19.All data and code are openly available(https://github.com/ZENGJingqi/GraphAI-for-TCM),providing a scalable and interpretable platform for TCM mechanism research and discovery of bioactive herbal constituents.展开更多
The increasing popularity of the Internet and the widespread use of information technology have led to a rise in the number and sophistication of network attacks and security threats.Intrusion detection systems are cr...The increasing popularity of the Internet and the widespread use of information technology have led to a rise in the number and sophistication of network attacks and security threats.Intrusion detection systems are crucial to network security,playing a pivotal role in safeguarding networks from potential threats.However,in the context of an evolving landscape of sophisticated and elusive attacks,existing intrusion detection methodologies often overlook critical aspects such as changes in network topology over time and interactions between hosts.To address these issues,this paper proposes a real-time network intrusion detection method based on graph neural networks.The proposedmethod leverages the advantages of graph neural networks and employs a straightforward graph construction method to represent network traffic as dynamic graph-structured data.Additionally,a graph convolution operation with a multi-head attention mechanism is utilized to enhance the model’s ability to capture the intricate relationships within the graph structure comprehensively.Furthermore,it uses an integrated graph neural network to address dynamic graphs’structural and topological changes at different time points and the challenges of edge embedding in intrusion detection data.The edge classification problem is effectively transformed into node classification by employing a line graph data representation,which facilitates fine-grained intrusion detection tasks on dynamic graph node feature representations.The efficacy of the proposed method is evaluated using two commonly used intrusion detection datasets,UNSW-NB15 and NF-ToN-IoT-v2,and results are compared with previous studies in this field.The experimental results demonstrate that our proposed method achieves 99.3%and 99.96%accuracy on the two datasets,respectively,and outperforms the benchmark model in several evaluation metrics.展开更多
Spectrum-based fault localization (SBFL) generates a ranked list of suspicious elements by using the program execution spectrum, but the excessive number of elements ranked in parallel results in low localization accu...Spectrum-based fault localization (SBFL) generates a ranked list of suspicious elements by using the program execution spectrum, but the excessive number of elements ranked in parallel results in low localization accuracy. Most researchers consider intra-class dependencies to improve localization accuracy. However, some studies show that inter-class method call type faults account for more than 20%, which means such methods still have certain limitations. To solve the above problems, this paper proposes a two-phase software fault localization based on relational graph convolutional neural networks (Two-RGCNFL). Firstly, in Phase 1, the method call dependence graph (MCDG) of the program is constructed, the intra-class and inter-class dependencies in MCDG are extracted by using the relational graph convolutional neural network, and the classifier is used to identify the faulty methods. Then, the GraphSMOTE algorithm is improved to alleviate the impact of class imbalance on classification accuracy. Aiming at the problem of parallel ranking of element suspicious values in traditional SBFL technology, in Phase 2, Doc2Vec is used to learn static features, while spectrum information serves as dynamic features. A RankNet model based on siamese multi-layer perceptron is constructed to score and rank statements in the faulty method. This work conducts experiments on 5 real projects of Defects4J benchmark. Experimental results show that, compared with the traditional SBFL technique and two baseline methods, our approach improves the Top-1 accuracy by 262.86%, 29.59% and 53.01%, respectively, which verifies the effectiveness of Two-RGCNFL. Furthermore, this work verifies the importance of inter-class dependencies through ablation experiments.展开更多
Accurate and efficient prediction of the distribution of surface loads on buildings subjected to explosive effects is crucial for rapidly calculating structural dynamic responses,establishing effective protective meas...Accurate and efficient prediction of the distribution of surface loads on buildings subjected to explosive effects is crucial for rapidly calculating structural dynamic responses,establishing effective protective measures,and designing civil defense engineering solutions.Current state-of-the-art methods face several issues:Experimental research is difficult and costly to implement,theoretical research is limited to simple geometries and lacks precision,and direct simulations require substantial computational resources.To address these challenges,this paper presents a data-driven method for predicting blast loads on building surfaces.This approach increases both the accuracy and computational efficiency of load predictions when the geometry of the building changes while the explosive yield remains constant,significantly improving its applicability in complex scenarios.This study introduces an innovative encoder-decoder graph neural network model named BlastGraphNet,which uses a message-passing mechanism to predict the overpressure and impulse load distributions on buildings with conventional and complex geometries during explosive events.The model also facilitates related downstream applications,such as damage mode identification and rapid assessment of virtual city explosions.The calculation results indicate that the prediction error of the model for conventional building tests is less than 2%,and its inference speed is 3-4 orders of magnitude faster than that of state-of-the-art numerical methods.In extreme test cases involving buildings with complex geometries and building clusters,the method achieved high accuracy and excellent generalizability.The strong adaptability and generalizability of BlastGraphNet confirm that this novel method enables precise real-time prediction of blast loads and provides a new paradigm for damage assessment in protective engineering.展开更多
The ability to accurately predict urban traffic flows is crucial for optimising city operations.Consequently,various methods for forecasting urban traffic have been developed,focusing on analysing historical data to u...The ability to accurately predict urban traffic flows is crucial for optimising city operations.Consequently,various methods for forecasting urban traffic have been developed,focusing on analysing historical data to understand complex mobility patterns.Deep learning techniques,such as graph neural networks(GNNs),are popular for their ability to capture spatio-temporal dependencies.However,these models often become overly complex due to the large number of hyper-parameters involved.In this study,we introduce Dynamic Multi-Graph Spatial-Temporal Graph Neural Ordinary Differential Equation Networks(DMST-GNODE),a framework based on ordinary differential equations(ODEs)that autonomously discovers effective spatial-temporal graph neural network(STGNN)architectures for traffic prediction tasks.The comparative analysis of DMST-GNODE and baseline models indicates that DMST-GNODE model demonstrates superior performance across multiple datasets,consistently achieving the lowest Root Mean Square Error(RMSE)and Mean Absolute Error(MAE)values,alongside the highest accuracy.On the BKK(Bangkok)dataset,it outperformed other models with an RMSE of 3.3165 and an accuracy of 0.9367 for a 20-min interval,maintaining this trend across 40 and 60 min.Similarly,on the PeMS08 dataset,DMST-GNODE achieved the best performance with an RMSE of 19.4863 and an accuracy of 0.9377 at 20 min,demonstrating its effectiveness over longer periods.The Los_Loop dataset results further emphasise this model’s advantage,with an RMSE of 3.3422 and an accuracy of 0.7643 at 20 min,consistently maintaining superiority across all time intervals.These numerical highlights indicate that DMST-GNODE not only outperforms baseline models but also achieves higher accuracy and lower errors across different time intervals and datasets.展开更多
Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based me...Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.展开更多
In this paper,a sparse graph neural network-aided(SGNN-aided)decoder is proposed for improving the decoding performance of polar codes under bursty interference.Firstly,a sparse factor graph is constructed using the e...In this paper,a sparse graph neural network-aided(SGNN-aided)decoder is proposed for improving the decoding performance of polar codes under bursty interference.Firstly,a sparse factor graph is constructed using the encoding characteristic to achieve high-throughput polar decoding.To further improve the decoding performance,a residual gated bipartite graph neural network is designed for updating embedding vectors of heterogeneous nodes based on a bidirectional message passing neural network.This framework exploits gated recurrent units and residual blocks to address the gradient disappearance in deep graph recurrent neural networks.Finally,predictions are generated by feeding the embedding vectors into a readout module.Simulation results show that the proposed decoder is more robust than the existing ones in the presence of bursty interference and exhibits high universality.展开更多
With the rapid development of deep learning neural networks,new solutions have emerged for addressing fluid flow problems in porous media.Combining data-driven approaches with physical constraints has become a hot res...With the rapid development of deep learning neural networks,new solutions have emerged for addressing fluid flow problems in porous media.Combining data-driven approaches with physical constraints has become a hot research direction,with physics-informed neural networks(PINNs) being the most popular hybrid model.PINNs have gained widespread attention in subsurface fluid flow simulations due to their low computational resource requirements,fast training speeds,strong generalization capabilities,and broad applicability.Despite success in homogeneous settings,standard PINNs face challenges in accurately calculating flux between irregular Eulerian cells with disparate properties and capturing global field influences on local cells.This limits their suitability for heterogeneous reservoirs and the irregular Eulerian grids frequently used in reservoir.To address these challenges,this study proposes a physics-informed graph neural network(PIGNN) model.The PIGNN model treats the entire field as a whole,integrating information from neighboring grids and physical laws into the solution for the target grid,thereby improving the accuracy of solving partial differential equations in heterogeneous and Eulerian irregular grids.The optimized model was applied to pressure field prediction in a spatially heterogeneous reservoir,achieving an average L_(2) error and R_(2) score of 6.710×10^(-4)and 0.998,respectively,which confirms the effectiveness of model.Compared to the conventional PINN model,the average L_(2) error was reduced by 76.93%,the average R_(2) score increased by 3.56%.Moreover,evaluating robustness,training the PIGNN model using only 54% and 76% of the original data yielded average relative L_(2) error reductions of 58.63% and 56.22%,respectively,compared to the PINN model.These results confirm the superior performance of this approach compared to PINN.展开更多
Cryptocurrency is a remarkable financial innovation that has affected the financial system in fundamental ways.Its increasingly complex interactions with the conventional financial market make precisely forecasting it...Cryptocurrency is a remarkable financial innovation that has affected the financial system in fundamental ways.Its increasingly complex interactions with the conventional financial market make precisely forecasting its volatility increasingly challenging.To this end,we propose a novel framework based on the evolving multiscale graph neural network(EMGNN).Specifically,we embed a graph that depicts the interactions between the cryptocurrency and conventional financial markets into the predictive process.Furthermore,we employ hierarchical evolving graph structure learners to model the dynamic and scale-specific interactions.We also evaluate our framework’s robustness and discuss its interpretability by extracting the learned graph structure.The empirical results show that(i)cryptocurrency volatility is not isolated from the conventional market,and the embedded graph can provide effective information for prediction;(ii)the EMGNN-based forecasting framework generally yields outstanding and robust performance in terms of multiple volatility estimators,cryptocurrency samples,forecasting horizons,and evaluation criteria;and(iii)the graph structure in the predictive process varies over time and scales and is well captured by our framework.Overall,our work provides new insights into risk management for market participants and into policy formulation for authorities.展开更多
Fault diagnosis occupies a pivotal position within the domain of machine and equipment management.Existing methods,however,often exhibit limitations in their scope of application,typically focusing on specific types o...Fault diagnosis occupies a pivotal position within the domain of machine and equipment management.Existing methods,however,often exhibit limitations in their scope of application,typically focusing on specific types of signals or faults in individual mechanical components while being constrained by data types and inherent characteristics.To address the limitations of existing methods,we propose a fault diagnosis method based on graph neural networks(GNNs)embedded with multirelationships of intrinsic mode functions(MIMF).The approach introduces a novel graph topological structure constructed from the features of intrinsic mode functions(IMFs)of monitored signals and their multirelationships.Additionally,a graph-level based fault diagnosis network model is designed to enhance feature learning capabilities for graph samples and enable flexible application across diverse signal sources and devices.Experimental validation with datasets including independent vibration signals for gear fault detection,mixed vibration signals for concurrent gear and bearing faults,and pressure signals for hydraulic cylinder leakage characterization demonstrates the model's adaptability and superior diagnostic accuracy across various types of signals and mechanical systems.展开更多
