Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local an...Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local and global network information.To comprehensively consider network information,we propose DHGT-DTI,a novel deep learning-based approach for DTI prediction.Specifically,we capture the local and global structural information of the network from both neighborhood and meta-path per-spectives.In the neighborhood perspective,we employ a heterogeneous graph neural network(HGNN),which extends Graph Sample and Aggregate(GraphSAGE)to handle diverse node and edge types,effectively learning local network structures.In the meta-path perspective,we introduce a Graph Transformer with residual connections to model higher-order relationships defined by meta-paths,such as"drug-disease-drug",and use an attention mechanism to fuse information across multiple meta-paths.The learned features from these dual perspectives are synergistically integrated for DTI prediction via a matrix decomposition method.Furthermore,DHGT-DTI reconstructs not only the DTI network but also auxiliary networks to bolster prediction accuracy.Comprehensive experiments on two benchmark datasets validate the superiority of DHGT-DTI over existing baseline methods.Additionally,case studies on six drugs used to treat Parkinson's disease not only validate the practical utility of DHGT-DTI but also highlight its broader potential in accelerating drug discovery for other diseases.展开更多
Graph Neural Networks(GNNs),as a deep learning framework specifically designed for graph-structured data,have achieved deep representation learning of graph data through message passing mechanisms and have become a co...Graph Neural Networks(GNNs),as a deep learning framework specifically designed for graph-structured data,have achieved deep representation learning of graph data through message passing mechanisms and have become a core technology in the field of graph analysis.However,current reviews on GNN models are mainly focused on smaller domains,and there is a lack of systematic reviews on the classification and applications of GNN models.This review systematically synthesizes the three canonical branches of GNN,Graph Convolutional Network(GCN),Graph Attention Network(GAT),and Graph Sampling Aggregation Network(GraphSAGE),and analyzes their integration pathways from both structural and feature perspectives.Drawing on representative studies,we identify three major integration patterns:cascaded fusion,where heterogeneous modules such as Convolutional Neural Network(CNN),Long Short-Term Memory(LSTM),and GraphSAGE are sequentially combined for hierarchical feature learning;parallel fusion,where multi-branch architectures jointly encode complementary graph features;and feature-level fusion,which employs concatenation,weighted summation,or attention-based gating to adaptively merge multi-source embeddings.Through these patterns,integrated GNNs achieve enhanced expressiveness,robustness,and scalability across domains including transportation,biomedicine,and cybersecurity.展开更多
基金the National Natural Science Foundation of China(Grant Nos.:62272288,U22A2041)Fundamental Research Funds for the Central Universities,Shaanxi Normal University(Grant No.:GK202302006)the Scientific Research Fund of Hunan Provincial Education Department of China(Grant No.:22B0097).
文摘Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local and global network information.To comprehensively consider network information,we propose DHGT-DTI,a novel deep learning-based approach for DTI prediction.Specifically,we capture the local and global structural information of the network from both neighborhood and meta-path per-spectives.In the neighborhood perspective,we employ a heterogeneous graph neural network(HGNN),which extends Graph Sample and Aggregate(GraphSAGE)to handle diverse node and edge types,effectively learning local network structures.In the meta-path perspective,we introduce a Graph Transformer with residual connections to model higher-order relationships defined by meta-paths,such as"drug-disease-drug",and use an attention mechanism to fuse information across multiple meta-paths.The learned features from these dual perspectives are synergistically integrated for DTI prediction via a matrix decomposition method.Furthermore,DHGT-DTI reconstructs not only the DTI network but also auxiliary networks to bolster prediction accuracy.Comprehensive experiments on two benchmark datasets validate the superiority of DHGT-DTI over existing baseline methods.Additionally,case studies on six drugs used to treat Parkinson's disease not only validate the practical utility of DHGT-DTI but also highlight its broader potential in accelerating drug discovery for other diseases.
基金funded by Guangzhou Huashang University(2024HSZD01,HS2023JYSZH01).
文摘Graph Neural Networks(GNNs),as a deep learning framework specifically designed for graph-structured data,have achieved deep representation learning of graph data through message passing mechanisms and have become a core technology in the field of graph analysis.However,current reviews on GNN models are mainly focused on smaller domains,and there is a lack of systematic reviews on the classification and applications of GNN models.This review systematically synthesizes the three canonical branches of GNN,Graph Convolutional Network(GCN),Graph Attention Network(GAT),and Graph Sampling Aggregation Network(GraphSAGE),and analyzes their integration pathways from both structural and feature perspectives.Drawing on representative studies,we identify three major integration patterns:cascaded fusion,where heterogeneous modules such as Convolutional Neural Network(CNN),Long Short-Term Memory(LSTM),and GraphSAGE are sequentially combined for hierarchical feature learning;parallel fusion,where multi-branch architectures jointly encode complementary graph features;and feature-level fusion,which employs concatenation,weighted summation,or attention-based gating to adaptively merge multi-source embeddings.Through these patterns,integrated GNNs achieve enhanced expressiveness,robustness,and scalability across domains including transportation,biomedicine,and cybersecurity.
