Automated Clinical Coding:What, Why, and Where We Are?

Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019 - early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.Comment: accepted for npj Digital Medicin

Automated clinical coding:What, why, and where we are?

Funding Information: The work is supported by WellCome Trust iTPA Awards (PIII009, PIII032), Health Data Research UK National Phenomics and Text Analytics Implementation Projects, and the United Kingdom Research and Innovation (grant EP/S02431X/1), UKRI Centre for Doctoral Training in Biomedical AI at the University of Edinburgh, School of Informatics. H.D. and J.C. are supported by the Engineering and Physical Sciences Research Council (EP/V050869/1) on “ConCur: Knowledge Base Construction and Curation”. HW was supported by Medical Research Council and Health Data Research UK (MR/S004149/1, MR/S004149/2); British Council (UCL-NMU-SEU international collaboration on Artificial Intelligence in Medicine: tackling challenges of low generalisability and health inequality); National Institute for Health Research (NIHR202639); Advanced Care Research Centre at the University of Edinburgh. We thank constructive comments from Murray Bell and Janice Watson in Terminology Service in Public Health Scotland, and information provided by Allison Reid in the coding department in NHS Lothian, Paul Mitchell, Nicola Symmers, and Barry Hewit in Edinburgh Cancer Informatics, and staff in Epic Systems Corporation. Thanks for the suggestions from Dr. Emma Davidson regarding clinical research. Thanks to the discussions with Dr. Kristiina Rannikmäe regarding the research on clinical coding and with Ruohua Han regarding the social and qualitative aspects of this research. In Fig. , the icon of “Clinical Coders” was from Freepik in Flaticon, https://www.flaticon.com/free-icon/user_747376 ; the icon of “Automated Coding System” was from Free Icon Library, https://icon-library.com/png/272370.html . Funding Information: The work is supported by WellCome Trust iTPA Awards (PIII009, PIII032), Health Data Research UK National Phenomics and Text Analytics Implementation Projects, and the United Kingdom Research and Innovation (grant EP/S02431X/1), UKRI Centre for Doctoral Training in Biomedical AI at the University of Edinburgh, School of Informatics. H.D. and J.C. are supported by the Engineering and Physical Sciences Research Council (EP/V050869/1) on “ConCur: Knowledge Base Construction and Curation”. HW was supported by Medical Research Council and Health Data Research UK (MR/S004149/1, MR/S004149/2); British Council (UCL-NMU-SEU international collaboration on Artificial Intelligence in Medicine: tackling challenges of low generalisability and health inequality); National Institute for Health Research (NIHR202639); Advanced Care Research Centre at the University of Edinburgh. We thank constructive comments from Murray Bell and Janice Watson in Terminology Service in Public Health Scotland, and information provided by Allison Reid in the coding department in NHS Lothian, Paul Mitchell, Nicola Symmers, and Barry Hewit in Edinburgh Cancer Informatics, and staff in Epic Systems Corporation. Thanks for the suggestions from Dr. Emma Davidson regarding clinical research. Thanks to the discussions with Dr. Kristiina Rannikmäe regarding the research on clinical coding and with Ruohua Han regarding the social and qualitative aspects of this research. In Fig. 1 , the icon of “Clinical Coders” was from Freepik in Flaticon, https://www.flaticon.com/free-icon/user_747376 ; the icon of “Automated Coding System” was from Free Icon Library, https://icon-library.com/png/272370.html. Publisher Copyright: © 2022, The Author(s).Clinical coding is the task of transforming medical information in a patient’s health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019–early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable processof a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.Peer reviewe

Automatic Discharge Summary Generation using Neural Network Models

東京都立大学Tokyo Metropolitan University博士（情報科学）doctoral thesi

Machine learning and electronic health records

In this work, we investigate the benefits and complications of using machine learning on EHR data. We survey some recent literature and conduct experiments on real data collected from hospital EHR systems.Masteroppgave i informatikkINF399MAMN-INFMAMN-PRO

Extreme multi-label deep neural classification of Spanish health records according to the International Classification of Diseases

111 p.Este trabajo trata sobre la minería de textos clínicos, un campo del Procesamiento del Lenguaje Natural aplicado al dominio biomédico. El objetivo es automatizar la tarea de codificación médica. Los registros electrónicos de salud (EHR) son documentos que contienen información clínica sobre la salud de unpaciente. Los diagnósticos y procedimientos médicos plasmados en la Historia Clínica Electrónica están codificados con respecto a la Clasificación Internacional de Enfermedades (CIE). De hecho, la CIE es la base para identificar estadísticas de salud internacionales y el estándar para informar enfermedades y condiciones de salud. Desde la perspectiva del aprendizaje automático, el objetivo es resolver un problema extremo de clasificación de texto de múltiples etiquetas, ya que a cada registro de salud se le asignan múltiples códigos ICD de un conjunto de más de 70 000 términos de diagnóstico. Una cantidad importante de recursos se dedican a la codificación médica, una laboriosa tarea que actualmente se realiza de forma manual. Los EHR son narraciones extensas, y los codificadores médicos revisan los registros escritos por los médicos y asignan los códigos ICD correspondientes. Los textos son técnicos ya que los médicos emplean una jerga médica especializada, aunque rica en abreviaturas, acrónimos y errores ortográficos, ya que los médicos documentan los registros mientras realizan la práctica clínica real. Paraabordar la clasificación automática de registros de salud, investigamos y desarrollamos un conjunto de técnicas de clasificación de texto de aprendizaje profundo

Advancing Clinical Natural Language Processing through Knowledge-Infused Language Models

Pre-trained Language Models (PLMs) have shown remarkable success in general-domain text tasks, but their application in the clinical domain is constrained by specialized language, terminology, and a lack of in-depth understanding of scientific and medical knowledge. As the adoption of Electronic Health Records (EHRs) and intricate clinical documents continues to grow, the need for domain-adapted PLMs in healthcare research and applications becomes increasingly vital. This research proposes innovative strategies to address these challenges, integrating domain-specific knowledge into PLMs to enhance their efficacy in healthcare. Our approach includes (i) fine-tuning models with knowledge graphs and domain-specific textual data, using graph representation learning and data augmentation techniques, and (ii) directly injecting domain knowledge into PLMs through the use of adapters. By employing these methods, the study aims to improve the performance of clinical language models in tasks such as interpreting EHRs, extracting information from clinical documents, and predicting patient outcomes. The advancements achieved in this work hold the potential to significantly influence the field of clinical Natural Language Processing (NLP) and contribute to improved patient care and healthcare innovation

Automated clinical coding: what, why, and where we are?

Clinical coding is the task of transforming medical information in a patient’s health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019–early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond