Graph Federated Learning(GFL)has shown great potential in privacy protection and distributed intelligence through distributed collaborative training of graph-structured data without sharing raw information.However,exi...Graph Federated Learning(GFL)has shown great potential in privacy protection and distributed intelligence through distributed collaborative training of graph-structured data without sharing raw information.However,existing GFL approaches often lack the capability for comprehensive feature extraction and adaptive optimization,particularly in non-independent and identically distributed(NON-IID)scenarios where balancing global structural understanding and local node-level detail remains a challenge.To this end,this paper proposes a novel framework called GFL-SAR(Graph Federated Collaborative Learning Framework Based on Structural Amplification and Attention Refinement),which enhances the representation learning capability of graph data through a dual-branch collaborative design.Specifically,we propose the Structural Insight Amplifier(SIA),which utilizes an improved Graph Convolutional Network(GCN)to strengthen structural awareness and improve modeling of topological patterns.In parallel,we propose the Attentive Relational Refiner(ARR),which employs an enhanced Graph Attention Network(GAT)to perform fine-grained modeling of node relationships and neighborhood features,thereby improving the expressiveness of local interactions and preserving critical contextual information.GFL-SAR effectively integrates multi-scale features from every branch via feature fusion and federated optimization,thereby addressing existing GFL limitations in structural modeling and feature representation.Experiments on standard benchmark datasets including Cora,Citeseer,Polblogs,and Cora_ML demonstrate that GFL-SAR achieves superior performance in classification accuracy,convergence speed,and robustness compared to existing methods,confirming its effectiveness and generalizability in GFL tasks.展开更多
The rapid growth of biomedical data,particularly multi-omics data including genomes,transcriptomics,proteomics,metabolomics,and epigenomics,medical research and clinical decision-making confront both new opportunities...The rapid growth of biomedical data,particularly multi-omics data including genomes,transcriptomics,proteomics,metabolomics,and epigenomics,medical research and clinical decision-making confront both new opportunities and obstacles.The huge and diversified nature of these datasets cannot always be managed using traditional data analysis methods.As a consequence,deep learning has emerged as a strong tool for analysing numerous omics data due to its ability to handle complex and non-linear relationships.This paper explores the fundamental concepts of deep learning and how they are used in multi-omics medical data mining.We demonstrate how autoencoders,variational autoencoders,multimodal models,attention mechanisms,transformers,and graph neural networks enable pattern analysis and recognition across all omics data.Deep learning has been found to be effective in illness classification,biomarker identification,gene network learning,and therapeutic efficacy prediction.We also consider critical problems like as data quality,model explainability,whether findings can be repeated,and computational power requirements.We now consider future elements of combining omics with clinical and imaging data,explainable AI,federated learning,and real-time diagnostics.Overall,this study emphasises the need of collaborating across disciplines to advance deep learning-based multi-omics research for precision medicine and comprehending complicated disorders.展开更多
This paper investigates the challenges associated with Unmanned Aerial Vehicle (UAV) collaborative search and target tracking in dynamic and unknown environments characterized by limited field of view. The primary obj...This paper investigates the challenges associated with Unmanned Aerial Vehicle (UAV) collaborative search and target tracking in dynamic and unknown environments characterized by limited field of view. The primary objective is to explore the unknown environments to locate and track targets effectively. To address this problem, we propose a novel Multi-Agent Reinforcement Learning (MARL) method based on Graph Neural Network (GNN). Firstly, a method is introduced for encoding continuous-space multi-UAV problem data into spatial graphs which establish essential relationships among agents, obstacles, and targets. Secondly, a Graph AttenTion network (GAT) model is presented, which focuses exclusively on adjacent nodes, learns attention weights adaptively and allows agents to better process information in dynamic environments. Reward functions are specifically designed to tackle exploration challenges in environments with sparse rewards. By introducing a framework that integrates centralized training and distributed execution, the advancement of models is facilitated. Simulation results show that the proposed method outperforms the existing MARL method in search rate and tracking performance with less collisions. The experiments show that the proposed method can be extended to applications with a larger number of agents, which provides a potential solution to the challenging problem of multi-UAV autonomous tracking in dynamic unknown environments.展开更多
Federated Graph Learning (FGL) enables model training without requiring each client to share local graph data, effectively breaking data silos by aggregating the training parameters from each terminal while safeguardi...Federated Graph Learning (FGL) enables model training without requiring each client to share local graph data, effectively breaking data silos by aggregating the training parameters from each terminal while safeguarding data privacy. Traditional FGL relies on a centralized server for model aggregation;however, this central server presents challenges such as a single point of failure and high communication overhead. Additionally, efficiently training a robust personalized local model for each client remains a significant objective in federated graph learning. To address these issues, we propose a decentralized Federated Graph Learning framework with efficient communication, termed Decentralized Federated Graph Learning via Surrogate Model (SD_FGL). In SD_FGL, each client is required to maintain two models: a private model and a surrogate model. The surrogate model is publicly shared and can exchange and update information directly with any client, eliminating the need for a central server and reducing communication overhead. The private model is independently trained by each client, allowing it to calculate similarity with other clients based on local data as well as information shared through the surrogate model. This enables the private model to better adjust its training strategy and selectively update its parameters. Additionally, local differential privacy is incorporated into the surrogate model training process to enhance privacy protection. Testing on three real-world graph datasets demonstrates that the proposed framework improves accuracy while achieving decentralized Federated Graph Learning with lower communication overhead and stronger privacy safeguards.展开更多
