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Patel PV, Davis C, Ralbovsky A, Tinoco D, Williams CYK, Slatter S, Naderalvojoud B, Rosen MJ, Hernandez-Boussard T, Rudrapatna V. Large language models outperform traditional natural language processing methods in extracting patient-reported outcomes in IBD. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.05.24313139. [PMID: 39281744 PMCID: PMC11398594 DOI: 10.1101/2024.09.05.24313139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Background and Aims Patient-reported outcomes (PROs) are vital in assessing disease activity and treatment outcomes in inflammatory bowel disease (IBD). However, manual extraction of these PROs from the free-text of clinical notes is burdensome. We aimed to improve data curation from free-text information in the electronic health record, making it more available for research and quality improvement. This study aimed to compare traditional natural language processing (tNLP) and large language models (LLMs) in extracting three IBD PROs (abdominal pain, diarrhea, fecal blood) from clinical notes across two institutions. Methods Clinic notes were annotated for each PRO using preset protocols. Models were developed and internally tested at the University of California San Francisco (UCSF), and then externally validated at Stanford University. We compared tNLP and LLM-based models on accuracy, sensitivity, specificity, positive and negative predictive value. Additionally, we conducted fairness and error assessments. Results Inter-rater reliability between annotators was >90%. On the UCSF test set (n=50), the top-performing tNLP models showcased accuracies of 92% (abdominal pain), 82% (diarrhea) and 80% (fecal blood), comparable to GPT-4, which was 96%, 88%, and 90% accurate, respectively. On external validation at Stanford (n=250), tNLP models failed to generalize (61-62% accuracy) while GPT-4 maintained accuracies >90%. PaLM-2 and GPT-4 showed similar performance. No biases were detected based on demographics or diagnosis. Conclusions LLMs are accurate and generalizable methods for extracting PROs. They maintain excellent accuracy across institutions, despite heterogeneity in note templates and authors. Widespread adoption of such tools has the potential to enhance IBD research and patient care.
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Affiliation(s)
- Perseus V Patel
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
- Division of Pediatric Gastroenterology, Stanford University School of Medicine, Palo Alto, CA
| | - Conner Davis
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA
| | - Amariel Ralbovsky
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Daniel Tinoco
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA
| | - Christopher Y K Williams
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA
| | - Shadera Slatter
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA
| | - Behzad Naderalvojoud
- Stanford Center for Biomedical Informatics Research, Department of Medicine, StanfordUniversity, Palo Alto, CA
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Stanford University School of Medicine, Palo Alto, CA
| | - Tina Hernandez-Boussard
- Stanford Center for Biomedical Informatics Research, Department of Medicine, StanfordUniversity, Palo Alto, CA
| | - Vivek Rudrapatna
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA
- Division of Gastroenterology, Department of Medicine, University of California San Francisco,San Francisco, CA
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Rojas-Carabali W, Agrawal R, Gutierrez-Sinisterra L, Baxter SL, Cifuentes-González C, Wei YC, Abisheganaden J, Kannapiran P, Wong S, Lee B, de-la-Torre A, Agrawal R. Natural Language Processing in medicine and ophthalmology: A review for the 21st-century clinician. Asia Pac J Ophthalmol (Phila) 2024; 13:100084. [PMID: 39059557 DOI: 10.1016/j.apjo.2024.100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Natural Language Processing (NLP) is a subfield of artificial intelligence that focuses on the interaction between computers and human language, enabling computers to understand, generate, and derive meaning from human language. NLP's potential applications in the medical field are extensive and vary from extracting data from Electronic Health Records -one of its most well-known and frequently exploited uses- to investigating relationships among genetics, biomarkers, drugs, and diseases for the proposal of new medications. NLP can be useful for clinical decision support, patient monitoring, or medical image analysis. Despite its vast potential, the real-world application of NLP is still limited due to various challenges and constraints, meaning that its evolution predominantly continues within the research domain. However, with the increasingly widespread use of NLP, particularly with the availability of large language models, such as ChatGPT, it is crucial for medical professionals to be aware of the status, uses, and limitations of these technologies.
