Sequential Diagnosis Prediction with Transformer and Ontological Representation

Sequential diagnosis prediction on the Electronic Health Record (EHR) has been proven crucial for predictive analytics in the medical domain. EHR data, sequential records of a patient’s interactions with healthcare systems, has numerous inherent characteristics of temporality, irregularity and data insufficiency. Some recent works train healthcare predictive models by making use of sequential information in EHR data, but they are vulnerable to irregular, temporal EHR data with the states of admission/discharge from hospital, and insufficient data. To mitigate this, we propose an end-to-end robust transformer-based model called SETOR, which exploits neural ordinary differential equation to handle both irregular intervals between a patient’s visits with admitted timestamps and length of stay in each visit, to alleviate the limitation of insufficient data by integrating medical ontology, and to capture the dependencies between the patient’s visits by employing multi-layer transformer blocks. Experiments conducted on two real-world healthcare datasets show that, our sequential diagnoses prediction model SETOR not only achieves better predictive results than previous state-of-the-art approaches, irrespective of sufficient or insufficient training data, but also derives more interpretable embeddings of medical codes. The experimental codes are available at the GitHub repository
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Github repository: https://github.com/Xueping/SETOR