How can natural language processing help model informed drug development?: a review

Abstract

Objective: To summarize applications of natural language processing (NLP) in model informed drug development (MIDD) and identify potential areas of improvement.

Materials and methods: Publications found on PubMed and Google Scholar, websites and GitHub repositories for NLP libraries and models. Publications describing applications of NLP in MIDD were reviewed. The applications were stratified into 3 stages: drug discovery, clinical trials, and pharmacovigilance. Key NLP functionalities used for these applications were assessed. Programming libraries and open-source resources for the implementation of NLP functionalities in MIDD were identified.

Results: NLP has been utilized to aid various processes in drug development lifecycle such as gene-disease mapping, biomarker discovery, patient-trial matching, adverse drug events detection, etc. These applications commonly use NLP functionalities of named entity recognition, word embeddings, entity resolution, assertion status detection, relation extraction, and topic modeling. The current state-of-the-art for implementing these functionalities in MIDD applications are transformer models that utilize transfer learning for enhanced performance. Various libraries in python, R, and Java like huggingface, sparkNLP, and KoRpus as well as open-source platforms such as DisGeNet, DeepEnroll, and Transmol have enabled convenient implementation of NLP models to MIDD applications.

Discussion: Challenges such as reproducibility, explainability, fairness, limited data, limited language-support, and security need to be overcome to ensure wider adoption of NLP in MIDD landscape. There are opportunities to improve the performance of existing models and expand the use of NLP in newer areas of MIDD.

Conclusions: This review provides an overview of the potential and pitfalls of current NLP approaches in MIDD.

Keywords: NLP; deep learning; drug development; machine learning.