The advent of computerized medical recording systems in healthcare facilities has made data retrieval tasks easier, compared to manual recording. Nevertheless, the potential of the information contained within medical records remains largely untapped, mostly due to the time and effort required to extract data from unstructured documents. Natural Language Processing (NLP) represents a promising solution to this challenge, as it enables the use of automated text-mining tools for clinical practitioners. In this work, we present the architecture of the Virtual Dementia Institute (IVD), a consortium of sixteen Italian hospitals, using the NLP Extraction and Management Tool (NEMT), a (semi-) automated end-to-end pipeline that extracts relevant information from clinical documents and stores it in a centralized REDCap database. After defining a common Case Report Form (CRF) across the IVD hospitals, we implemented NEMT, the core of which is a Question Answering Bot (QABot) based on a modern NLP model. This QABot is fine-tuned on thousands of examples from IVD centers. Detailed descriptions of the process to define a common minimum dataset, Inter-Annotator Agreement calculated on clinical documents, and NEMT results are provided. The best QABot performance show an Exact Match score (EM) of 78.1%, a F1-score of 84.7%, a Lenient Accuracy (LAcc) of 0.834, and a Mean Reciprocal Rank (MRR) of 0.810. EM and F1 scores outperform the same metrics obtained with ChatGPTv3.5 (68.9% and 52.5%, respectively). With NEMT the IVD has been able to populate a database that will contain data from thousands of Italian patients, all screened with the same procedure. NEMT represents an efficient tool that paves the way for medical information extraction and exploitation for new research studies.
Medical Information Extraction With NLP-Powered QABots: A Real-World Scenario / Crema, C.; Verde, F.; Tiraboschi, P.; Marra, C.; Arighi, A.; Fostinelli, S.; Giuffre, G. M.; Maschio, V. P. D.; L'Abbate, F.; Solca, F.; Poletti, B.; Silani, V.; Rotondo, E.; Borracci, V.; Vimercati, R.; Crepaldi, V.; Inguscio, E.; Filippi, M.; Caso, F.; Rosati, A. M.; Quaranta, D.; Binetti, G.; Pagnoni, I.; Morreale, M.; Burgio, F.; Maserati, M. S.; Capellari, S.; Pardini, M.; Girtler, N.; Piras, F.; Piras, F.; Lalli, S.; Perdixi, E.; Lombardi, G.; Tella, S. D.; Costa, A.; Capelli, M.; Fundaro, C.; Manera, M.; Muscio, C.; Pellencin, E.; Lodi, R.; Tagliavini, F.; Redolfi, A.. - In: IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS. - ISSN 2168-2194. - 28:11(2024), pp. 6906-6917. [10.1109/JBHI.2024.3450118]
Medical Information Extraction With NLP-Powered QABots: A Real-World Scenario
Filippi M.;Piras F.;Piras F.;Lombardi G.;Costa A.;
2024-01-01
Abstract
The advent of computerized medical recording systems in healthcare facilities has made data retrieval tasks easier, compared to manual recording. Nevertheless, the potential of the information contained within medical records remains largely untapped, mostly due to the time and effort required to extract data from unstructured documents. Natural Language Processing (NLP) represents a promising solution to this challenge, as it enables the use of automated text-mining tools for clinical practitioners. In this work, we present the architecture of the Virtual Dementia Institute (IVD), a consortium of sixteen Italian hospitals, using the NLP Extraction and Management Tool (NEMT), a (semi-) automated end-to-end pipeline that extracts relevant information from clinical documents and stores it in a centralized REDCap database. After defining a common Case Report Form (CRF) across the IVD hospitals, we implemented NEMT, the core of which is a Question Answering Bot (QABot) based on a modern NLP model. This QABot is fine-tuned on thousands of examples from IVD centers. Detailed descriptions of the process to define a common minimum dataset, Inter-Annotator Agreement calculated on clinical documents, and NEMT results are provided. The best QABot performance show an Exact Match score (EM) of 78.1%, a F1-score of 84.7%, a Lenient Accuracy (LAcc) of 0.834, and a Mean Reciprocal Rank (MRR) of 0.810. EM and F1 scores outperform the same metrics obtained with ChatGPTv3.5 (68.9% and 52.5%, respectively). With NEMT the IVD has been able to populate a database that will contain data from thousands of Italian patients, all screened with the same procedure. NEMT represents an efficient tool that paves the way for medical information extraction and exploitation for new research studies.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
