Discharge summary hospital course summarisation of in patient Electronic Health Record text with clinical concept guided deep pre-trained Transformer models

Thomas Searle*, Zina Ibrahim, James Teo, Richard J.B. Dobson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 Citations (Scopus)

Abstract

Brief Hospital Course (BHC) summaries are succinct summaries of an entire hospital encounter, embedded within discharge summaries, written by senior clinicians responsible for the overall care of a patient. Methods to automatically produce summaries from inpatient documentation would be invaluable in reducing clinician manual burden of summarising documents under high time-pressure to admit and discharge patients. Automatically producing these summaries from the inpatient course, is a complex, multi-document summarisation task, as source notes are written from various perspectives (e.g. nursing, doctor, radiology), during the course of the hospitalisation. We demonstrate a range of methods for BHC summarisation demonstrating the performance of deep learning summarisation models across extractive and abstractive summarisation scenarios. We also test a novel ensemble extractive and abstractive summarisation model that incorporates a medical concept ontology (SNOMED) as a clinical guidance signal and shows superior performance in 2 real-world clinical data sets.

Original languageEnglish
Article number104358
JournalJOURNAL OF BIOMEDICAL INFORMATICS
Volume141
DOIs
Publication statusPublished - May 2023

Keywords

  • Clinical natural language processing
  • Clinical text summarisation
  • Pre-trained, deep learning, fine-tuned models for clinical summarisation

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