MADEx: A System for Detecting Medications, Adverse Drug Events, and Their Relations from Clinical Notes

Abstract

Introduction: Early detection of adverse drug events (ADEs) from electronic health records is an important, challenging task to support pharmacovigilance and drug safety surveillance. A well-known challenge to use clinical text for detection of ADEs is that much of the detailed information is documented in a narrative manner. Clinical natural language processing (NLP) is the key technology to extract information from unstructured clinical text. Objective: We present a machine learning-based clinical NLP system—MADEx—for detecting medications, ADEs, and their relations from clinical notes. Methods: We developed a recurrent neural network (RNN) model using a long short-term memory (LSTM) strategy for clinical name entity recognition (NER) and compared it with baseline conditional random fields (CRFs). We also developed a modified training strategy for the RNN, which outperformed the widely used early stop strategy. For relation extraction, we compared support vector machines (SVMs) and random forests on single-sentence relations and cross-sentence relations. In addition, we developed an integrated pipeline to extract entities and relations together by combining RNNs and SVMs. Results: MADEx achieved the top-three best performances (F1 score of 0.8233) for clinical NER in the 2018 Medication and Adverse Drug Events (MADE1.0) challenge. The post-challenge evaluation showed that the relation extraction module and integrated pipeline (identify entity and relation together) of MADEx are comparable with the best systems developed in this challenge. Conclusion: This study demonstrated the efficiency of deep learning methods for automatic extraction of medications, ADEs, and their relations from clinical text to support pharmacovigilance and drug safety surveillance.