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Electronic Health Records (EHRs) are digital records associated with hospitalization, diagnosis, medications and so on. Secondary use of EHRs can promote the clinical informatics applications and the development of healthcare undertaking. EHRs have the unique characteristic where the patient visits are temporally ordered but the diagnosis codes within a visit are randomly ordered. The hierarchical structure requires a multi-layer network to explore the different relational information of EHRs. In this paper, we propos