Computational analysis can accurately detect drug-gene interactions(DGIs)cost-effectively.However,transductive learning models are the hotspot to reveal the promising performance for unknown DGIs(both drugs and genes ...Computational analysis can accurately detect drug-gene interactions(DGIs)cost-effectively.However,transductive learning models are the hotspot to reveal the promising performance for unknown DGIs(both drugs and genes are present in the training model),without special attention to the unseen DGIs(both drugs and genes are absent in the training model).In view of this,this study,for the first time,proposed an inductive learning-based model for the precise identification of unseen DGIs.In our study,by integrating disease nodes to avoid data sparsity,a multi-relational drug-disease-gene(DDG)graph was constructed to achieve effective fusion of data on DDG intro-relationships and inter-actions.Following the extraction of graph features by utilizing graph embedding algorithms,our next step was the retrieval of the attributes of individual gene and drug nodes.In this way,a hybrid feature characterization was represented by integrating graph features and node attributes.Machine learning(ML)models were built,enabling the fulfillment of transductive predictions of unknown DGIs.To realize inductive learning,this study generated an innovative idea of transforming known node vectors derived from the DDG graph into representations of unseen nodes using node similarities as weights,enabling inductive predictions for the unseen DGIs.Consequently,the final model was superior to existing models,with significant improvement in predicting both external unknown and unseen DGIs.The practical feasibility of our model was further confirmed through case study and molecular docking.In summary,this study establishes an efficient data-driven approach through the proposed modeling,suggesting its value as a promising tool for accelerating drug discovery and repurposing.展开更多
Graph similarity learning aims to calculate the similarity between pairs of graphs.Existing unsupervised graph similarity learning methods based on contrastive learning encounter challenges related to random graph aug...Graph similarity learning aims to calculate the similarity between pairs of graphs.Existing unsupervised graph similarity learning methods based on contrastive learning encounter challenges related to random graph augmentation strategies,which can harm the semantic and structural information of graphs and overlook the rich structural information present in subgraphs.To address these issues,we propose a graph similarity learning model based on learnable augmentation and multi-level contrastive learning.First,to tackle the problem of random augmentation disrupting the semantics and structure of the graph,we design a learnable augmentation method to selectively choose nodes and edges within the graph.To enhance contrastive levels,we employ a biased random walk method to generate corresponding subgraphs,enriching the contrastive hierarchy.Second,to solve the issue of previous work not considering multi-level contrastive learning,we utilize graph convolutional networks to learn node representations of augmented views and the original graph and calculate the interaction information between the attribute-augmented and structure-augmented views and the original graph.The goal is to maximize node consistency between different views and learn node matching between different graphs,resulting in node-level representations for each graph.Subgraph representations are then obtained through pooling operations,and we conduct contrastive learning utilizing both node and subgraph representations.Finally,the graph similarity score is computed according to different downstream tasks.We conducted three sets of experiments across eight datasets,and the results demonstrate that the proposed model effectively mitigates the issues of random augmentation damaging the original graph’s semantics and structure,as well as the insufficiency of contrastive levels.Additionally,the model achieves the best overall performance.展开更多
Graphs have been widely used in fields ranging from chemical informatics to social network analysis.Graph-related problems become increasingly significant,with subgraph matching standing out as one of the most challen...Graphs have been widely used in fields ranging from chemical informatics to social network analysis.Graph-related problems become increasingly significant,with subgraph matching standing out as one of the most challenging tasks.The goal of subgraph matching is to find all subgraphs in the data graph that are isomorphic to the query graph.Traditional methods mostly rely on search strategies with high computational complexity and are hard to apply to large-scale real datasets.With the advent of graph neural networks(GNNs),researchers have turned to GNNs to address subgraph matching problems.However,the multi-attributed features on nodes and edges are overlooked during the learning of graphs,which causes inaccurate results in real-world scenarios.To tackle this problem,we propose a novel model called subgraph matching on multi-attributed graph network(SGMAN).SGMAN first utilizes improved line graphs to capture node and edge features.Then,SGMAN integrates GNN and contrastive learning(CL)to derive graph representation embeddings and calculate the matching matrix to represent the matching results.We conduct experiments on public datasets,and the results affirm the superior performance of our model.展开更多
Social media has significantly accelerated the rapid dissemination of information,but it also boosts propagation of fake news,posing serious challenges to public awareness and social stability.In real-world contexts,t...Social media has significantly accelerated the rapid dissemination of information,but it also boosts propagation of fake news,posing serious challenges to public awareness and social stability.In real-world contexts,the volume of trustable information far exceeds that of rumors,resulting in a class imbalance that leads models to prioritize the majority class during training.This focus diminishes the model’s ability to recognize minority class samples.Furthermore,models may experience overfitting when encountering these minority samples,further compromising their generalization capabilities.Unlike node-level classification tasks,fake news detection in social networks operates on graph-level samples,where traditional interpolation and oversampling methods struggle to effectively generate high-quality graph-level samples.This challenge complicates the identification of new instances of false information.To address this issue,this paper introduces the FHGraph(Fake News Hunting Graph)framework,which employs a generative data augmentation approach and a latent diffusion model to create graph structures that align with news communication patterns.Using the few-sample learning capabilities of large language models(LLMs),the framework generates diverse texts for minority class nodes.FHGraph comprises a hierarchical multiview graph contrastive learning module,in which two horizontal views and three vertical levels are utilized for self-supervised learning,resulting in more optimized representations.Experimental results show that FHGraph significantly outperforms state-of-the-art(SOTA)graph-level class imbalance methods and SOTA graph-level contrastive learning methods.Specifically,FHGraph has achieved a 2%increase in F1 Micro and a 2.5%increase in F1 Macro in the PHEME dataset,as well as a 3.5%improvement in F1 Micro and a 4.3%improvement in F1 Macro on RumorEval dataset.展开更多
Existing wireless networks are flooded with video data transmissions,and the demand for high-speed and low-latency video services continues to surge.This has brought with it challenges to networks in the form of conge...Existing wireless networks are flooded with video data transmissions,and the demand for high-speed and low-latency video services continues to surge.This has brought with it challenges to networks in the form of congestion as well as the need for more resources and more dedicated caching schemes.Recently,Multi-access Edge Computing(MEC)-enabled heterogeneous networks,which leverage edge caches for proximity delivery,have emerged as a promising solution to all of these problems.Designing an effective edge caching scheme is critical to its success,however,in the face of limited resources.We propose a novel Knowledge Graph(KG)-based Dueling Deep Q-Network(KG-DDQN)for cooperative caching in MEC-enabled heterogeneous networks.The KGDDQN scheme leverages a KG to uncover video relations,providing valuable insights into user preferences for the caching scheme.Specifically,the KG guides the selection of related videos as caching candidates(i.e.,actions in the DDQN),thus providing a rich reference for implementing a personalized caching scheme while also improving the decision efficiency of the DDQN.Extensive simulation results validate the convergence effectiveness of the KG-DDQN,and it also outperforms baselines regarding cache hit rate and service delay.展开更多