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Affiliation(s)
- William Rojas-Carabali
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Tan Tock Seng Hospital, National Healthcare Group Eye Institute, Singapore
| | - Rajdeep Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Sally L Baxter
- Division of Ophthalmology Informatics and Data Science, Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Carlos Cifuentes-González
- Neuroscience Research Group (NEUROS), Neurovitae Center for Neuroscience, Institute of Translational Medicine (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Yap Chun Wei
- Health Services and Outcomes Research, National Healthcare Group, Singapore
| | - John Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Health Services and Outcomes Research, National Healthcare Group, Singapore; Department of Respiratory Medicine, Tan Tock Seng Hospital, Singapore
| | | | - Sunny Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Bernett Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Alejandra de-la-Torre
- Neuroscience Research Group (NEUROS), Neurovitae Center for Neuroscience, Institute of Translational Medicine (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Rupesh Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Tan Tock Seng Hospital, National Healthcare Group Eye Institute, Singapore; Singapore Eye Research Institute, Singapore; Duke NUS Medical School, National University of Singapore, Singapore.
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Pinton P. Impact of artificial intelligence on prognosis, shared decision-making, and precision medicine for patients with inflammatory bowel disease: a perspective and expert opinion. Ann Med 2024; 55:2300670. [PMID: 38163336 PMCID: PMC10763920 DOI: 10.1080/07853890.2023.2300670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION Artificial intelligence (AI) is expected to impact all facets of inflammatory bowel disease (IBD) management, including disease assessment, treatment decisions, discovery and development of new biomarkers and therapeutics, as well as clinician-patient communication. AREAS COVERED This perspective paper provides an overview of the application of AI in the clinical management of IBD through a review of the currently available AI models that could be potential tools for prognosis, shared decision-making, and precision medicine. This overview covers models that measure treatment response based on statistical or machine-learning methods, or a combination of the two. We briefly discuss a computational model that allows integration of immune/biological system knowledge with mathematical modeling and also involves a 'digital twin', which allows measurement of temporal trends in mucosal inflammatory activity for predicting treatment response. A viewpoint on AI-enabled wearables and nearables and their use to improve IBD management is also included. EXPERT OPINION Although challenges regarding data quality, privacy, and security; ethical concerns; technical limitations; and regulatory barriers remain to be fully addressed, a growing body of evidence suggests a tremendous potential for integration of AI into daily clinical practice to enable precision medicine and shared decision-making.
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Affiliation(s)
- Philippe Pinton
- Clinical and Translational Sciences, Ferring Pharmaceuticals, Kastrup, Denmark
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4
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Ferro Desideri L, Roth J, Zinkernagel M, Anguita R. "Application and accuracy of artificial intelligence-derived large language models in patients with age related macular degeneration". Int J Retina Vitreous 2023; 9:71. [PMID: 37980501 PMCID: PMC10657493 DOI: 10.1186/s40942-023-00511-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023] Open
Abstract
INTRODUCTION Age-related macular degeneration (AMD) affects millions of people globally, leading to a surge in online research of putative diagnoses, causing potential misinformation and anxiety in patients and their parents. This study explores the efficacy of artificial intelligence-derived large language models (LLMs) like in addressing AMD patients' questions. METHODS ChatGPT 3.5 (2023), Bing AI (2023), and Google Bard (2023) were adopted as LLMs. Patients' questions were subdivided in two question categories, (a) general medical advice and (b) pre- and post-intravitreal injection advice and classified as (1) accurate and sufficient (2) partially accurate but sufficient and (3) inaccurate and not sufficient. Non-parametric test has been done to compare the means between the 3 LLMs scores and also an analysis of variance and reliability tests were performed among the 3 groups. RESULTS In category a) of questions, the average score was 1.20 (± 0.41) with ChatGPT 3.5, 1.60 (± 0.63) with Bing AI and 1.60 (± 0.73) with Google Bard, showing no significant differences among the 3 groups (p = 0.129). The average score in category b was 1.07 (± 0.27) with ChatGPT 3.5, 1.69 (± 0.63) with Bing AI and 1.38 (± 0.63) with Google Bard, showing a significant difference among the 3 groups (p = 0.0042). Reliability statistics showed Chronbach's α of 0.237 (range 0.448, 0.096-0.544). CONCLUSION ChatGPT 3.5 consistently offered the most accurate and satisfactory responses, particularly with technical queries. While LLMs displayed promise in providing precise information about AMD; however, further improvements are needed especially in more technical questions.