Schizophrenia(SZ)stands as a severe psychiatric disorder.This study applied diffusion tensor imaging(DTI)data in conjunction with graph neural networks to distinguish SZ patients from normal controls(NCs)and showcases...Schizophrenia(SZ)stands as a severe psychiatric disorder.This study applied diffusion tensor imaging(DTI)data in conjunction with graph neural networks to distinguish SZ patients from normal controls(NCs)and showcases the superior performance of a graph neural network integrating combined fractional anisotropy and fiber number brain network features,achieving an accuracy of 73.79%in distinguishing SZ patients from NCs.Beyond mere discrimination,our study delved deeper into the advantages of utilizing white matter brain network features for identifying SZ patients through interpretable model analysis and gene expression analysis.These analyses uncovered intricate interrelationships between brain imaging markers and genetic biomarkers,providing novel insights into the neuropathological basis of SZ.In summary,our findings underscore the potential of graph neural networks applied to multimodal DTI data for enhancing SZ detection through an integrated analysis of neuroimaging and genetic features.展开更多
Objective:Prostate cancer(PCa)exhibits significant genomic differences between Western and Asian populations.This study aimed to design a predictive model applicable across diverse populations while selecting a limite...Objective:Prostate cancer(PCa)exhibits significant genomic differences between Western and Asian populations.This study aimed to design a predictive model applicable across diverse populations while selecting a limited set of genes suitable for clinical implementation.Methods:We utilized an integrated dataset of 1360 whole-exome and whole-genome sequences from Chinese and Western PCa cohorts to develop and evaluate the model.External validation was conducted using an independent cohort of patients.A graph neural network architecture,termed the pathway-aware multi-layered hierarchical network-Western and Asian(P-NETwa),was developed and trained on combined genomic profiles from Chinese and Western cohorts.The model employed a multilayer perceptron(MLP)to identify key signature genes from multiomics data,enabling precise prediction of PCa metastasis.Results:The model achieved an accuracy of 0.87 and an F1-score of 0.85 on Western population datasets.The application of integrated Chinese and Western population data improved the accuracy to 0.88,achieving an F1-score of 0.75.The analysis identified 18 signature genes implicated in PCa progression,including established markers(AR and TP53)and novel candidates(MUC16,MUC4,and ASB12).For clinical adoption,the model was optimized for commercially available gene panels while maintaining high classification accuracy.Additionally,a user-friendly web interface was developed to facilitate real-time prediction of primary versus metastatic status using the pre-trained P-NETwa-MLP model.Conclusion:The P-NETwa-MLP model integrates a query system that allows for efficient retrieval of prediction outcomes and associated genomic signatures via sample ID,enhancing its potential for seamless integration into clinical workflows.展开更多
Graph Neural Networks(GNNs)have demonstrated outstanding capabilities in processing graph-structured data and are increasingly being integrated into large-scale pre-trained models,such as Large Language Models(LLMs),t...Graph Neural Networks(GNNs)have demonstrated outstanding capabilities in processing graph-structured data and are increasingly being integrated into large-scale pre-trained models,such as Large Language Models(LLMs),to enhance structural reasoning,knowledge retrieval,and memory management.The expansion of their application scope imposes higher requirements on the robustness of GNNs.However,as GNNs are applied to more dynamic and heterogeneous environments,they become increasingly vulnerable to real-world perturbations.In particular,graph data frequently encounters joint adversarial perturbations that simultaneously affect both structures and features,which are significantly more challenging than isolated attacks.These disruptions,caused by incomplete data,malicious attacks,or inherent noise,pose substantial threats to the stable and reliable performance of traditional GNN models.To address this issue,this study proposes the Dual-Shield Graph Neural Network(DSGNN),a defense model that simultaneously mitigates structural and feature perturbations.DSGNN utilizes two parallel GNN channels to independently process structural noise and feature noise,and introduces an adaptive fusion mechanism that integrates information from both pathways to generate robust node representations.Theoretical analysis demonstrates that DSGNN achieves a tighter robustness boundary under joint perturbations compared to conventional single-channel methods.Experimental evaluations across Cora,CiteSeer,and Industry datasets show that DSGNN achieves the highest average classification accuracy under various adversarial settings,reaching 81.24%,71.94%,and 81.66%,respectively,outperforming GNNGuard,GCN-Jaccard,GCN-SVD,RGCN,and NoisyGNN.These results underscore the importance of multi-view perturbation decoupling in constructing resilient GNN models for real-world applications.展开更多
Metal–organic frameworks(MOFs)hold great potential for gas separation and storage,and graph neural networks have proven to be a powerful tool for exploring material structure–property relationships and discovering n...Metal–organic frameworks(MOFs)hold great potential for gas separation and storage,and graph neural networks have proven to be a powerful tool for exploring material structure–property relationships and discovering new materials.Unlike traditional molecular graphs,crystal graphs require consideration of periodic invariance and modes.In addition,MOF structures such as covalent bonds,functional groups,and global structures impact adsorption performance in different ways.However,redundant atomic interactions can disrupt training accuracy,potentially leading to overfitting.In this paper,we propose a multi-scale crystal graph for describing periodic crystal structures,modeling interatomic interactions at different scales while preserving periodicity invariance.We also propose a multi-head attention crystal graph network in multi-scale graphs(MHACGN-MS),which learns structural characteristics by focusing on interatomic interactions at different scales,thereby reducing interference from redundant interactions.Using MOF adsorption for gases as an example,we demonstrate that MHACGN-MS outperforms traditional graph neural networks in predicting multi-component gas adsorption.We also visualize attention scores to validate effective learning and demonstrate the model’s interpretability.展开更多
Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,e...Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).展开更多
Federated Graph Neural Networks (FedGNNs) have achieved significant success in representation learning for graph data, enabling collaborative training among multiple parties without sharing their raw graph data and so...Federated Graph Neural Networks (FedGNNs) have achieved significant success in representation learning for graph data, enabling collaborative training among multiple parties without sharing their raw graph data and solving the data isolation problem faced by centralized GNNs in data-sensitive scenarios. Despite the plethora of prior work on inference attacks against centralized GNNs, the vulnerability of FedGNNs to inference attacks has not yet been widely explored. It is still unclear whether the privacy leakage risks of centralized GNNs will also be introduced in FedGNNs. To bridge this gap, we present PIAFGNN, the first property inference attack (PIA) against FedGNNs. Compared with prior works on centralized GNNs, in PIAFGNN, the attacker can only obtain the global embedding gradient distributed by the central server. The attacker converts the task of stealing the target user’s local embeddings into a regression problem, using a regression model to generate the target graph node embeddings. By training shadow models and property classifiers, the attacker can infer the basic property information within the target graph that is of interest. Experiments on three benchmark graph datasets demonstrate that PIAFGNN achieves attack accuracy of over 70% in most cases, even approaching the attack accuracy of inference attacks against centralized GNNs in some instances, which is much higher than the attack accuracy of the random guessing method. Furthermore, we observe that common defense mechanisms cannot mitigate our attack without affecting the model’s performance on mainly classification tasks.展开更多