Recommendation systems(RSs)are crucial in personalizing user experiences in digital environments by suggesting relevant content or items.Collaborative filtering(CF)is a widely used personalization technique that lever...Recommendation systems(RSs)are crucial in personalizing user experiences in digital environments by suggesting relevant content or items.Collaborative filtering(CF)is a widely used personalization technique that leverages user-item interactions to generate recommendations.However,it struggles with challenges like the cold-start problem,scalability issues,and data sparsity.To address these limitations,we develop a Graph Convolutional Networks(GCNs)model that captures the complex network of interactions between users and items,identifying subtle patterns that traditional methods may overlook.We integrate this GCNs model into a federated learning(FL)framework,enabling themodel to learn fromdecentralized datasets.This not only significantly enhances user privacy—a significant improvement over conventionalmodels but also reassures users about the safety of their data.Additionally,by securely incorporating demographic information,our approach further personalizes recommendations and mitigates the coldstart issue without compromising user data.We validate our RSs model using the openMovieLens dataset and evaluate its performance across six key metrics:Precision,Recall,Area Under the Receiver Operating Characteristic Curve(ROC-AUC),F1 Score,Normalized Discounted Cumulative Gain(NDCG),and Mean Reciprocal Rank(MRR).The experimental results demonstrate significant enhancements in recommendation quality,underscoring that combining GCNs with CF in a federated setting provides a transformative solution for advanced recommendation systems.展开更多
The increase in population and vehicles exacerbates traffic congestion and management difficulties.Therefore,achieving accurate and efficient traffic flow prediction is crucial for urban transportation.For that reason...The increase in population and vehicles exacerbates traffic congestion and management difficulties.Therefore,achieving accurate and efficient traffic flow prediction is crucial for urban transportation.For that reason,we propose a graph federated learning-based digital twin traffic flow prediction method(GFLDT)by integrating the benefits of collaborative intelligence and computation of intelligent IoT.Specifically,we construct a digital twin network for predicting traffic flow,which is divided into client twin and global twin.Based on this,we adopt the concept of graph federated learning to learn the temporal dependence of traffic flow using local data from client twins,and the spatial dependence of traffic flow using global information from global twins.In addition,we validate on a real traffic dataset,and the results show that through collaborative training of the client twins and the global twins,GFLDT achieves accurate traffic flow prediction while protecting data security.展开更多
Container-based virtualization technology has been more widely used in edge computing environments recently due to its advantages of lighter resource occupation, faster startup capability, and better resource utilizat...Container-based virtualization technology has been more widely used in edge computing environments recently due to its advantages of lighter resource occupation, faster startup capability, and better resource utilization efficiency. To meet the diverse needs of tasks, it usually needs to instantiate multiple network functions in the form of containers interconnect various generated containers to build a Container Cluster(CC). Then CCs will be deployed on edge service nodes with relatively limited resources. However, the increasingly complex and timevarying nature of tasks brings great challenges to optimal placement of CC. This paper regards the charges for various resources occupied by providing services as revenue, the service efficiency and energy consumption as cost, thus formulates a Mixed Integer Programming(MIP) model to describe the optimal placement of CC on edge service nodes. Furthermore, an Actor-Critic based Deep Reinforcement Learning(DRL) incorporating Graph Convolutional Networks(GCN) framework named as RL-GCN is proposed to solve the optimization problem. The framework obtains an optimal placement strategy through self-learning according to the requirements and objectives of the placement of CC. Particularly, through the introduction of GCN, the features of the association relationship between multiple containers in CCs can be effectively extracted to improve the quality of placement.The experiment results show that under different scales of service nodes and task requests, the proposed method can obtain the improved system performance in terms of placement error ratio, time efficiency of solution output and cumulative system revenue compared with other representative baseline methods.展开更多
Fault sensing in wind turbine(WT)generator bearings is essential for ensuring reliability and holding down maintenance costs.Feeding raw sensor data to machine learning(ML)model often overlooks the enveloping interdep...Fault sensing in wind turbine(WT)generator bearings is essential for ensuring reliability and holding down maintenance costs.Feeding raw sensor data to machine learning(ML)model often overlooks the enveloping interdependencies between system elements.This study proposes a new hybrid method that combines the domain knowledge via knowledge graphs(KGs)and the traditional feature-based data.Incorporation of contextual relationships through construction of graph embedding methods,such as Node2Vec,can capture meaningful information,such as the relationships among key parameters(e.g.wind speed,rotor Revolutions Per Minute(RPM),and temperature)in the enriched feature representations.These node embeddings,when augmented with the original data,can be used to allow the model to learn and generalize better.As shown in results achieved on experimental data,the augmented ML model(with KG)is much better at predicting with the help of accuracy and error measure compared to traditional ML methods.Paired t-test analysis proves the statistical validity of this improvement.Moreover,graph-based feature importance increases the interpretability of the model and helps to uncover the structurally significant variables that are otherwise ignored by the common methods.The approach provides an excellent,knowledge-guided manner through which intelligent fault detection can be executed on WT systems.展开更多
Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches ofte...Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.展开更多
Recently,Network Functions Virtualization(NFV)has become a critical resource for optimizing capability utilization in the 5G/B5G era.NFV decomposes the network resource paradigm,demonstrating the efficient utilization...Recently,Network Functions Virtualization(NFV)has become a critical resource for optimizing capability utilization in the 5G/B5G era.NFV decomposes the network resource paradigm,demonstrating the efficient utilization of Network Functions(NFs)to enable configurable service priorities and resource demands.Telecommunications Service Providers(TSPs)face challenges in network utilization,as the vast amounts of data generated by the Internet of Things(IoT)overwhelm existing infrastructures.IoT applications,which generate massive volumes of diverse data and require real-time communication,contribute to bottlenecks and congestion.In this context,Multiaccess Edge Computing(MEC)is employed to support resource and priority-aware IoT applications by implementing Virtual Network Function(VNF)sequences within Service Function Chaining(SFC).This paper proposes the use of Deep Reinforcement Learning(DRL)combined with Graph Neural Networks(GNN)to enhance network processing,performance,and resource pooling capabilities.GNN facilitates feature extraction through Message-Passing Neural Network(MPNN)mechanisms.Together with DRL,Deep Q-Networks(DQN)are utilized to dynamically allocate resources based on IoT network priorities and demands.Our focus is on minimizing delay times for VNF instance execution,ensuring effective resource placement,and allocation in SFC deployments,offering flexibility to adapt to real-time changes in priority and workload.Simulation results demonstrate that our proposed scheme outperforms reference models in terms of reward,delay,delivery,service drop ratios,and average completion ratios,proving its potential for IoT applications.展开更多