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Affiliation(s)
- Lorenzo Ferro Desideri
- Department of Ophthalmology, Inselspital, University Hospital of Bern, Bern, Switzerland.
- Bern Photographic Reading Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
| | - Janice Roth
- Department of Ophthalmology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Martin Zinkernagel
- Department of Ophthalmology, Inselspital, University Hospital of Bern, Bern, Switzerland
- Bern Photographic Reading Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Rodrigo Anguita
- Department of Ophthalmology, Inselspital, University Hospital of Bern, Bern, Switzerland
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, EC1V 2PD, UK
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5
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Griffin AC, Khairat S, Bailey SC, Chung AE. A chatbot for hypertension self-management support: user-centered design, development, and usability testing. JAMIA Open 2023; 6:ooad073. [PMID: 37693367 PMCID: PMC10491950 DOI: 10.1093/jamiaopen/ooad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/02/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023] Open
Abstract
Objectives Health-related chatbots have demonstrated early promise for improving self-management behaviors but have seldomly been utilized for hypertension. This research focused on the design, development, and usability evaluation of a chatbot for hypertension self-management, called "Medicagent." Materials and Methods A user-centered design process was used to iteratively design and develop a text-based chatbot using Google Cloud's Dialogflow natural language understanding platform. Then, usability testing sessions were conducted among patients with hypertension. Each session was comprised of: (1) background questionnaires, (2) 10 representative tasks within Medicagent, (3) System Usability Scale (SUS) questionnaire, and (4) a brief semi-structured interview. Sessions were video and audio recorded using Zoom. Qualitative and quantitative analyses were used to assess effectiveness, efficiency, and satisfaction of the chatbot. Results Participants (n = 10) completed nearly all tasks (98%, 98/100) and spent an average of 18 min (SD = 10 min) interacting with Medicagent. Only 11 (8.6%) utterances were not successfully mapped to an intent. Medicagent achieved a mean SUS score of 78.8/100, which demonstrated acceptable usability. Several participants had difficulties navigating the conversational interface without menu and back buttons, felt additional information would be useful for redirection when utterances were not recognized, and desired a health professional persona within the chatbot. Discussion The text-based chatbot was viewed favorably for assisting with blood pressure and medication-related tasks and had good usability. Conclusion Flexibility of interaction styles, handling unrecognized utterances gracefully, and having a credible persona were highlighted as design components that may further enrich the user experience of chatbots for hypertension self-management.
