Natural language processing to identify lupus nephritis phenotype in electronic health records

Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data. We developed four algorithms: a rule-based algorithm using only structured data (baseline algorithm) and three algorithms using different NLP models. The three NLP models are based on regularized logistic regression and use different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components respectively. The baseline algorithm and the best performed NLP algorithm were external validated on a dataset from Vanderbilt University Medical Center (VUMC). Our best performing NLP model incorporating features from both structured data, regular expression concepts, and mapped CUIs improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.62 vs 0.96) datasets compared to the baseline lupus nephritis algorithm.

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

The automatic development of phenotype algorithms from Electronic Health Record data with machine learning (ML) techniques is of great interest given the current practice is very time-consuming and resource intensive. The extraction of design patterns from phenotype algorithms is essential to understand their rationale and standard, with great potential to automate the development process. In this pilot study, we perform network visualization on the design patterns and their associations with phenotypes and sites. We classify design patterns using the fragments from previously annotated phenotype algorithms as the ground truth. The classification performance is used as a proxy for coherence at the attribution level. The bag-of-words representation with knowledge-based features generated a good performance in the classification task (0.79 macro-f1 scores). Good classification accuracy with simple features demonstrated the attribution coherence and the feasibility of automatic identification of design patterns. Our results point to both the feasibility and challenges of automatic identification of phenotyping design patterns, which would power the automatic development of phenotype algorithms.