With the availability of high-performance computing technology and the development of advanced numerical simulation methods, Computational Fluid Dynamics (CFD) is becoming more and more practical and efficient in engi...With the availability of high-performance computing technology and the development of advanced numerical simulation methods, Computational Fluid Dynamics (CFD) is becoming more and more practical and efficient in engineering. As one of the high-precision representative algorithms, the high-order Discontinuous Galerkin Method (DGM) has not only attracted widespread attention from scholars in the CFD research community, but also received strong development. However, when DGM is extended to high-speed aerodynamic flow field calculations, non-physical numerical Gibbs oscillations near shock waves often significantly affect the numerical accuracy and even cause calculation failure. Data driven approaches based on machine learning techniques can be used to learn the characteristics of Gibbs noise, which motivates us to use it in high-speed DG applications. To achieve this goal, labeled data need to be generated in order to train the machine learning models. This paper proposes a new method for denoising modeling of Gibbs phenomenon using a machine learning technique, the zero-shot learning strategy, to eliminate acquiring large amounts of CFD data. The model adopts a graph convolutional network combined with graph attention mechanism to learn the denoising paradigm from synthetic Gibbs noise data and generalize to DGM numerical simulation data. Numerical simulation results show that the Gibbs denoising model proposed in this paper can suppress the numerical oscillation near shock waves in the high-order DGM. Our work automates the extension of DGM to high-speed aerodynamic flow field calculations with higher generalization and lower cost.展开更多
Self-powered neutron detectors(SPNDs)play a critical role in monitoring the safety margins and overall health of reactors,directly affecting safe operation within the reactor.In this work,a novel fault identification ...Self-powered neutron detectors(SPNDs)play a critical role in monitoring the safety margins and overall health of reactors,directly affecting safe operation within the reactor.In this work,a novel fault identification method based on graph convolutional networks(GCN)and Stacking ensemble learning is proposed for SPNDs.The GCN is employed to extract the spatial neighborhood information of SPNDs at different positions,and residuals are obtained by nonlinear fitting of SPND signals.In order to completely extract the time-varying features from residual sequences,the Stacking fusion model,integrated with various algorithms,is developed and enables the identification of five conditions for SPNDs:normal,drift,bias,precision degradation,and complete failure.The results demonstrate that the integration of diverse base-learners in the GCN-Stacking model exhibits advantages over a single model as well as enhances the stability and reliability in fault identification.Additionally,the GCN-Stacking model maintains higher accuracy in identifying faults at different reactor power levels.展开更多
Graph learning is an effective manner to analyze the intrinsic properties of data.It has been widely used in the fields of dimensionality reduction and classification for data.In this paper,we focus on the graph learn...Graph learning is an effective manner to analyze the intrinsic properties of data.It has been widely used in the fields of dimensionality reduction and classification for data.In this paper,we focus on the graph learning-based dimensionality reduction for a hyperspectral image.Firstly,we review the development of graph learning and its application in a hyperspectral image.Then,we mainly discuss several representative graph methods including two manifold learning methods,two sparse graph learning methods,and two hypergraph learning methods.For manifold learning,we analyze neighborhood preserving embedding and locality preserving projections which are two classic manifold learning methods and can be transformed into the form of a graph.For sparse graph,we introduce sparsity preserving graph embedding and sparse graph-based discriminant analysis which can adaptively reveal data structure to construct a graph.For hypergraph learning,we review binary hypergraph and discriminant hyper-Laplacian projection which can represent the high-order relationship of data.展开更多
P-glycoprotein(P-gp)is a transmembrane protein widely involved in the absorption,distribution,metabolism,excretion,and toxicity(ADMET)of drugs within the human body.Accurate prediction of Pgp inhibitors and substrates...P-glycoprotein(P-gp)is a transmembrane protein widely involved in the absorption,distribution,metabolism,excretion,and toxicity(ADMET)of drugs within the human body.Accurate prediction of Pgp inhibitors and substrates is crucial for drug discovery and toxicological assessment.However,existing models rely on limited molecular information,leading to suboptimal model performance for predicting P-gp inhibitors and substrates.To overcome this challenge,we compiled an extensive dataset from public databases and literature,consisting of 5,943 P-gp inhibitors and 4,018 substrates,notable for their high quantity,quality,and structural uniqueness.In addition,we curated two external test sets to validate the model's generalization capability.Subsequently,we developed a multimodal graph contrastive learning(GCL)model for the prediction of P-gp inhibitors and substrates(MC-PGP).This framework integrates three types of features from Simplified Molecular Input Line Entry System(SMILES)sequences,molecular fingerprints,and molecular graphs using an attention-based fusion strategy to generate a unified molecular representation.Furthermore,we employed a GCL approach to enhance structural representations by aligning local and global structures.Extensive experimental results highlight the superior performance of MC-PGP,which achieves improvements in the area under the curve of receiver operating characteristic(AUC-ROC)of 9.82%and 10.62%on the external P-gp inhibitor and external P-gp substrate datasets,respectively,compared with 12 state-of-the-art methods.Furthermore,the interpretability analysis of all three molecular feature types offers comprehensive and complementary insights,demonstrating that MC-PGP effectively identifies key functional groups involved in P-gp interactions.These chemically intuitive insights provide valuable guidance for the design and optimization of drug candidates.展开更多
Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug rese...Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug research.Given the rapid and accurate characteristics of computational methods,their role in predicting drug properties is increasingly important.Although many pK_(a) prediction models currently exist,they often focus on enhancing model precision while neglecting interpretability.In this study,we present GraFpKa,a pK_(a) prediction model using graph neural networks(GNNs)and molecular finger-prints.The results show that our acidic and basic models achieved mean absolute errors(MAEs)of 0.621 and 0.402,respectively,on the test set,demonstrating good predictive performance.Notably,to improve interpretability,GraFpKa also incorporates Integrated Gradients(IGs),providing a clearer visual description of the atoms significantly affecting the pK_(a) values.The high reliability and interpretability of GraFpKa ensure accurate pKa predictions while also facilitating a deeper understanding of the relation-ship between molecular structure and pK_(a) values,making it a valuable tool in the field of pK_(a) prediction.展开更多
基金supported by National Natural Science Foundation of China(62466045)Inner Mongolia Natural Science Foundation Project(2021LHMS06003)Inner Mongolia University Basic Research Business Fee Project(114).
