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

Searle, Thomas; Ibrahim, Zina; Teo, James; Dobson, Richard JB; (2023) Discharge summary hospital course summarisation of in patient Electronic Health Record text with clinical concept guided deep pre-trained Transformer models. Journal of Biomedical Informatics , 141 , Article 104358. 10.1016/j.jbi.2023.104358. Green open access

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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.

Type: Article
Title: Discharge summary hospital course summarisation of in patient Electronic Health Record text with clinical concept guided deep pre-trained Transformer models
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.jbi.2023.104358
Publisher version: https://doi.org/10.1016/j.jbi.2023.104358
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Clinical natural language processing, Clinical text summarisation, Pre-trained, deep learning, fine-tuned models for clinical summarisation
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Health Informatics
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Health Informatics > Clinical Epidemiology
URI: https://discovery.ucl.ac.uk/id/eprint/10169753
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