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Affiliation(s)
- Ashley C Griffin
- VA Palo Alto Health Care System, Palo Alto, CA 94025, United States
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Saif Khairat
- Carolina Health Informatics Program, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC 27599, United States
- School of Nursing, UNC, Chapel Hill, NC 27599, United States
| | - Stacy C Bailey
- Division of General Internal Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Arlene E Chung
- Department of Biostatistics & Bioinformatics, Duke School of Medicine, Durham, NC 27710, United States
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Thaxton C, Dardik A. Computer Science meets Vascular Surgery: Keeping a pulse on artificial intelligence. Semin Vasc Surg 2023; 36:419-425. [PMID: 37863614 PMCID: PMC10589450 DOI: 10.1053/j.semvascsurg.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/24/2023] [Indexed: 10/22/2023]
Abstract
Artificial intelligence (AI)-based technologies have garnered interest across a range of disciplines in the past several years, with an even more recent interest in various health care fields, including Vascular Surgery. AI offers a unique ability to analyze health data more quickly and efficiently than could be done by humans alone and can be used for clinical applications such as diagnosis, risk stratification, and follow-up, as well as patient-used applications to improve both patient and provider experiences, mitigate health care disparities, and individualize treatment. As with all novel technologies, AI is not without its risks and carries with it unique ethical considerations that will need to be addressed before its broad integration into health care systems. AI has the potential to revolutionize the way care is provided to patients, including those requiring vascular care.
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Affiliation(s)
- Carly Thaxton
- Department of Surgery, Yale School of Medicine, 10 Amistad Street, Room 437, New Haven, CT 06519; The Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT
| | - Alan Dardik
- Department of Surgery, Yale School of Medicine, 10 Amistad Street, Room 437, New Haven, CT 06519; The Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT.
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7
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Patil NS, Huang RS, van der Pol CB, Larocque N. Comparative Performance of ChatGPT and Bard in a Text-Based Radiology Knowledge Assessment. Can Assoc Radiol J 2023:8465371231193716. [PMID: 37578849 DOI: 10.1177/08465371231193716] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
PURPOSE Bard by Google, a direct competitor to ChatGPT, was recently released. Understanding the relative performance of these different chatbots can provide important insight into their strengths and weaknesses as well as which roles they are most suited to fill. In this project, we aimed to compare the most recent version of ChatGPT, ChatGPT-4, and Bard by Google, in their ability to accurately respond to radiology board examination practice questions. METHODS Text-based questions were collected from the 2017-2021 American College of Radiology's Diagnostic Radiology In-Training (DXIT) examinations. ChatGPT-4 and Bard were queried, and their comparative accuracies, response lengths, and response times were documented. Subspecialty-specific performance was analyzed as well. RESULTS 318 questions were included in our analysis. ChatGPT answered significantly more accurately than Bard (87.11% vs 70.44%, P < .0001). ChatGPT's response length was significantly shorter than Bard's (935.28 ± 440.88 characters vs 1437.52 ± 415.91 characters, P < .0001). ChatGPT's response time was significantly longer than Bard's (26.79 ± 3.27 seconds vs 7.55 ± 1.88 seconds, P < .0001). ChatGPT performed superiorly to Bard in neuroradiology, (100.00% vs 86.21%, P = .03), general & physics (85.39% vs 68.54%, P < .001), nuclear medicine (80.00% vs 56.67%, P < .01), pediatric radiology (93.75% vs 68.75%, P = .03), and ultrasound (100.00% vs 63.64%, P < .001). In the remaining subspecialties, there were no significant differences between ChatGPT and Bard's performance. CONCLUSION ChatGPT displayed superior radiology knowledge compared to Bard. While both chatbots display reasonable radiology knowledge, they should be used with conscious knowledge of their limitations and fallibility. Both chatbots provided incorrect or illogical answer explanations and did not always address the educational content of the question.
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Affiliation(s)
- Nikhil S Patil
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Ryan S Huang
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Christian B van der Pol
- Department of Diagnostic Imaging, Hamilton Health Sciences, Juravinski Hospital and Cancer Centre, Hamilton, ON, Canada
| | - Natasha Larocque
- Department of Radiology, McMaster University, Hamilton, ON, Canada
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Feldman K, Nehme F. Beyond Clinical Accuracy: Considerations for the Use of Generative Artificial Intelligence Models in Gastrointestinal Care. Gastroenterology 2023; 165:336-338. [PMID: 37321355 DOI: 10.1053/j.gastro.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Keith Feldman
- Division of Health Services and Outcomes Research, Children's Mercy Kansas City, Kansas City, Missouri; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Fredy Nehme
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana.
