Natural language processing for EHR-based computational phenotyping

Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo

Research output: Contribution to journalArticlepeer-review


This article reviews recent advances in applying natural language processing (NLP) to Electronic Health Records (EHRs) for computational phenotyping. NLP-based computational phenotyping has numerous applications including diagnosis categorization, novel phenotype discovery, clinical trial screening, pharmacogenomics, drug-drug interaction (DDI) and adverse drug event (ADE) detection, as well as genome-wide and phenome-wide association studies. Significant progress has been made in algorithm development and resource construction for computational phenotyping. Among the surveyed methods, well-designed keyword search and rule-based systems often achieve good performance. However, the construction of keyword and rule lists requires significant manual effort, which is difficult to scale. Supervised machine learning models have been favored because they are capable of acquiring both classification patterns and structures from data. Recently, deep learning and unsupervised learning have received growing attention, with the former favored for its performance and the latter for its ability to find novel phenotypes. Integrating heterogeneous data sources have become increasingly important and have shown promise in improving model performance. Often better performance is achieved by combining multiple modalities of information. Despite these many advances, challenges and opportunities remain for NLP-based computational phenotyping, including better model interpretability and generalizability, and proper characterization of feature relations in clinical narratives.

Original languageEnglish (US)
JournalUnknown Journal
StatePublished - Jun 12 2018


  • Computational Phenotyping
  • Electronic Health Records
  • Machine Learning
  • Natural Language Processing

ASJC Scopus subject areas

  • General

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