There are challenges for analyzing the narrative clinical notes in Electronic Health Records (EHRs) because of their unstructured nature. Mining the associations between the clinical concepts within the clinical notes can support physicians in making decisions, and provide researchers evidence about disease development and treatment. In this paper, in order to model and analyze disease and symptom relationships in the clinical notes, we present a concept association mining framework that is based on word embedding learned through neural networks. The approach is tested using 154,738 clinical notes from 500 patients, which are extracted from the Indiana University Health's Electronic Health Records system. All patients are diagnosed with more than one type of disease. The results show that this concept association mining framework can identify related diseases and symptoms. We also propose a method to visualize a patients' diseases and related symptoms in chronological order. This visualization can provide physicians an overview of the medical history of a patient and support decision making. The presented approach can also be expanded to analyze the associations of other clinical concepts, such as social history, family history, medications, etc.
Keywords: Clinical notes; Concept association mining; Electronic health records; Natural language processing; Neural networks.