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Chua JYX, Choolani M, Chee CYI, Chan YH, Lalor JG, Chong YS, Shorey S. Insights of Parents and Parents-To-Be in Using Chatbots to Improve Their Preconception, Pregnancy, and Postpartum Health: A Mixed Studies Review. J Midwifery Womens Health 2023; 68:480-489. [PMID: 36734375 DOI: 10.1111/jmwh.13472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Chatbots, which are also known as conversational or virtual agents, are digital programs that can interact with humans using voice, text, or animation. They have shown promise in providing preconception, pregnancy, and postpartum care. This review aims to consolidate the insights of parents and parents-to-be in using chatbots to improve their preconception, pregnancy, and postpartum health. METHODS Seven electronic databases were searched from their inception dates until April 2022 (PubMed, Embase, CINAHL, PsycINFO, Web of Science, Scopus, and ProQuest Dissertations and Theses Global) for relevant studies. English language primary studies that were conducted on parents or parents-to-be aged ≥18 years old who had undergone interventions involving the use of any type of chatbot were included in this review. The quality of included studies was appraised using the Mixed Methods Appraisal Tool. A convergent qualitative synthesis design for mixed studies reviews was used to synthesize the findings, and results were thematically analyzed. RESULTS Fifteen studies met the inclusion criteria: quantitative (n = 11), qualitative (n = 1), and mixed method (n = 3). Three main themes were identified: (1) welcoming a new health resource, (2) obstacles blocking the way, and (3) moving toward a digital health era. DISCUSSION Parents and parents-to-be appreciated the informational, socioemotional, and psychological support provided by chatbots. Recommendations for technological improvements in the functionality of the chatbots were made that include training sessions for health care providers to familiarize them with this new digital technology. Multidisciplinary chatbot development teams could also be established to develop more comprehensive chatbot-delivered health programs for more diverse populations.
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Affiliation(s)
- Joelle Yan Xin Chua
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | | | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Yap Seng Chong
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Shefaly Shorey
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Padoan A, Musso G, Contran N, Basso D. Inflammation, Autoinflammation and Autoimmunity in Inflammatory Bowel Diseases. Curr Issues Mol Biol 2023; 45:5534-5557. [PMID: 37504266 PMCID: PMC10378236 DOI: 10.3390/cimb45070350] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023] Open
Abstract
In this review, the role of innate and adaptive immunity in the pathogenesis of inflammatory bowel diseases (IBD) is reported. In IBD, an altered innate immunity is often found, with increased Th17 and decreased Treg cells infiltrating the intestinal mucosa. An associated increase in inflammatory cytokines, such as IL-1 and TNF-α, and a decrease in anti-inflammatory cytokines, such as IL-10, concur in favoring the persistent inflammation of the gut mucosa. Autoinflammation is highlighted with insights in the role of inflammasomes, which activation by exogenous or endogenous triggers might be favored by mutations of NOD and NLRP proteins. Autoimmunity mechanisms also take place in IBD pathogenesis and in this context of a persistent immune stimulation by bacterial antigens and antigens derived from intestinal cells degradation, the adaptive immune response takes place and results in antibodies and autoantibodies production, a frequent finding in these diseases. Inflammation, autoinflammation and autoimmunity concur in altering the mucus layer and enhancing intestinal permeability, which sustains the vicious cycle of further mucosal inflammation.