Recently,numerous estimation issues have been solved due to the developments in data-driven artificial neural networks(ANN)and graph neural networks(GNN).The primary limitation of previous methodologies has been the d...Recently,numerous estimation issues have been solved due to the developments in data-driven artificial neural networks(ANN)and graph neural networks(GNN).The primary limitation of previous methodologies has been the dependence on data that can be structured in a grid format.However,physiological recordings often exhibit irregular and unordered patterns,posing a significant challenge in conceptualising them as matrices.As a result,GNNs which comprise interactive nodes connected by edges whose weights are defined by anatomical junctions or temporal relationships have received a lot of consideration by leveraging implicit data that exists in a biological system.Additionally,our study incorporates a structural GNN to effectively differentiate between different degrees of infection in both the left and right hemispheres of the brain.Subsequently,demographic data are included,and a multi-task learning architecture is devised,integrating classification and regression tasks.The trials used an authentic dataset,including 800 brain x-ray pictures,consisting of 560 instances classified as moderate cases and 240 instances classified as severe cases.Based on empirical evidence,our methodology demonstrates superior performance in classification,surpassing other comparison methods with a notable achievement of 92.27%in terms of area under the curve as well as a correlation coefficient of 0.62.展开更多
Quantum error correction is a technique that enhances a system’s ability to combat noise by encoding logical information into additional quantum bits,which plays a key role in building practical quantum computers.The...Quantum error correction is a technique that enhances a system’s ability to combat noise by encoding logical information into additional quantum bits,which plays a key role in building practical quantum computers.The XZZX surface code,with only one stabilizer generator on each face,demonstrates significant application potential under biased noise.However,the existing minimum weight perfect matching(MWPM)algorithm has high computational complexity and lacks flexibility in large-scale systems.Therefore,this paper proposes a decoding method that combines graph neural networks(GNN)with multi-classifiers,the syndrome is transformed into an undirected graph,and the features are aggregated by convolutional layers,providing a more efficient and accurate decoding strategy.In the experiments,we evaluated the performance of the XZZX code under different biased noise conditions(bias=1,20,200)and different code distances(d=3,5,7,9,11).The experimental results show that under low bias noise(bias=1),the GNN decoder achieves a threshold of 0.18386,an improvement of approximately 19.12%compared to the MWPM decoder.Under high bias noise(bias=200),the GNN decoder reaches a threshold of 0.40542,improving by approximately 20.76%,overcoming the limitations of the conventional decoder.They demonstrate that the GNN decoding method exhibits superior performance and has broad application potential in the error correction of XZZX code.展开更多
The increasing frequency of offshore engineering activities,particularly the expansion of offshore oil transport and the rise in the number of oil platforms,has greatly increased the potential risk of marine oil spill...The increasing frequency of offshore engineering activities,particularly the expansion of offshore oil transport and the rise in the number of oil platforms,has greatly increased the potential risk of marine oil spill incidents.Historically,several large oil spills have had long-term adverse effects on marine ecosystems and economic development,highlighting the importance of accurate-ly delineating and monitoring oil spill areas.In this study,graph neural network technology is introduced to implement semantic seg-mentation of SAR images,and two graph neural network models based on Graph-FCN and Graph-DeepLabV3+with the introduction of an attention mechanism are constructed and evaluated to improve the accuracy and efficiency of oil spill detection.By com-paring the Swin-Unet model,the Graph-DeepLabV3+model performs better in complex scenarios,especially in edge detail recognition.This not only provides strong technical support for marine oil spill monitoring but also provides an effective solution to deal with the potential risks brought by the increase of marine engineering activities,which is of great practical significance as it helps to safeguard the health and sustainable development of marine ecosystems and reduce the economic losses.展开更多
基金funded by the Deanship of Graduate Studies and Scientific Research at Jouf University under grant No.(DGSSR-2025-02-01296).
文摘Skin diseases affect millions worldwide.Early detection is key to preventing disfigurement,lifelong disability,or death.Dermoscopic images acquired in primary-care settings show high intra-class visual similarity and severe class imbalance,and occasional imaging artifacts can create ambiguity for state-of-the-art convolutional neural networks(CNNs).We frame skin lesion recognition as graph-based reasoning and,to ensure fair evaluation and avoid data leakage,adopt a strict lesion-level partitioning strategy.Each image is first over-segmented using SLIC(Simple Linear Iterative Clustering)to produce perceptually homogeneous superpixels.These superpixels form the nodes of a region-adjacency graph whose edges encode spatial continuity.Node attributes are 1280-dimensional embeddings extracted with a lightweight yet expressive EfficientNet-B0 backbone,providing strong representational power at modest computational cost.The resulting graphs are processed by a five-layer Graph Attention Network(GAT)that learns to weight inter-node relationships dynamically and aggregates multi-hop context before classifying lesions into seven classes with a log-softmax output.Extensive experiments on the DermaMNIST benchmark show the proposed pipeline achieves 88.35%accuracy and 98.04%AUC,outperforming contemporary CNNs,AutoML approaches,and alternative graph neural networks.An ablation study indicates EfficientNet-B0 produces superior node descriptors compared with ResNet-18 and DenseNet,and that roughly five GAT layers strike a good balance between being too shallow and over-deep while avoiding oversmoothing.The method requires no data augmentation or external metadata,making it a drop-in upgrade for clinical computer-aided diagnosis systems.
基金supported by the National Natural Science Foundation of China(Grant No.:82230117).
