Biomedical Knowledge Graph Embedding with Householder Projection (Student Abstract)

Abstract

Researchers have applied knowledge graph embedding (KGE) techniques with advanced neural network techniques, such as capsule networks, for predicting drug-drug interactions (DDIs) and achieved remarkable results. However, most ignore molecular structure and position features between drug pairs. They cannot model the biomedical field's significant relational mapping properties (RMPs,1-N, N-1, N-N) relation. To solve these problems, we innovatively propose CDHse that consists of two crucial modules: 1) Entity embedding module, we obtain position feature obtained by PubMedBERT and Convolutional Neural Network (CNN), obtain molecular structure feature with Graphic Nuaral Network (GNN), obtain entity embedding feature of drug pairs, and then incorporate these features into one synthetic feature. 2) Knowledge graph embedding module, the synthetic feature is Householder projections and then embedded in the complex vector space for training. In this paper, we have selected several advanced models for the DDIs task and performed experiments on three standard BioKG to validate the effectiveness of CDHse.