计算机科学
嵌入
图形
代表(政治)
节点(物理)
编码器
链接(几何体)
分子图
卷积神经网络
联想(心理学)
人工智能
自编码
数据挖掘
人工神经网络
理论计算机科学
模式识别(心理学)
法学
操作系统
哲学
工程类
政治学
认识论
政治
结构工程
计算机网络
作者
Chuanze Kang,Han Zhang,Zhuo Liu,Shenwei Huang,Yanbin Yin
摘要
In biomedical networks, molecular associations are important to understand biological processes and functions. Many computational methods, such as link prediction methods based on graph neural networks (GNNs), have been successfully applied in discovering molecular relationships with biological significance. However, it remains a challenge to explore a method that relies on representation learning of links for accurately predicting molecular associations. In this paper, we present a novel GNN based on link representation (LR-GNN) to identify potential molecular associations. LR-GNN applies a graph convolutional network (GCN)-encoder to obtain node embedding. To represent associations between molecules, we design a propagation rule that captures the node embedding of each GCN-encoder layer to construct the LR. Furthermore, the LRs of all layers are fused in output by a designed layer-wise fusing rule, which enables LR-GNN to output more accurate results. Experiments on four biomedical network data, including lncRNA-disease association, miRNA-disease association, protein-protein interaction and drug-drug interaction, show that LR-GNN outperforms state-of-the-art methods and achieves robust performance. Case studies are also presented on two datasets to verify the ability to predict unknown associations. Finally, we validate the effectiveness of the LR by visualization.
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