Construction of Cohorts of Similar Patients From Automatic Extraction of Medical Concepts: Phenotype Extraction Study

Improving Phenotyping of Patients With Immune-Mediated Inflammatory Diseases Through Automated Processing of Discharge Summaries: Multicenter Cohort Study

BACKGROUND

Valuable insights gathered by clinicians during their inquiries and documented in textual reports are often unavailable in the structured data recorded in electronic health records (EHRs).

OBJECTIVE

This study aimed to highlight that mining unstructured textual data with natural language processing techniques complements the available structured data and enables more comprehensive patient phenotyping. A proof-of-concept for patients diagnosed with specific autoimmune diseases is presented, in which the extraction of information on laboratory tests and drug treatments is performed.

METHODS

We collected EHRs available in the clinical data warehouse of the Greater Paris University Hospitals from 2012 to 2021 for patients hospitalized and diagnosed with 1 of 4 immune-mediated inflammatory diseases: systemic lupus erythematosus, systemic sclerosis, antiphospholipid syndrome, and Takayasu arteritis. Then, we built, trained, and validated natural language processing algorithms on 103 discharge summaries selected from the cohort and annotated by a clinician. Finally, all discharge summaries in the cohort were processed with the algorithms, and the extracted data on laboratory tests and drug treatments were compared with the structured data.

RESULTS

Named entity recognition followed by normalization yielded F1-scores of 71.1 (95% CI 63.6-77.8) for the laboratory tests and 89.3 (95% CI 85.9-91.6) for the drugs. Application of the algorithms to 18,604 EHRs increased the detection of antibody results and drug treatments. For instance, among patients in the systemic lupus erythematosus cohort with positive antinuclear antibodies, the rate increased from 18.34% (752/4102) to 71.87% (2949/4102), making the results more consistent with the literature.

CONCLUSIONS

While challenges remain in standardizing laboratory tests, particularly with abbreviations, this work, based on secondary use of clinical data, demonstrates that automated processing of discharge summaries enriched the information available in structured data and facilitated more comprehensive patient profiling.

Year 2022 in Medical Natural Language Processing: Availability of Language Models as a Step in the Democratization of NLP in the Biomedical Area

OBJECTIVES

To analyse the content of publications within the medical Natural Language Processing (NLP) domain in 2022.

METHODS

Automatic and manual preselection of publications to be reviewed, and selection of the best NLP papers of the year. Analysis of the important issues.

RESULTS

Three best papers have been selected. We also propose an analysis of the content of the NLP publications in 2022, stressing on some of the topics.

CONCLUSION

The main trend in 2022 is certainly related to the availability of large language models, especially those based on Transformers, and to their use by non-NLP researchers. This leads to the democratization of the NLP methods. We also observe the renewal of interest to languages other than English, the continuation of research on information extraction and prediction, the massive use of data from social media, and the consideration of needs and interests of patients.