Natural language processing with deep learning for medical adverse event detection from free-text medical narratives: A case study of detecting total hip replacement dislocation

Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In t...

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Veröffentlicht in:Computers in biology and medicine 2021-02, Vol.129, p.104140-104140, Article 104140
Hauptverfasser: Borjali, Alireza, Magnéli, Martin, Shin, David, Malchau, Henrik, Muratoglu, Orhun K., Varadarajan, Kartik M.
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container_title Computers in biology and medicine
container_volume 129
creator Borjali, Alireza
Magnéli, Martin
Shin, David
Malchau, Henrik
Muratoglu, Orhun K.
Varadarajan, Kartik M.
description Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate hip dislocation AE detection following primary total hip replacement from standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). On the other hand, the ICD/CPT codes of the patients who sustained a hip dislocation AE were only 75.24% accurate. We demonstrated that a DL-NLP model can be used in largescale orthopaedic registries for accurate and efficient detection of hip dislocation AEs. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This NLP model could potentially be implemented in other Epic-based EMR systems to improve AE detection, and consequently, quality of care and patient outcomes. •Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging.•We developed deep learning based natural language processing models for efficient and accurate hip dislocation AE detection.•A convolutional neural network (CNN) model achieved the best overall performance detecting hip dislocation AE.•Such a CNN model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives is challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models f
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Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate hip dislocation AE detection following primary total hip replacement from standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). On the other hand, the ICD/CPT codes of the patients who sustained a hip dislocation AE were only 75.24% accurate. We demonstrated that a DL-NLP model can be used in largescale orthopaedic registries for accurate and efficient detection of hip dislocation AEs. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This NLP model could potentially be implemented in other Epic-based EMR systems to improve AE detection, and consequently, quality of care and patient outcomes. •Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging.•We developed deep learning based natural language processing models for efficient and accurate hip dislocation AE detection.•A convolutional neural network (CNN) model achieved the best overall performance detecting hip dislocation AE.•Such a CNN model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives is challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate detection of hip dislocation AEs following primary total hip replacement using standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). In comparison, the ICD/CPT codings of the patients who sustained a hip dislocation AE were only 75.24% accurate. We showed that a DL-NLP model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This model could be implemented in other Epic-based EMR systems for AE detection to improve the quality of care and patient outcomes.</description><identifier>ISSN: 0010-4825</identifier><identifier>EISSN: 1879-0534</identifier><identifier>DOI: 10.1016/j.compbiomed.2020.104140</identifier><identifier>PMID: 33278631</identifier><language>eng</language><publisher>OXFORD: Elsevier Ltd</publisher><subject>Accuracy ; Artificial neural networks ; Biology ; Biomedical materials ; Codes ; Computer Science ; Computer Science, Interdisciplinary Applications ; Deep learning ; Electronic health records ; Electronic medical records ; Engineering ; Engineering, Biomedical ; Hip ; Hip dislocation ; Hospitals ; Joint surgery ; Language ; Learning algorithms ; Life Sciences &amp; Biomedicine ; Life Sciences &amp; Biomedicine - Other Topics ; Machine learning ; Mathematical &amp; Computational Biology ; Medical adverse event ; Model accuracy ; Narratives ; Natural language processing ; Neural networks ; Orthopedics ; Patients ; Radiology ; Science &amp; Technology ; Surgical implants ; Technology ; Terminology ; Total hip arthroplasty</subject><ispartof>Computers in biology and medicine, 2021-02, Vol.129, p.104140-104140, Article 104140</ispartof><rights>2020 Elsevier Ltd</rights><rights>Copyright © 2020 Elsevier Ltd. All rights reserved.</rights><rights>2020. Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>31</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000613926300006</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c440t-44d5652b39e33b96df650cb51a599dacffa7787d971afb5fec14cdd3993e27853</citedby><cites>FETCH-LOGICAL-c440t-44d5652b39e33b96df650cb51a599dacffa7787d971afb5fec14cdd3993e27853</cites><orcidid>0000-0003-1039-3314 ; 0000-0001-6291-5327 ; 0000-0002-7997-9543</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.proquest.com/docview/2479989447?pq-origsite=primo$$EHTML$$P50$$Gproquest$$H</linktohtml><link.rule.ids>230,314,777,781,882,3537,27905,27906,45976,64364,64366,64368,72218</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33278631$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:146020761$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Borjali, Alireza</creatorcontrib><creatorcontrib>Magnéli, Martin</creatorcontrib><creatorcontrib>Shin, David</creatorcontrib><creatorcontrib>Malchau, Henrik</creatorcontrib><creatorcontrib>Muratoglu, Orhun K.</creatorcontrib><creatorcontrib>Varadarajan, Kartik M.</creatorcontrib><title>Natural language processing with deep learning for medical adverse event detection from free-text medical narratives: A case study of detecting total hip replacement dislocation</title><title>Computers in biology and medicine</title><addtitle>COMPUT BIOL MED</addtitle><addtitle>Comput Biol Med</addtitle><description>Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate hip dislocation AE detection following primary total hip replacement from standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). On the other hand, the ICD/CPT codes of the patients who sustained a hip dislocation AE were only 75.24% accurate. We demonstrated that a DL-NLP model can be used in largescale orthopaedic registries for accurate and efficient detection of hip dislocation AEs. