Heterogeneous Similarity Graph Neural Network on Electronic Health Records

Abstract

Mining Electronic Health Records (EHRs) becomes a promising topic because of the rich information they contain. By learning from EHRs, machine learning models can be built to help human expert to make medical decisions and thus improve healthcare quality. Recently, many models based on sequential or graph model are proposed to achieve this goal. EHRs contain multiple entities and relations, and can be viewed as a heterogeneous graph. However, previous studies ignore the heterogeneity in EHRs. On the other hand, current heterogeneous graph neural networks cannot be simply used on EHR graph because of the existence of hub nodes in it. To address this issue, we propose Heterogeneous Similarity Graph Neural Network (HSGNN) to analyze EHRs with a novel heterogeneous GNN. Our framework consists of two parts: one is a preprocessing method and the other is an end-to-end GNN. The preprocessing method normalizes edges and splits the EHR graph into multiple homogeneous graphs while each homogeneous graph contains partial information of the original EHR graph. The GNN takes all homogeneous graphs as input and fuses all of them into one graph to make prediction. Experimental results show that HSGNN outperforms other baselines in the diagnosis prediction task.