文摘Graph Federated Learning(GFL)has shown great potential in privacy protection and distributed intelligence through distributed collaborative training of graph-structured data without sharing raw information.However,existing GFL approaches often lack the capability for comprehensive feature extraction and adaptive optimization,particularly in non-independent and identically distributed(NON-IID)scenarios where balancing global structural understanding and local node-level detail remains a challenge.To this end,this paper proposes a novel framework called GFL-SAR(Graph Federated Collaborative Learning Framework Based on Structural Amplification and Attention Refinement),which enhances the representation learning capability of graph data through a dual-branch collaborative design.Specifically,we propose the Structural Insight Amplifier(SIA),which utilizes an improved Graph Convolutional Network(GCN)to strengthen structural awareness and improve modeling of topological patterns.In parallel,we propose the Attentive Relational Refiner(ARR),which employs an enhanced Graph Attention Network(GAT)to perform fine-grained modeling of node relationships and neighborhood features,thereby improving the expressiveness of local interactions and preserving critical contextual information.GFL-SAR effectively integrates multi-scale features from every branch via feature fusion and federated optimization,thereby addressing existing GFL limitations in structural modeling and feature representation.Experiments on standard benchmark datasets including Cora,Citeseer,Polblogs,and Cora_ML demonstrate that GFL-SAR achieves superior performance in classification accuracy,convergence speed,and robustness compared to existing methods,confirming its effectiveness and generalizability in GFL tasks.
文摘The rapid growth of biomedical data,particularly multi-omics data including genomes,transcriptomics,proteomics,metabolomics,and epigenomics,medical research and clinical decision-making confront both new opportunities and obstacles.The huge and diversified nature of these datasets cannot always be managed using traditional data analysis methods.As a consequence,deep learning has emerged as a strong tool for analysing numerous omics data due to its ability to handle complex and non-linear relationships.This paper explores the fundamental concepts of deep learning and how they are used in multi-omics medical data mining.We demonstrate how autoencoders,variational autoencoders,multimodal models,attention mechanisms,transformers,and graph neural networks enable pattern analysis and recognition across all omics data.Deep learning has been found to be effective in illness classification,biomarker identification,gene network learning,and therapeutic efficacy prediction.We also consider critical problems like as data quality,model explainability,whether findings can be repeated,and computational power requirements.We now consider future elements of combining omics with clinical and imaging data,explainable AI,federated learning,and real-time diagnostics.Overall,this study emphasises the need of collaborating across disciplines to advance deep learning-based multi-omics research for precision medicine and comprehending complicated disorders.
基金supported by the National Natural Science Foundation of China(Nos.12272104,U22B2013).
文摘This paper investigates the challenges associated with Unmanned Aerial Vehicle (UAV) collaborative search and target tracking in dynamic and unknown environments characterized by limited field of view. The primary objective is to explore the unknown environments to locate and track targets effectively. To address this problem, we propose a novel Multi-Agent Reinforcement Learning (MARL) method based on Graph Neural Network (GNN). Firstly, a method is introduced for encoding continuous-space multi-UAV problem data into spatial graphs which establish essential relationships among agents, obstacles, and targets. Secondly, a Graph AttenTion network (GAT) model is presented, which focuses exclusively on adjacent nodes, learns attention weights adaptively and allows agents to better process information in dynamic environments. Reward functions are specifically designed to tackle exploration challenges in environments with sparse rewards. By introducing a framework that integrates centralized training and distributed execution, the advancement of models is facilitated. Simulation results show that the proposed method outperforms the existing MARL method in search rate and tracking performance with less collisions. The experiments show that the proposed method can be extended to applications with a larger number of agents, which provides a potential solution to the challenging problem of multi-UAV autonomous tracking in dynamic unknown environments.
基金supported by InnerMongolia Natural Science Foundation Project(2021LHMS06003)Inner Mongolia University Basic Research Business Fee Project(114).
文摘Federated Graph Learning (FGL) enables model training without requiring each client to share local graph data, effectively breaking data silos by aggregating the training parameters from each terminal while safeguarding data privacy. Traditional FGL relies on a centralized server for model aggregation;however, this central server presents challenges such as a single point of failure and high communication overhead. Additionally, efficiently training a robust personalized local model for each client remains a significant objective in federated graph learning. To address these issues, we propose a decentralized Federated Graph Learning framework with efficient communication, termed Decentralized Federated Graph Learning via Surrogate Model (SD_FGL). In SD_FGL, each client is required to maintain two models: a private model and a surrogate model. The surrogate model is publicly shared and can exchange and update information directly with any client, eliminating the need for a central server and reducing communication overhead. The private model is independently trained by each client, allowing it to calculate similarity with other clients based on local data as well as information shared through the surrogate model. This enables the private model to better adjust its training strategy and selectively update its parameters. Additionally, local differential privacy is incorporated into the surrogate model training process to enhance privacy protection. Testing on three real-world graph datasets demonstrates that the proposed framework improves accuracy while achieving decentralized Federated Graph Learning with lower communication overhead and stronger privacy safeguards.
基金funded by the National Natural Science Foundation of China(Grant No.:22173065)the Sichuan International Science and Technology Innovation Cooperation Project,China(Grant No.:24GJHZ0431).
文摘Computational analysis can accurately detect drug-gene interactions(DGIs)cost-effectively.However,transductive learning models are the hotspot to reveal the promising performance for unknown DGIs(both drugs and genes are present in the training model),without special attention to the unseen DGIs(both drugs and genes are absent in the training model).In view of this,this study,for the first time,proposed an inductive learning-based model for the precise identification of unseen DGIs.In our study,by integrating disease nodes to avoid data sparsity,a multi-relational drug-disease-gene(DDG)graph was constructed to achieve effective fusion of data on DDG intro-relationships and inter-actions.Following the extraction of graph features by utilizing graph embedding algorithms,our next step was the retrieval of the attributes of individual gene and drug nodes.In this way,a hybrid feature characterization was represented by integrating graph features and node attributes.Machine learning(ML)models were built,enabling the fulfillment of transductive predictions of unknown DGIs.To realize inductive learning,this study generated an innovative idea of transforming known node vectors derived from the DDG graph into representations of unseen nodes using node similarities as weights,enabling inductive predictions for the unseen DGIs.Consequently,the final model was superior to existing models,with significant improvement in predicting both external unknown and unseen DGIs.The practical feasibility of our model was further confirmed through case study and molecular docking.In summary,this study establishes an efficient data-driven approach through the proposed modeling,suggesting its value as a promising tool for accelerating drug discovery and repurposing.
