MedGCN: Medication recommendation and lab test imputation via graph convolutional networks

Chengsheng Mao, Liang Yao, Yuan Luo*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Laboratory testing and medication prescription are two of the most important routines in daily clinical practice. Developing an artificial intelligence system that can automatically make lab test imputations and medication recommendations can save costs on potentially redundant lab tests and inform physicians of a more effective prescription. We present an intelligent medical system (named MedGCN) that can automatically recommend the patients’ medications based on their incomplete lab tests, and can even accurately estimate the lab values that have not been taken. In our system, we integrate the complex relations between multiple types of medical entities with their inherent features in a heterogeneous graph. Then we model the graph to learn a distributed representation for each entity in the graph based on graph convolutional networks (GCN). By the propagation of graph convolutional networks, the entity representations can incorporate multiple types of medical information that can benefit multiple medical tasks. Moreover, we introduce a cross regularization strategy to reduce overfitting for multi-task training by the interaction between the multiple tasks. In this study, we construct a graph to associate 4 types of medical entities, i.e., patients, encounters, lab tests, and medications, and applied a graph neural network to learn node embeddings for medication recommendation and lab test imputation. we validate our MedGCN model on two real-world datasets: NMEDW and MIMIC-III. The experimental results on both datasets demonstrate that our model can outperform the state-of-the-art in both tasks. We believe that our innovative system can provide a promising and reliable way to assist physicians to make medication prescriptions and to save costs on potentially redundant lab tests.

Original languageEnglish (US)
Article number104000
JournalJournal of Biomedical Informatics
StatePublished - Mar 2022


  • Electronic health records
  • Graph convolutional networks
  • Lab test imputation
  • Medication recommendation
  • Multi-task learning

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics


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