文摘Traditional Chinese medicine(TCM)features complex compatibility mechanisms involving multicomponent,multi-target,and multi-pathway interactions.This study presents an interpretable graph artificial intelligence(GraphAI)framework to quantify such mechanisms in Chinese herbal formulas(CHFs).A multidimensional TCM knowledge graph(TCM-MKG;https://zenodo.org/records/13763953)was constructed,integrating seven standardized modules:TCM terminology,Chinese patent medicines(CPMs),Chinese herbal pieces(CHPs),pharmacognostic origins(POs),chemical compounds,biological targets,and diseases.A neighbor-diffusion strategy was used to address the sparsity of compound-target associations,increasing target coverage from 12.0%to 98.7%.Graph neural networks(GNNs)with attention mechanisms were applied to 6,080 CHFs,modeled as graphs with CHPs as nodes.To embed domain-specific semantics,virtual nodes medicinal properties,i.e.,therapeutic nature,flavor,and meridian tropism,were introduced,enabling interpretable modeling of inter-CHP relationships.The model quantitatively captured classical compatibility roles such as“monarch-minister-assistant-guide”,and uncovered TCM etiological types derived from diagnostic and efficacy patterns.Model validation using 215 CHFs used for coronavirus disease 2019(COVID-19)management highlighted Radix Astragali-Rhizoma Phragmitis as a high-attention herb pair.Mass spectrometry(MS)and target prediction identified three active compounds,i.e.,methylinissolin-3-O-glucoside,corydalin,and pingbeinine,which converge on pathways such as neuroactive ligand-receptor interaction,xenobiotic response,and neuronal function,supporting their neuroimmune and detoxification potential.Given their high safety and dietary compatibility,this herb pair may offer therapeutic value for managing long COVID-19.All data and code are openly available(https://github.com/ZENGJingqi/GraphAI-for-TCM),providing a scalable and interpretable platform for TCM mechanism research and discovery of bioactive herbal constituents.
文摘The increasing popularity of the Internet and the widespread use of information technology have led to a rise in the number and sophistication of network attacks and security threats.Intrusion detection systems are crucial to network security,playing a pivotal role in safeguarding networks from potential threats.However,in the context of an evolving landscape of sophisticated and elusive attacks,existing intrusion detection methodologies often overlook critical aspects such as changes in network topology over time and interactions between hosts.To address these issues,this paper proposes a real-time network intrusion detection method based on graph neural networks.The proposedmethod leverages the advantages of graph neural networks and employs a straightforward graph construction method to represent network traffic as dynamic graph-structured data.Additionally,a graph convolution operation with a multi-head attention mechanism is utilized to enhance the model’s ability to capture the intricate relationships within the graph structure comprehensively.Furthermore,it uses an integrated graph neural network to address dynamic graphs’structural and topological changes at different time points and the challenges of edge embedding in intrusion detection data.The edge classification problem is effectively transformed into node classification by employing a line graph data representation,which facilitates fine-grained intrusion detection tasks on dynamic graph node feature representations.The efficacy of the proposed method is evaluated using two commonly used intrusion detection datasets,UNSW-NB15 and NF-ToN-IoT-v2,and results are compared with previous studies in this field.The experimental results demonstrate that our proposed method achieves 99.3%and 99.96%accuracy on the two datasets,respectively,and outperforms the benchmark model in several evaluation metrics.
基金funded by the Youth Fund of the National Natural Science Foundation of China(Grant No.42261070).
文摘Spectrum-based fault localization (SBFL) generates a ranked list of suspicious elements by using the program execution spectrum, but the excessive number of elements ranked in parallel results in low localization accuracy. Most researchers consider intra-class dependencies to improve localization accuracy. However, some studies show that inter-class method call type faults account for more than 20%, which means such methods still have certain limitations. To solve the above problems, this paper proposes a two-phase software fault localization based on relational graph convolutional neural networks (Two-RGCNFL). Firstly, in Phase 1, the method call dependence graph (MCDG) of the program is constructed, the intra-class and inter-class dependencies in MCDG are extracted by using the relational graph convolutional neural network, and the classifier is used to identify the faulty methods. Then, the GraphSMOTE algorithm is improved to alleviate the impact of class imbalance on classification accuracy. Aiming at the problem of parallel ranking of element suspicious values in traditional SBFL technology, in Phase 2, Doc2Vec is used to learn static features, while spectrum information serves as dynamic features. A RankNet model based on siamese multi-layer perceptron is constructed to score and rank statements in the faulty method. This work conducts experiments on 5 real projects of Defects4J benchmark. Experimental results show that, compared with the traditional SBFL technique and two baseline methods, our approach improves the Top-1 accuracy by 262.86%, 29.59% and 53.01%, respectively, which verifies the effectiveness of Two-RGCNFL. Furthermore, this work verifies the importance of inter-class dependencies through ablation experiments.
基金supported by the National Natural Science Founion of China(U2241285).
文摘Accurate and efficient prediction of the distribution of surface loads on buildings subjected to explosive effects is crucial for rapidly calculating structural dynamic responses,establishing effective protective measures,and designing civil defense engineering solutions.Current state-of-the-art methods face several issues:Experimental research is difficult and costly to implement,theoretical research is limited to simple geometries and lacks precision,and direct simulations require substantial computational resources.To address these challenges,this paper presents a data-driven method for predicting blast loads on building surfaces.This approach increases both the accuracy and computational efficiency of load predictions when the geometry of the building changes while the explosive yield remains constant,significantly improving its applicability in complex scenarios.This study introduces an innovative encoder-decoder graph neural network model named BlastGraphNet,which uses a message-passing mechanism to predict the overpressure and impulse load distributions on buildings with conventional and complex geometries during explosive events.The model also facilitates related downstream applications,such as damage mode identification and rapid assessment of virtual city explosions.The calculation results indicate that the prediction error of the model for conventional building tests is less than 2%,and its inference speed is 3-4 orders of magnitude faster than that of state-of-the-art numerical methods.In extreme test cases involving buildings with complex geometries and building clusters,the method achieved high accuracy and excellent generalizability.The strong adaptability and generalizability of BlastGraphNet confirm that this novel method enables precise real-time prediction of blast loads and provides a new paradigm for damage assessment in protective engineering.