文摘Graph similarity learning aims to calculate the similarity between pairs of graphs.Existing unsupervised graph similarity learning methods based on contrastive learning encounter challenges related to random graph augmentation strategies,which can harm the semantic and structural information of graphs and overlook the rich structural information present in subgraphs.To address these issues,we propose a graph similarity learning model based on learnable augmentation and multi-level contrastive learning.First,to tackle the problem of random augmentation disrupting the semantics and structure of the graph,we design a learnable augmentation method to selectively choose nodes and edges within the graph.To enhance contrastive levels,we employ a biased random walk method to generate corresponding subgraphs,enriching the contrastive hierarchy.Second,to solve the issue of previous work not considering multi-level contrastive learning,we utilize graph convolutional networks to learn node representations of augmented views and the original graph and calculate the interaction information between the attribute-augmented and structure-augmented views and the original graph.The goal is to maximize node consistency between different views and learn node matching between different graphs,resulting in node-level representations for each graph.Subgraph representations are then obtained through pooling operations,and we conduct contrastive learning utilizing both node and subgraph representations.Finally,the graph similarity score is computed according to different downstream tasks.We conducted three sets of experiments across eight datasets,and the results demonstrate that the proposed model effectively mitigates the issues of random augmentation damaging the original graph’s semantics and structure,as well as the insufficiency of contrastive levels.Additionally,the model achieves the best overall performance.
文摘Graphs have been widely used in fields ranging from chemical informatics to social network analysis.Graph-related problems become increasingly significant,with subgraph matching standing out as one of the most challenging tasks.The goal of subgraph matching is to find all subgraphs in the data graph that are isomorphic to the query graph.Traditional methods mostly rely on search strategies with high computational complexity and are hard to apply to large-scale real datasets.With the advent of graph neural networks(GNNs),researchers have turned to GNNs to address subgraph matching problems.However,the multi-attributed features on nodes and edges are overlooked during the learning of graphs,which causes inaccurate results in real-world scenarios.To tackle this problem,we propose a novel model called subgraph matching on multi-attributed graph network(SGMAN).SGMAN first utilizes improved line graphs to capture node and edge features.Then,SGMAN integrates GNN and contrastive learning(CL)to derive graph representation embeddings and calculate the matching matrix to represent the matching results.We conduct experiments on public datasets,and the results affirm the superior performance of our model.
基金supported by the National Key R&D Program of China(Grant No.2022YFB3104601)the Big Data Computing Center of Southeast University.
文摘Social media has significantly accelerated the rapid dissemination of information,but it also boosts propagation of fake news,posing serious challenges to public awareness and social stability.In real-world contexts,the volume of trustable information far exceeds that of rumors,resulting in a class imbalance that leads models to prioritize the majority class during training.This focus diminishes the model’s ability to recognize minority class samples.Furthermore,models may experience overfitting when encountering these minority samples,further compromising their generalization capabilities.Unlike node-level classification tasks,fake news detection in social networks operates on graph-level samples,where traditional interpolation and oversampling methods struggle to effectively generate high-quality graph-level samples.This challenge complicates the identification of new instances of false information.To address this issue,this paper introduces the FHGraph(Fake News Hunting Graph)framework,which employs a generative data augmentation approach and a latent diffusion model to create graph structures that align with news communication patterns.Using the few-sample learning capabilities of large language models(LLMs),the framework generates diverse texts for minority class nodes.FHGraph comprises a hierarchical multiview graph contrastive learning module,in which two horizontal views and three vertical levels are utilized for self-supervised learning,resulting in more optimized representations.Experimental results show that FHGraph significantly outperforms state-of-the-art(SOTA)graph-level class imbalance methods and SOTA graph-level contrastive learning methods.Specifically,FHGraph has achieved a 2%increase in F1 Micro and a 2.5%increase in F1 Macro in the PHEME dataset,as well as a 3.5%improvement in F1 Micro and a 4.3%improvement in F1 Macro on RumorEval dataset.
基金supported by the National Natural Science Foundation of China(Nos.62201419,62372357)the Natural Science Foundation of Chongqing(CSTB2023NSCQ-LMX0032)the ISN State Key Laboratory.
文摘Existing wireless networks are flooded with video data transmissions,and the demand for high-speed and low-latency video services continues to surge.This has brought with it challenges to networks in the form of congestion as well as the need for more resources and more dedicated caching schemes.Recently,Multi-access Edge Computing(MEC)-enabled heterogeneous networks,which leverage edge caches for proximity delivery,have emerged as a promising solution to all of these problems.Designing an effective edge caching scheme is critical to its success,however,in the face of limited resources.We propose a novel Knowledge Graph(KG)-based Dueling Deep Q-Network(KG-DDQN)for cooperative caching in MEC-enabled heterogeneous networks.The KGDDQN scheme leverages a KG to uncover video relations,providing valuable insights into user preferences for the caching scheme.Specifically,the KG guides the selection of related videos as caching candidates(i.e.,actions in the DDQN),thus providing a rich reference for implementing a personalized caching scheme while also improving the decision efficiency of the DDQN.Extensive simulation results validate the convergence effectiveness of the KG-DDQN,and it also outperforms baselines regarding cache hit rate and service delay.
基金funded by Soonchunhyang University,Grant Numbers 20241422BK21 FOUR(Fostering Outstanding Universities for Research,Grant Number 5199990914048).
