Volume 10, Number 1

Attention-Based Deep Learning System for Negation and Assertion Detection in Clinical Notes


Long Chen, Med Data Quest, USA


Natural language processing (NLP) has been recently used to extract clinical information from free text in Electronic Health Record (EHR). In clinical NLP one challenge is that the meaning of clinical entities is heavily affected by assertion modifiers such as negation, uncertain, hypothetical, experiencer and so on. Incorrect assertion assignment could cause inaccurate diagnosis of patients’ condition or negatively influence following study like disease modelling. Thus, high-performance clinical NLP systems which can automatically detect negation and other assertion status of given target medical findings (e.g. disease, symptom) in clinical context are highly demanded. Here in this work, we propose a deep-learning system based on word embedding and Attention-based Bidirectional Long Short-Term Memory networks (AttBiLSTM) for assertion detection in clinical notes. Unlike previous state-of-art methods which require knowledge input, our system is a knowledge poor machine learning system and can be easily extended or transferred to other domains. The evaluation of our system on public benchmarking corpora demonstrates that a knowledge poor deep-learning system can also achieve high performance for detecting negation and assertions comparing to state-of-the-art systems.


Natural language processing, Deep learning, BiLSTM, Clinical assertion, Attention