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Affiliation(s)
- Andrea Padoan
- Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
| | - Giulia Musso
- Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
| | - Nicole Contran
- Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
| | - Daniela Basso
- Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padova, Italy
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Rani S, Jain A. Optimizing healthcare system by amalgamation of text processing and deep learning: a systematic review. MULTIMEDIA TOOLS AND APPLICATIONS 2023:1-25. [PMID: 37362695 PMCID: PMC10183315 DOI: 10.1007/s11042-023-15539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 05/18/2022] [Accepted: 04/19/2023] [Indexed: 06/28/2023]
Abstract
The explosion of clinical textual data has drawn the attention of researchers. Owing to the abundance of clinical data, it is becoming difficult for healthcare professionals to take real-time measures. The tools and methods are lacking when compared to the amount of clinical data generated every day. This review aims to survey the text processing pipeline with deep learning methods such as CNN, RNN, LSTM, and GRU in the healthcare domain and discuss various applications such as clinical concept detection and extraction, medically aware dialogue systems, sentiment analysis of drug reviews shared online, clinical trial matching, and pharmacovigilance. In addition, we highlighted the major challenges in deploying text processing with deep learning to clinical textual data and identified the scope of research in this domain. Furthermore, we have discussed various resources that can be used in the future to optimize the healthcare domain by amalgamating text processing and deep learning.
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Affiliation(s)
- Somiya Rani
- Department of Computer Science and Engineering, NSUT East Campus (erstwhile AIACTR), Affiliated to Guru Gobind Singh Indraprastha University, Delhi, India
| | - Amita Jain
- Department of Computer Science and Engineering, Netaji Subhas University of Technology, Delhi, India
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12
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Schick A, Feine J, Morana S, Maedche A, Reininghaus U. Validity of Chatbot Use for Mental Health Assessment: Experimental Study. JMIR Mhealth Uhealth 2022; 10:e28082. [PMID: 36315228 PMCID: PMC9664331 DOI: 10.2196/28082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/09/2021] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Mental disorders in adolescence and young adulthood are major public health concerns. Digital tools such as text-based conversational agents (ie, chatbots) are a promising technology for facilitating mental health assessment. However, the human-like interaction style of chatbots may induce potential biases, such as socially desirable responding (SDR), and may require further effort to complete assessments. OBJECTIVE This study aimed to investigate the convergent and discriminant validity of chatbots for mental health assessments, the effect of assessment mode on SDR, and the effort required by participants for assessments using chatbots compared with established modes. METHODS In a counterbalanced within-subject design, we assessed 2 different constructs-psychological distress (Kessler Psychological Distress Scale and Brief Symptom Inventory-18) and problematic alcohol use (Alcohol Use Disorders Identification Test-3)-in 3 modes (chatbot, paper-and-pencil, and web-based), and examined convergent and discriminant validity. In addition, we investigated the effect of mode on SDR, controlling for perceived sensitivity of items and individuals' tendency to respond in a socially desirable way, and we also assessed the perceived social presence of modes. Including a between-subject condition, we further investigated whether SDR is increased in chatbot assessments when applied in a self-report setting versus when human interaction may be expected. Finally, the effort (ie, complexity, difficulty, burden, and time) required to complete the assessments was investigated. RESULTS A total of 146 young adults (mean age 24, SD 6.42 years; n=67, 45.9% female) were recruited from a research panel for laboratory experiments. The results revealed high positive correlations (all P<.001) of measures of the same construct across different modes, indicating the convergent validity of chatbot assessments. Furthermore, there were no correlations between the distinct constructs, indicating discriminant validity. Moreover, there were no differences in SDR between modes and whether human interaction was expected, although the perceived social presence of the chatbot mode was higher than that of the established modes (P<.001). Finally, greater effort (all P<.05) and more time were needed to complete chatbot assessments than for completing the established modes (P<.001). CONCLUSIONS Our findings suggest that chatbots may yield valid results. Furthermore, an understanding of chatbot design trade-offs in terms of potential strengths (ie, increased social presence) and limitations (ie, increased effort) when assessing mental health were established.