文摘The ability to accurately predict urban traffic flows is crucial for optimising city operations.Consequently,various methods for forecasting urban traffic have been developed,focusing on analysing historical data to understand complex mobility patterns.Deep learning techniques,such as graph neural networks(GNNs),are popular for their ability to capture spatio-temporal dependencies.However,these models often become overly complex due to the large number of hyper-parameters involved.In this study,we introduce Dynamic Multi-Graph Spatial-Temporal Graph Neural Ordinary Differential Equation Networks(DMST-GNODE),a framework based on ordinary differential equations(ODEs)that autonomously discovers effective spatial-temporal graph neural network(STGNN)architectures for traffic prediction tasks.The comparative analysis of DMST-GNODE and baseline models indicates that DMST-GNODE model demonstrates superior performance across multiple datasets,consistently achieving the lowest Root Mean Square Error(RMSE)and Mean Absolute Error(MAE)values,alongside the highest accuracy.On the BKK(Bangkok)dataset,it outperformed other models with an RMSE of 3.3165 and an accuracy of 0.9367 for a 20-min interval,maintaining this trend across 40 and 60 min.Similarly,on the PeMS08 dataset,DMST-GNODE achieved the best performance with an RMSE of 19.4863 and an accuracy of 0.9377 at 20 min,demonstrating its effectiveness over longer periods.The Los_Loop dataset results further emphasise this model’s advantage,with an RMSE of 3.3422 and an accuracy of 0.7643 at 20 min,consistently maintaining superiority across all time intervals.These numerical highlights indicate that DMST-GNODE not only outperforms baseline models but also achieves higher accuracy and lower errors across different time intervals and datasets.
基金supported by Macao Science and Technology Development Fund,Macao SAR,China(Grant No.:0043/2023/AFJ)the National Natural Science Foundation of China(Grant No.:22173038)Macao Polytechnic University,Macao SAR,China(Grant No.:RP/FCA-01/2022).
文摘Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.
文摘In this paper,a sparse graph neural network-aided(SGNN-aided)decoder is proposed for improving the decoding performance of polar codes under bursty interference.Firstly,a sparse factor graph is constructed using the encoding characteristic to achieve high-throughput polar decoding.To further improve the decoding performance,a residual gated bipartite graph neural network is designed for updating embedding vectors of heterogeneous nodes based on a bidirectional message passing neural network.This framework exploits gated recurrent units and residual blocks to address the gradient disappearance in deep graph recurrent neural networks.Finally,predictions are generated by feeding the embedding vectors into a readout module.Simulation results show that the proposed decoder is more robust than the existing ones in the presence of bursty interference and exhibits high universality.
基金supported by the National Natural Science Foundation of China (No. 52274048)Beijing Natural Science Foundation (No. 3222037)。
文摘With the rapid development of deep learning neural networks,new solutions have emerged for addressing fluid flow problems in porous media.Combining data-driven approaches with physical constraints has become a hot research direction,with physics-informed neural networks(PINNs) being the most popular hybrid model.PINNs have gained widespread attention in subsurface fluid flow simulations due to their low computational resource requirements,fast training speeds,strong generalization capabilities,and broad applicability.Despite success in homogeneous settings,standard PINNs face challenges in accurately calculating flux between irregular Eulerian cells with disparate properties and capturing global field influences on local cells.This limits their suitability for heterogeneous reservoirs and the irregular Eulerian grids frequently used in reservoir.To address these challenges,this study proposes a physics-informed graph neural network(PIGNN) model.The PIGNN model treats the entire field as a whole,integrating information from neighboring grids and physical laws into the solution for the target grid,thereby improving the accuracy of solving partial differential equations in heterogeneous and Eulerian irregular grids.The optimized model was applied to pressure field prediction in a spatially heterogeneous reservoir,achieving an average L_(2) error and R_(2) score of 6.710×10^(-4)and 0.998,respectively,which confirms the effectiveness of model.Compared to the conventional PINN model,the average L_(2) error was reduced by 76.93%,the average R_(2) score increased by 3.56%.Moreover,evaluating robustness,training the PIGNN model using only 54% and 76% of the original data yielded average relative L_(2) error reductions of 58.63% and 56.22%,respectively,compared to the PINN model.These results confirm the superior performance of this approach compared to PINN.
基金financial support from the National Natural Science Foundation of China(Grant Nos.71971079,72271087,and 71871088)the Major Projects of the National Social Science Foundation of China(Grant No.21ZDA114)+1 种基金the National Social Science Foundation of China(Grant No.19BTJ018)the Hunan Provincial Natural Science Foundation of China(Grant No.21JJ20019).
文摘Cryptocurrency is a remarkable financial innovation that has affected the financial system in fundamental ways.Its increasingly complex interactions with the conventional financial market make precisely forecasting its volatility increasingly challenging.To this end,we propose a novel framework based on the evolving multiscale graph neural network(EMGNN).Specifically,we embed a graph that depicts the interactions between the cryptocurrency and conventional financial markets into the predictive process.Furthermore,we employ hierarchical evolving graph structure learners to model the dynamic and scale-specific interactions.We also evaluate our framework’s robustness and discuss its interpretability by extracting the learned graph structure.The empirical results show that(i)cryptocurrency volatility is not isolated from the conventional market,and the embedded graph can provide effective information for prediction;(ii)the EMGNN-based forecasting framework generally yields outstanding and robust performance in terms of multiple volatility estimators,cryptocurrency samples,forecasting horizons,and evaluation criteria;and(iii)the graph structure in the predictive process varies over time and scales and is well captured by our framework.Overall,our work provides new insights into risk management for market participants and into policy formulation for authorities.
文摘Fault diagnosis occupies a pivotal position within the domain of machine and equipment management.Existing methods,however,often exhibit limitations in their scope of application,typically focusing on specific types of signals or faults in individual mechanical components while being constrained by data types and inherent characteristics.To address the limitations of existing methods,we propose a fault diagnosis method based on graph neural networks(GNNs)embedded with multirelationships of intrinsic mode functions(MIMF).The approach introduces a novel graph topological structure constructed from the features of intrinsic mode functions(IMFs)of monitored signals and their multirelationships.Additionally,a graph-level based fault diagnosis network model is designed to enhance feature learning capabilities for graph samples and enable flexible application across diverse signal sources and devices.Experimental validation with datasets including independent vibration signals for gear fault detection,mixed vibration signals for concurrent gear and bearing faults,and pressure signals for hydraulic cylinder leakage characterization demonstrates the model's adaptability and superior diagnostic accuracy across various types of signals and mechanical systems.