文摘Recommendation systems(RSs)are crucial in personalizing user experiences in digital environments by suggesting relevant content or items.Collaborative filtering(CF)is a widely used personalization technique that leverages user-item interactions to generate recommendations.However,it struggles with challenges like the cold-start problem,scalability issues,and data sparsity.To address these limitations,we develop a Graph Convolutional Networks(GCNs)model that captures the complex network of interactions between users and items,identifying subtle patterns that traditional methods may overlook.We integrate this GCNs model into a federated learning(FL)framework,enabling themodel to learn fromdecentralized datasets.This not only significantly enhances user privacy—a significant improvement over conventionalmodels but also reassures users about the safety of their data.Additionally,by securely incorporating demographic information,our approach further personalizes recommendations and mitigates the coldstart issue without compromising user data.We validate our RSs model using the openMovieLens dataset and evaluate its performance across six key metrics:Precision,Recall,Area Under the Receiver Operating Characteristic Curve(ROC-AUC),F1 Score,Normalized Discounted Cumulative Gain(NDCG),and Mean Reciprocal Rank(MRR).The experimental results demonstrate significant enhancements in recommendation quality,underscoring that combining GCNs with CF in a federated setting provides a transformative solution for advanced recommendation systems.
基金supported by the National Natural Science Foundation of China(U23A20272,U22A2069,62272146)Natural Science Foundation of Henan(252300421237).
文摘The increase in population and vehicles exacerbates traffic congestion and management difficulties.Therefore,achieving accurate and efficient traffic flow prediction is crucial for urban transportation.For that reason,we propose a graph federated learning-based digital twin traffic flow prediction method(GFLDT)by integrating the benefits of collaborative intelligence and computation of intelligent IoT.Specifically,we construct a digital twin network for predicting traffic flow,which is divided into client twin and global twin.Based on this,we adopt the concept of graph federated learning to learn the temporal dependence of traffic flow using local data from client twins,and the spatial dependence of traffic flow using global information from global twins.In addition,we validate on a real traffic dataset,and the results show that through collaborative training of the client twins and the global twins,GFLDT achieves accurate traffic flow prediction while protecting data security.
文摘Container-based virtualization technology has been more widely used in edge computing environments recently due to its advantages of lighter resource occupation, faster startup capability, and better resource utilization efficiency. To meet the diverse needs of tasks, it usually needs to instantiate multiple network functions in the form of containers interconnect various generated containers to build a Container Cluster(CC). Then CCs will be deployed on edge service nodes with relatively limited resources. However, the increasingly complex and timevarying nature of tasks brings great challenges to optimal placement of CC. This paper regards the charges for various resources occupied by providing services as revenue, the service efficiency and energy consumption as cost, thus formulates a Mixed Integer Programming(MIP) model to describe the optimal placement of CC on edge service nodes. Furthermore, an Actor-Critic based Deep Reinforcement Learning(DRL) incorporating Graph Convolutional Networks(GCN) framework named as RL-GCN is proposed to solve the optimization problem. The framework obtains an optimal placement strategy through self-learning according to the requirements and objectives of the placement of CC. Particularly, through the introduction of GCN, the features of the association relationship between multiple containers in CCs can be effectively extracted to improve the quality of placement.The experiment results show that under different scales of service nodes and task requests, the proposed method can obtain the improved system performance in terms of placement error ratio, time efficiency of solution output and cumulative system revenue compared with other representative baseline methods.
文摘Fault sensing in wind turbine(WT)generator bearings is essential for ensuring reliability and holding down maintenance costs.Feeding raw sensor data to machine learning(ML)model often overlooks the enveloping interdependencies between system elements.This study proposes a new hybrid method that combines the domain knowledge via knowledge graphs(KGs)and the traditional feature-based data.Incorporation of contextual relationships through construction of graph embedding methods,such as Node2Vec,can capture meaningful information,such as the relationships among key parameters(e.g.wind speed,rotor Revolutions Per Minute(RPM),and temperature)in the enriched feature representations.These node embeddings,when augmented with the original data,can be used to allow the model to learn and generalize better.As shown in results achieved on experimental data,the augmented ML model(with KG)is much better at predicting with the help of accuracy and error measure compared to traditional ML methods.Paired t-test analysis proves the statistical validity of this improvement.Moreover,graph-based feature importance increases the interpretability of the model and helps to uncover the structurally significant variables that are otherwise ignored by the common methods.The approach provides an excellent,knowledge-guided manner through which intelligent fault detection can be executed on WT systems.
基金supported by the National Natural Science Foundation of China(Grant No.:62101087)the China Postdoctoral Science Foundation(Grant No.:2021MD703942)+2 种基金the Chongqing Postdoctoral Research Project Special Funding,China(Grant No.:2021XM2016)the Science Foundation of Chongqing Municipal Commission of Education,China(Grant No.:KJQN202100642)the Chongqing Natural Science Foundation,China(Grant No.:cstc2021jcyj-msxmX0834).
文摘Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
基金supported by Institute of Information&Communications Technology Planning and Evaluation(IITP)grant funded by the Korean government(MSIT)(No.RS-2022-00167197,Development of Intelligent 5G/6G Infrastructure Technology for the Smart City)in part by the National Research Foundation of Korea(NRF),Ministry of Education,through the Basic Science Research Program under Grant NRF-2020R1I1A3066543+1 种基金in part by BK21 FOUR(Fostering Outstanding Universities for Research)under Grant 5199990914048in part by the Soonchunhyang University Research Fund.
文摘Recently,Network Functions Virtualization(NFV)has become a critical resource for optimizing capability utilization in the 5G/B5G era.NFV decomposes the network resource paradigm,demonstrating the efficient utilization of Network Functions(NFs)to enable configurable service priorities and resource demands.Telecommunications Service Providers(TSPs)face challenges in network utilization,as the vast amounts of data generated by the Internet of Things(IoT)overwhelm existing infrastructures.IoT applications,which generate massive volumes of diverse data and require real-time communication,contribute to bottlenecks and congestion.In this context,Multiaccess Edge Computing(MEC)is employed to support resource and priority-aware IoT applications by implementing Virtual Network Function(VNF)sequences within Service Function Chaining(SFC).This paper proposes the use of Deep Reinforcement Learning(DRL)combined with Graph Neural Networks(GNN)to enhance network processing,performance,and resource pooling capabilities.GNN facilitates feature extraction through Message-Passing Neural Network(MPNN)mechanisms.Together with DRL,Deep Q-Networks(DQN)are utilized to dynamically allocate resources based on IoT network priorities and demands.Our focus is on minimizing delay times for VNF instance execution,ensuring effective resource placement,and allocation in SFC deployments,offering flexibility to adapt to real-time changes in priority and workload.Simulation results demonstrate that our proposed scheme outperforms reference models in terms of reward,delay,delivery,service drop ratios,and average completion ratios,proving its potential for IoT applications.
基金co-supported by the Aeronautical Science Foundation of China(Nos.2018ZA52002,2019ZA052011).