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This NLP model could potentially be implemented in other Epic-based EMR systems to improve AE detection, and consequently, quality of care and patient outcomes. •Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging.•We developed deep learning based natural language processing models for efficient and accurate hip dislocation AE detection.•A convolutional neural network (CNN) model achieved the best overall performance detecting hip dislocation AE.•Such a CNN model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives is challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate detection of hip dislocation AEs following primary total hip replacement using standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). In comparison, the ICD/CPT codings of the patients who sustained a hip dislocation AE were only 75.24% accurate. We showed that a DL-NLP model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This model could be implemented in other Epic-based EMR systems for AE detection to improve the quality of care and patient outcomes.</description><subject>Accuracy</subject><subject>Artificial neural networks</subject><subject>Biology</subject><subject>Biomedical materials</subject><subject>Codes</subject><subject>Computer Science</subject><subject>Computer Science, Interdisciplinary Applications</subject><subject>Deep learning</subject><subject>Electronic health records</subject><subject>Electronic medical records</subject><subject>Engineering</subject><subject>Engineering, Biomedical</subject><subject>Hip</subject><subject>Hip dislocation</subject><subject>Hospitals</subject><subject>Joint surgery</subject><subject>Language</subject><subject>Learning algorithms</subject><subject>Life Sciences &amp; Biomedicine</subject><subject>Life Sciences &amp; Biomedicine - Other Topics</subject><subject>Machine learning</subject><subject>Mathematical &amp; Computational Biology</subject><subject>Medical adverse event</subject><subject>Model accuracy</subject><subject>Narratives</subject><subject>Natural language processing</subject><subject>Neural networks</subject><subject>Orthopedics</subject><subject>Patients</subject><subject>Radiology</subject><subject>Science &amp; 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Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate hip dislocation AE detection following primary total hip replacement from standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). On the other hand, the ICD/CPT codes of the patients who sustained a hip dislocation AE were only 75.24% accurate. We demonstrated that a DL-NLP model can be used in largescale orthopaedic registries for accurate and efficient detection of hip dislocation AEs. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This NLP model could potentially be implemented in other Epic-based EMR systems to improve AE detection, and consequently, quality of care and patient outcomes. •Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives can be challenging.•We developed deep learning based natural language processing models for efficient and accurate hip dislocation AE detection.•A convolutional neural network (CNN) model achieved the best overall performance detecting hip dislocation AE.•Such a CNN model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. Accurate and timely detection of medical adverse events (AEs) from free-text medical narratives is challenging. Natural language processing (NLP) with deep learning has already shown great potential for analyzing free-text data, but its application for medical AE detection has been limited. In this study, we developed deep learning based NLP (DL-NLP) models for efficient and accurate detection of hip dislocation AEs following primary total hip replacement using standard (radiology notes) and non-standard (follow-up telephone notes) free-text medical narratives. We benchmarked these proposed models with traditional machine learning based NLP (ML-NLP) models, and also assessed the accuracy of International Classification of Diseases (ICD) and Current Procedural Terminology (CPT) codes in capturing these hip dislocation AEs in a multi-center orthopaedic registry. All DL-NLP models outperformed all of the ML-NLP models, with a convolutional neural network (CNN) model achieving the best overall performance (Kappa = 0.97 for radiology notes, and Kappa = 1.00 for follow-up telephone notes). In comparison, the ICD/CPT codings of the patients who sustained a hip dislocation AE were only 75.24% accurate. We showed that a DL-NLP model can be used in large-scale orthopaedic registries for accurate and efficient hip dislocation AE detection. The NLP model in this study was developed with data from the most frequently used electronic medical record (EMR) system in the U.S., Epic. This model could be implemented in other Epic-based EMR systems for AE detection to improve the quality of care and patient outcomes.</abstract><cop>OXFORD</cop><pub>Elsevier Ltd</pub><pmid>33278631</pmid><doi>10.1016/j.compbiomed.2020.104140</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0003-1039-3314</orcidid><orcidid>https://orcid.org/0000-0001-6291-5327</orcidid><orcidid>https://orcid.org/0000-0002-7997-9543</orcidid></addata></record>
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identifier ISSN: 0010-4825
ispartof Computers in biology and medicine, 2021-02, Vol.129, p.104140-104140, Article 104140
issn 0010-4825
1879-0534
language eng
recordid cdi_swepub_primary_oai_swepub_ki_se_466070
source Elsevier ScienceDirect Journals; ProQuest Central UK/Ireland
subjects Accuracy
Artificial neural networks
Biology
Biomedical materials
Codes
Computer Science
Computer Science, Interdisciplinary Applications
Deep learning
Electronic health records
Electronic medical records
Engineering
Engineering, Biomedical
Hip
Hip dislocation
Hospitals
Joint surgery
Language
Learning algorithms
Life Sciences & Biomedicine
Life Sciences & Biomedicine - Other Topics
Machine learning
Mathematical & Computational Biology
Medical adverse event
Model accuracy
Narratives
Natural language processing
Neural networks
Orthopedics
Patients
Radiology
Science & Technology
Surgical implants
Technology
Terminology
Total hip arthroplasty
title Natural language processing with deep learning for medical adverse event detection from free-text medical narratives: A case study of detecting total hip replacement dislocation
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