Tan, Wee-Ming and Teoh, Kean-Hooi and Ganggayah, Mogana and Mohd Taib, Nur Aishah and Zaini, Hana and Dhillon, Sarinder Kaur (2022) Automated generation of synoptic reports from narrative pathology reports in University Malaya Medical Centre using natural language processing. Diagnostics, 12 (4). ISSN 2075-4418, DOI https://doi.org/10.3390/diagnostics12040879.
Full text not available from this repository.Abstract
Pathology reports represent a primary source of information for cancer registries. University Malaya Medical Centre (UMMC) is a tertiary hospital responsible for training pathologists; thus narrative reporting becomes important. However, the unstructured free-text reports made the information extraction process tedious for clinical audits and data analysis-related research. This study aims to develop an automated natural language processing (NLP) algorithm to summarize the existing narrative breast pathology report from UMMC to a narrower structured synoptic pathology report with a checklist-style report template to ease the creation of pathology reports. The development of the rule-based NLP algorithm was based on the R programming language by using 593 pathology specimens from 174 patients provided by the Department of Pathology, UMMC. The pathologist provides specific keywords for data elements to define the semantic rules of the NLP. The system was evaluated by calculating the precision, recall, and F1-score. The proposed NLP algorithm achieved a micro-F1 score of 99.50% and a macro-F1 score of 98.97% on 178 specimens with 25 data elements. This achievement correlated to clinicians' needs, which could improve communication between pathologists and clinicians. The study presented here is significant, as structured data is easily minable and could generate important insights.
| Item Type: | Article |
|---|---|
| Funders: | UNSPECIFIED |
| Uncontrolled Keywords: | Pathology reporting; Synoptic reporting; Information extraction; Text mining; Natural language processing; Rule based |
| Subjects: | R Medicine |
| Divisions: | Faculty of Medicine > Surgery Department Faculty of Science > Institute of Biological Sciences |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 10 Sep 2023 03:49 |
| Last Modified: | 10 Sep 2023 03:49 |
| URI: | http://eprints.um.edu.my/id/eprint/42941 |
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