基金supported by the National Natural Science Foundation of China(62276049,61701078,61872068,and 62006038)the Natural Science Foundation of Sichuan Province(2025ZNSFSC0487)+3 种基金the Science and Technology Innovation 2030-Brain Science and Brain-Inspired Intelligence Project(2021ZD0200200)the National Key R&D Program of China(2023YFE0118600)Sichuan Province Science and Technology Support Program(2019YJ0193,2021YFG0126,2021YFG0366,and 2022YFS0180)Medico-Engineering Cooperation Funds from the University of Electronic Science and Technology of China(ZYGX2021YGLH014).
文摘Schizophrenia(SZ)stands as a severe psychiatric disorder.This study applied diffusion tensor imaging(DTI)data in conjunction with graph neural networks to distinguish SZ patients from normal controls(NCs)and showcases the superior performance of a graph neural network integrating combined fractional anisotropy and fiber number brain network features,achieving an accuracy of 73.79%in distinguishing SZ patients from NCs.Beyond mere discrimination,our study delved deeper into the advantages of utilizing white matter brain network features for identifying SZ patients through interpretable model analysis and gene expression analysis.These analyses uncovered intricate interrelationships between brain imaging markers and genetic biomarkers,providing novel insights into the neuropathological basis of SZ.In summary,our findings underscore the potential of graph neural networks applied to multimodal DTI data for enhancing SZ detection through an integrated analysis of neuroimaging and genetic features.
基金supported by the National Key R&D Program of China(2022YFA1305700 to Li J)the“Dawn”Program of Shanghai Education Commission,China(21SG33 to Li J)The National Natural Science Foundation of China(82272793 to Gao X).
文摘Objective:Prostate cancer(PCa)exhibits significant genomic differences between Western and Asian populations.This study aimed to design a predictive model applicable across diverse populations while selecting a limited set of genes suitable for clinical implementation.Methods:We utilized an integrated dataset of 1360 whole-exome and whole-genome sequences from Chinese and Western PCa cohorts to develop and evaluate the model.External validation was conducted using an independent cohort of patients.A graph neural network architecture,termed the pathway-aware multi-layered hierarchical network-Western and Asian(P-NETwa),was developed and trained on combined genomic profiles from Chinese and Western cohorts.The model employed a multilayer perceptron(MLP)to identify key signature genes from multiomics data,enabling precise prediction of PCa metastasis.Results:The model achieved an accuracy of 0.87 and an F1-score of 0.85 on Western population datasets.The application of integrated Chinese and Western population data improved the accuracy to 0.88,achieving an F1-score of 0.75.The analysis identified 18 signature genes implicated in PCa progression,including established markers(AR and TP53)and novel candidates(MUC16,MUC4,and ASB12).For clinical adoption,the model was optimized for commercially available gene panels while maintaining high classification accuracy.Additionally,a user-friendly web interface was developed to facilitate real-time prediction of primary versus metastatic status using the pre-trained P-NETwa-MLP model.Conclusion:The P-NETwa-MLP model integrates a query system that allows for efficient retrieval of prediction outcomes and associated genomic signatures via sample ID,enhancing its potential for seamless integration into clinical workflows.
基金funded by the Key Research and Development Program of Zhejiang Province No.2023C01141the Science and Technology Innovation Community Project of the Yangtze River Delta No.23002410100suported by the Open Research Fund of the State Key Laboratory of Blockchain and Data Security,Zhejiang University.
文摘Graph Neural Networks(GNNs)have demonstrated outstanding capabilities in processing graph-structured data and are increasingly being integrated into large-scale pre-trained models,such as Large Language Models(LLMs),to enhance structural reasoning,knowledge retrieval,and memory management.The expansion of their application scope imposes higher requirements on the robustness of GNNs.However,as GNNs are applied to more dynamic and heterogeneous environments,they become increasingly vulnerable to real-world perturbations.In particular,graph data frequently encounters joint adversarial perturbations that simultaneously affect both structures and features,which are significantly more challenging than isolated attacks.These disruptions,caused by incomplete data,malicious attacks,or inherent noise,pose substantial threats to the stable and reliable performance of traditional GNN models.To address this issue,this study proposes the Dual-Shield Graph Neural Network(DSGNN),a defense model that simultaneously mitigates structural and feature perturbations.DSGNN utilizes two parallel GNN channels to independently process structural noise and feature noise,and introduces an adaptive fusion mechanism that integrates information from both pathways to generate robust node representations.Theoretical analysis demonstrates that DSGNN achieves a tighter robustness boundary under joint perturbations compared to conventional single-channel methods.Experimental evaluations across Cora,CiteSeer,and Industry datasets show that DSGNN achieves the highest average classification accuracy under various adversarial settings,reaching 81.24%,71.94%,and 81.66%,respectively,outperforming GNNGuard,GCN-Jaccard,GCN-SVD,RGCN,and NoisyGNN.These results underscore the importance of multi-view perturbation decoupling in constructing resilient GNN models for real-world applications.
基金supported by the National Natural Science Foundation of China(NSFC)(61821005).
文摘Metal–organic frameworks(MOFs)hold great potential for gas separation and storage,and graph neural networks have proven to be a powerful tool for exploring material structure–property relationships and discovering new materials.Unlike traditional molecular graphs,crystal graphs require consideration of periodic invariance and modes.In addition,MOF structures such as covalent bonds,functional groups,and global structures impact adsorption performance in different ways.However,redundant atomic interactions can disrupt training accuracy,potentially leading to overfitting.In this paper,we propose a multi-scale crystal graph for describing periodic crystal structures,modeling interatomic interactions at different scales while preserving periodicity invariance.We also propose a multi-head attention crystal graph network in multi-scale graphs(MHACGN-MS),which learns structural characteristics by focusing on interatomic interactions at different scales,thereby reducing interference from redundant interactions.Using MOF adsorption for gases as an example,we demonstrate that MHACGN-MS outperforms traditional graph neural networks in predicting multi-component gas adsorption.We also visualize attention scores to validate effective learning and demonstrate the model’s interpretability.
基金supported in part by funds from the Ministry of Science and Technology(2022FY101104).
