preprints.org > computer science and mathematics > information systems > doi: 10.20944/preprints202309.1986.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Version 1 : Received: 27 September 2023 / Approved: 28 September 2023 / Online: 28 September 2023 (09:56:28 CEST)

Background: Although electronic health records (EHR) provide useful insights into disease patterns and patient treatment optimisation, their reliance on unstructured data presents a difficulty. Because of their narrative structure, echocardiography reports, which provide extensive pathology information for cardiovascular patients, are particularly challenging to extract and analyse. Although natural language processing (NLP) has been utilised successfully in a variety of medical fields, it is not commonly used in echocardiography analysis. Objectives: To develop an NLP-based approach for extracting and categorizing data from echocardiography reports by accurately converting continuous (e.g. LVOT VTI, AV VTI, and TR Vmax) and discrete (e.g. Regurgitation severity) outcomes in semi-structured narrative format into structured and categorized format, allowing for future research or clinical use. Methods: 135,062 Trans-Thoracic Echocardiogram (TTE) reports were derived from 146967 baseline Echocardiogram reports and split into three cohorts: Training and Validation (n = 1075), Test Dataset (n = 98) and Application Dataset (n = 133,889). The NLP system was developed and iteratively refined using medical expert knowledge. The system was used to curate a moderate-fidelity database from extractions of 133,889 reports. A hold-out validation set of 98 reports was blindly annotated and extracted by two clinicians for comparison with the NLP extraction. Agreement, discrimination, accuracy and calibration of outcome measure extractions were evaluated. Results: Continuous outcomes including LVOT VTI, AV VTI, and TR Vmax exhibited perfect inter-rater reliability using intra-class correlation scores (ICC=1.00, P< 0.05) alongside high R2 values, demonstrating an ideal alignment between the NLP system and clinicians. Good level (ICC =0.75-0.9, P<0.05) of inter-rater reliability were observed for outcomes such as LVOT Diam, Lateral MAPSE, Peak E Velocity, Lateral E' Velocity, PV Vmax, Sinuses of Valsalva, and Ascending Aorta diameters. Furthermore, the accuracy rate for discrete outcome measures was 91.38% in the confusion matrix analysis, indicating effective performance. Conclusions: The NLP-based technique yielded good results when it came to extracting and categorising data from echocardiography reports. The system demonstrated a high degree of agreement and concordance with clinician extractions. This study contributes to the effective use of semi-structured data by providing a useful tool for converting semi-structured text to structured echo report that can be used for data management. Additional validation and implementation in healthcare settings can improve data availability and support research and clinical decision-making.

electronic health records; big Data; unstructured data; echo report; echocardiography analysis; natural language processing; data extraction; validation

Computer Science and Mathematics, Information Systems

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