Adverse drug event detection using natural language processing: A scoping review of supervised learning methods

Abstract

To reduce adverse drug events (ADEs), hospitals need a system to support them in monitoring ADE occurrence routinely, rapidly, and at scale. Natural language processing (NLP), a computerized approach to analyze text data, has shown promising results for the purpose of ADE detection in the context of pharmacovigilance. However, a detailed qualitative assessment and critical appraisal of NLP methods for ADE detection in the context of ADE monitoring in hospitals is lacking. Therefore, we have conducted a scoping review to close this knowledge gap, and to provide directions for future research and practice. We included articles where NLP was applied to detect ADEs in clinical narratives within electronic health records of inpatients. Quantitative and qualitative data items relating to NLP methods were extracted and critically appraised. Out of 1,065 articles screened for eligibility, 29 articles met the inclusion criteria. Most frequent tasks included named entity recognition (n = 17; 58.6%) and relation extraction/classification (n = 15; 51.7%). Clinical involvement was reported in nine studies (31%). Multiple NLP modelling approaches seem suitable, with Long Short Term Memory and Conditional Random Field methods most commonly used. Although reported overall performance of the systems was high, it provides an inflated impression given a steep drop in performance when predicting the ADE entity or ADE relation class. When annotating corpora, treating an ADE as a relation between a drug and non-drug entity seems the best practice. Future research should focus on semi-automated methods to reduce the manual annotation effort, and examine implementation of the NLP methods in practice.

Fig 1. PRISMA flow diagram.

Fig 2. A framework for NLP workflow in clinical setting according to CRISP-DM reference model [18].

Fig 3

a. Number of articles published each year; search was conducted on 1^st July 2021. b. Number of articles by country of author institution.

Fig 4. Patient type studied in each article (chord diagram from circlize [61]).

Fig 5. Definition of an ADE as an entity or as a relation in the text; solid coloured rectangles represent entities and dashed line boxes over linking arrows represent relationships between entities.