文摘Recognizing essential proteins within bacteriophages is fundamental to uncovering their replication and survival mechanisms and contributes to advances in phage-based antibacterial therapies.Despite notable progress,existing computational techniques struggle to represent the interplay between sequence-derived and structuredependent protein features.To overcome this limitation,we introduce GLM-EP,a unified framework that fuses protein language models with equivariant graph neural networks.Bymerging semantic embeddings extracted from amino acid sequences with geometry-aware graph representations,GLM-EP enables an in-depth depiction of phage proteins and enhances essential protein identification.Evaluation on diverse benchmark datasets confirms that GLM-EP surpasses conventional sequence-based and independent deep-learning methods,yielding higher F1 and AUROC outcomes.Component-wise analysis demonstrates that GCNII,EGNN,and the gated multi-head attention mechanism function in a complementary manner to encode complex molecular attributes.In summary,GLM-EP serves as a robust and efficient tool for bacteriophage genomic analysis and provides valuable methodological perspectives for the discovery of antibiotic-resistance therapeutic targets.The corresponding code repository is available at:https://github.com/MiJia-ID/GLM-EP(accessed on 01 November 2025).
基金supported by the National Natural Science Foundation of China(Nos.62176122 and 62061146002).
文摘Federated Graph Neural Networks (FedGNNs) have achieved significant success in representation learning for graph data, enabling collaborative training among multiple parties without sharing their raw graph data and solving the data isolation problem faced by centralized GNNs in data-sensitive scenarios. Despite the plethora of prior work on inference attacks against centralized GNNs, the vulnerability of FedGNNs to inference attacks has not yet been widely explored. It is still unclear whether the privacy leakage risks of centralized GNNs will also be introduced in FedGNNs. To bridge this gap, we present PIAFGNN, the first property inference attack (PIA) against FedGNNs. Compared with prior works on centralized GNNs, in PIAFGNN, the attacker can only obtain the global embedding gradient distributed by the central server. The attacker converts the task of stealing the target user’s local embeddings into a regression problem, using a regression model to generate the target graph node embeddings. By training shadow models and property classifiers, the attacker can infer the basic property information within the target graph that is of interest. Experiments on three benchmark graph datasets demonstrate that PIAFGNN achieves attack accuracy of over 70% in most cases, even approaching the attack accuracy of inference attacks against centralized GNNs in some instances, which is much higher than the attack accuracy of the random guessing method. Furthermore, we observe that common defense mechanisms cannot mitigate our attack without affecting the model’s performance on mainly classification tasks.
文摘Recently,numerous estimation issues have been solved due to the developments in data-driven artificial neural networks(ANN)and graph neural networks(GNN).The primary limitation of previous methodologies has been the dependence on data that can be structured in a grid format.However,physiological recordings often exhibit irregular and unordered patterns,posing a significant challenge in conceptualising them as matrices.As a result,GNNs which comprise interactive nodes connected by edges whose weights are defined by anatomical junctions or temporal relationships have received a lot of consideration by leveraging implicit data that exists in a biological system.Additionally,our study incorporates a structural GNN to effectively differentiate between different degrees of infection in both the left and right hemispheres of the brain.Subsequently,demographic data are included,and a multi-task learning architecture is devised,integrating classification and regression tasks.The trials used an authentic dataset,including 800 brain x-ray pictures,consisting of 560 instances classified as moderate cases and 240 instances classified as severe cases.Based on empirical evidence,our methodology demonstrates superior performance in classification,surpassing other comparison methods with a notable achievement of 92.27%in terms of area under the curve as well as a correlation coefficient of 0.62.
基金supported by the Natural Science Foundation of Shandong Province,China(Grant No.ZR2021MF049)the Joint Fund of Natural Science Foundation of Shandong Province,China(Grant Nos.ZR2022LL.Z012 and ZR2021LLZ001)the Key Research and Development Program of Shandong Province,China(Grant No.2023CXGC010901).
文摘Quantum error correction is a technique that enhances a system’s ability to combat noise by encoding logical information into additional quantum bits,which plays a key role in building practical quantum computers.The XZZX surface code,with only one stabilizer generator on each face,demonstrates significant application potential under biased noise.However,the existing minimum weight perfect matching(MWPM)algorithm has high computational complexity and lacks flexibility in large-scale systems.Therefore,this paper proposes a decoding method that combines graph neural networks(GNN)with multi-classifiers,the syndrome is transformed into an undirected graph,and the features are aggregated by convolutional layers,providing a more efficient and accurate decoding strategy.In the experiments,we evaluated the performance of the XZZX code under different biased noise conditions(bias=1,20,200)and different code distances(d=3,5,7,9,11).The experimental results show that under low bias noise(bias=1),the GNN decoder achieves a threshold of 0.18386,an improvement of approximately 19.12%compared to the MWPM decoder.Under high bias noise(bias=200),the GNN decoder reaches a threshold of 0.40542,improving by approximately 20.76%,overcoming the limitations of the conventional decoder.They demonstrate that the GNN decoding method exhibits superior performance and has broad application potential in the error correction of XZZX code.
基金supported by the Natural Science Foun-dation of Shandong Province,China(No.ZR2024QF057)the Natural Science Foundation of Jiangsu Province,China(No.BK20240937)+1 种基金the Natural Science Foundation of China(No.42276215)the China University of Mining and Technology(CUMT)Open Sharing Fund for Large-Scale Instruments and Equipment(No.DYGX-2024-86).
文摘The increasing frequency of offshore engineering activities,particularly the expansion of offshore oil transport and the rise in the number of oil platforms,has greatly increased the potential risk of marine oil spill incidents.Historically,several large oil spills have had long-term adverse effects on marine ecosystems and economic development,highlighting the importance of accurate-ly delineating and monitoring oil spill areas.In this study,graph neural network technology is introduced to implement semantic seg-mentation of SAR images,and two graph neural network models based on Graph-FCN and Graph-DeepLabV3+with the introduction of an attention mechanism are constructed and evaluated to improve the accuracy and efficiency of oil spill detection.By com-paring the Swin-Unet model,the Graph-DeepLabV3+model performs better in complex scenarios,especially in edge detail recognition.This not only provides strong technical support for marine oil spill monitoring but also provides an effective solution to deal with the potential risks brought by the increase of marine engineering activities,which is of great practical significance as it helps to safeguard the health and sustainable development of marine ecosystems and reduce the economic losses.
