“Note Bloat” impacts deep learning-based NLP models for clinical prediction tasks

One unintended consequence of the Electronic Health Records (EHR) implementation is the overuse of content-importing technology, such as copy-and-paste, that creates “bloated” notes containing large amounts of textual redundancy. Despite the rising interest in applying machine learning models to learn from real-patient data, it is unclear how the phenomenon of note bloat might affect the Natural Language Processing (NLP) models derived from these notes. Therefore, in this work we examine the impact of redundancy on deep learning-based NLP models, considering four clinical prediction tasks using a publicly available EHR database. We applied two deduplication methods to the hospital notes, identifying large quantities of redundancy, and found that removing the redundancy usually has little negative impact on downstream performances, and can in certain circumstances assist models to achieve significantly better results. We also showed it is possible to attack model predictions by simply adding note duplicates, causing changes of correct predictions made by trained models into wrong predictions. In conclusion, we demonstrated that EHR text redundancy substantively affects NLP models for clinical prediction tasks, showing that the awareness of clinical contexts and robust modeling methods are important to create effective and reliable NLP systems in healthcare contexts.