文摘With the availability of high-performance computing technology and the development of advanced numerical simulation methods, Computational Fluid Dynamics (CFD) is becoming more and more practical and efficient in engineering. As one of the high-precision representative algorithms, the high-order Discontinuous Galerkin Method (DGM) has not only attracted widespread attention from scholars in the CFD research community, but also received strong development. However, when DGM is extended to high-speed aerodynamic flow field calculations, non-physical numerical Gibbs oscillations near shock waves often significantly affect the numerical accuracy and even cause calculation failure. Data driven approaches based on machine learning techniques can be used to learn the characteristics of Gibbs noise, which motivates us to use it in high-speed DG applications. To achieve this goal, labeled data need to be generated in order to train the machine learning models. This paper proposes a new method for denoising modeling of Gibbs phenomenon using a machine learning technique, the zero-shot learning strategy, to eliminate acquiring large amounts of CFD data. The model adopts a graph convolutional network combined with graph attention mechanism to learn the denoising paradigm from synthetic Gibbs noise data and generalize to DGM numerical simulation data. Numerical simulation results show that the Gibbs denoising model proposed in this paper can suppress the numerical oscillation near shock waves in the high-order DGM. Our work automates the extension of DGM to high-speed aerodynamic flow field calculations with higher generalization and lower cost.
基金the Industry-University Cooperation Project in Fujian Province University(No.2022H6020)。
文摘Self-powered neutron detectors(SPNDs)play a critical role in monitoring the safety margins and overall health of reactors,directly affecting safe operation within the reactor.In this work,a novel fault identification method based on graph convolutional networks(GCN)and Stacking ensemble learning is proposed for SPNDs.The GCN is employed to extract the spatial neighborhood information of SPNDs at different positions,and residuals are obtained by nonlinear fitting of SPND signals.In order to completely extract the time-varying features from residual sequences,the Stacking fusion model,integrated with various algorithms,is developed and enables the identification of five conditions for SPNDs:normal,drift,bias,precision degradation,and complete failure.The results demonstrate that the integration of diverse base-learners in the GCN-Stacking model exhibits advantages over a single model as well as enhances the stability and reliability in fault identification.Additionally,the GCN-Stacking model maintains higher accuracy in identifying faults at different reactor power levels.
基金This work is supported by the National Natural Science Foundation of China[grant number 61801336]the China Postdoctoral Science Foundation[grant number 2019M662717 and 2017M622521]the China Postdoctoral Program for Innovative Talent[grant number BX201700182].
文摘Graph learning is an effective manner to analyze the intrinsic properties of data.It has been widely used in the fields of dimensionality reduction and classification for data.In this paper,we focus on the graph learning-based dimensionality reduction for a hyperspectral image.Firstly,we review the development of graph learning and its application in a hyperspectral image.Then,we mainly discuss several representative graph methods including two manifold learning methods,two sparse graph learning methods,and two hypergraph learning methods.For manifold learning,we analyze neighborhood preserving embedding and locality preserving projections which are two classic manifold learning methods and can be transformed into the form of a graph.For sparse graph,we introduce sparsity preserving graph embedding and sparse graph-based discriminant analysis which can adaptively reveal data structure to construct a graph.For hypergraph learning,we review binary hypergraph and discriminant hyper-Laplacian projection which can represent the high-order relationship of data.
基金supported by the National Key Research and Development Program of China(Program No.:2022YFF1203003)the National Natural Science Foundation of China(Grant No.:82373791).
文摘P-glycoprotein(P-gp)is a transmembrane protein widely involved in the absorption,distribution,metabolism,excretion,and toxicity(ADMET)of drugs within the human body.Accurate prediction of Pgp inhibitors and substrates is crucial for drug discovery and toxicological assessment.However,existing models rely on limited molecular information,leading to suboptimal model performance for predicting P-gp inhibitors and substrates.To overcome this challenge,we compiled an extensive dataset from public databases and literature,consisting of 5,943 P-gp inhibitors and 4,018 substrates,notable for their high quantity,quality,and structural uniqueness.In addition,we curated two external test sets to validate the model's generalization capability.Subsequently,we developed a multimodal graph contrastive learning(GCL)model for the prediction of P-gp inhibitors and substrates(MC-PGP).This framework integrates three types of features from Simplified Molecular Input Line Entry System(SMILES)sequences,molecular fingerprints,and molecular graphs using an attention-based fusion strategy to generate a unified molecular representation.Furthermore,we employed a GCL approach to enhance structural representations by aligning local and global structures.Extensive experimental results highlight the superior performance of MC-PGP,which achieves improvements in the area under the curve of receiver operating characteristic(AUC-ROC)of 9.82%and 10.62%on the external P-gp inhibitor and external P-gp substrate datasets,respectively,compared with 12 state-of-the-art methods.Furthermore,the interpretability analysis of all three molecular feature types offers comprehensive and complementary insights,demonstrating that MC-PGP effectively identifies key functional groups involved in P-gp interactions.These chemically intuitive insights provide valuable guidance for the design and optimization of drug candidates.
基金upported by the National Key Research and Development Program of China(Grant No.:2023YFF1204904)the National Natural Science Foundation of China(Grant Nos.:U23A20530 and 82173746)Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism(Shanghai Municipal Education Commission,China).
文摘Negative logarithm of the acid dissociation constant(pK_(a))significantly influences the absorption,dis-tribution,metabolism,excretion,and toxicity(ADMET)properties of molecules and is a crucial indicator in drug research.Given the rapid and accurate characteristics of computational methods,their role in predicting drug properties is increasingly important.Although many pK_(a) prediction models currently exist,they often focus on enhancing model precision while neglecting interpretability.In this study,we present GraFpKa,a pK_(a) prediction model using graph neural networks(GNNs)and molecular finger-prints.The results show that our acidic and basic models achieved mean absolute errors(MAEs)of 0.621 and 0.402,respectively,on the test set,demonstrating good predictive performance.Notably,to improve interpretability,GraFpKa also incorporates Integrated Gradients(IGs),providing a clearer visual description of the atoms significantly affecting the pK_(a) values.The high reliability and interpretability of GraFpKa ensure accurate pKa predictions while also facilitating a deeper understanding of the relation-ship between molecular structure and pK_(a) values,making it a valuable tool in the field of pK_(a) prediction.