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Affiliation(s)
- Anita Schick
- Department of Public Mental Health, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jasper Feine
- Institute of Information Systems and Marketing, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stefan Morana
- Junior Professorship for Digital Transformation and Information Systems, Saarland University, Saarbruecken, Germany
| | - Alexander Maedche
- Institute of Information Systems and Marketing, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ulrich Reininghaus
- Department of Public Mental Health, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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13
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Chen JS, Baxter SL. Applications of natural language processing in ophthalmology: present and future. Front Med (Lausanne) 2022; 9:906554. [PMID: 36004369 PMCID: PMC9393550 DOI: 10.3389/fmed.2022.906554] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in technology, including novel ophthalmic imaging devices and adoption of the electronic health record (EHR), have resulted in significantly increased data available for both clinical use and research in ophthalmology. While artificial intelligence (AI) algorithms have the potential to utilize these data to transform clinical care, current applications of AI in ophthalmology have focused mostly on image-based deep learning. Unstructured free-text in the EHR represents a tremendous amount of underutilized data in big data analyses and predictive AI. Natural language processing (NLP) is a type of AI involved in processing human language that can be used to develop automated algorithms using these vast quantities of available text data. The purpose of this review was to introduce ophthalmologists to NLP by (1) reviewing current applications of NLP in ophthalmology and (2) exploring potential applications of NLP. We reviewed current literature published in Pubmed and Google Scholar for articles related to NLP and ophthalmology, and used ancestor search to expand our references. Overall, we found 19 published studies of NLP in ophthalmology. The majority of these publications (16) focused on extracting specific text such as visual acuity from free-text notes for the purposes of quantitative analysis. Other applications included: domain embedding, predictive modeling, and topic modeling. Future ophthalmic applications of NLP may also focus on developing search engines for data within free-text notes, cleaning notes, automated question-answering, and translating ophthalmology notes for other specialties or for patients, especially with a growing interest in open notes. As medicine becomes more data-oriented, NLP offers increasing opportunities to augment our ability to harness free-text data and drive innovations in healthcare delivery and treatment of ophthalmic conditions.
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Affiliation(s)
- Jimmy S. Chen
- Division of Ophthalmology Informatics and Data Science, Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
- Health Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, United States
| | - Sally L. Baxter
- Division of Ophthalmology Informatics and Data Science, Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
- Health Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, United States
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14
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Aramaki E, Wakamiya S, Yada S, Nakamura Y. Natural Language Processing: from Bedside to Everywhere. Yearb Med Inform 2022; 31:243-253. [PMID: 35654422 PMCID: PMC9719781 DOI: 10.1055/s-0042-1742510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES Owing to the rapid progress of natural language processing (NLP), the role of NLP in the medical field has radically gained considerable attention from both NLP and medical informatics. Although numerous medical NLP papers are published annually, there is still a gap between basic NLP research and practical product development. This gap raises questions, such as what has medical NLP achieved in each medical field, and what is the burden for the practical use of NLP? This paper aims to clarify the above questions. METHODS We explore the literature on potential NLP products/services applied to various medical/clinical/healthcare areas. RESULTS This paper introduces clinical applications (bedside applications), in which we introduce the use of NLP for each clinical department, internal medicine, pre-surgery, post-surgery, oncology, radiology, pathology, psychiatry, rehabilitation, obstetrics, and gynecology. Also, we clarify technical problems to be addressed for encouraging bedside applications based on NLP. CONCLUSIONS These results contribute to discussions regarding potentially feasible NLP applications and highlight research gaps for future studies.
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Affiliation(s)
- Eiji Aramaki
- Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Shoko Wakamiya
- Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Shuntaro Yada
- Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Yuta Nakamura
- Division of Radiology and Biomedical Engineering, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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15
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Pernencar C, Saboia I, Dias JC. How Far Can Conversational Agents Contribute to IBD Patient Health Care—A Review of the Literature. Front Public Health 2022; 10:862432. [PMID: 35844879 PMCID: PMC9282671 DOI: 10.3389/fpubh.2022.862432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Modern societies are facing health and healthcare challenges as never seen before. The digital world in which we are living today considers digital health interventions such as “internet-delivered” therapy (e-Therapy) or mobile apps as an integrated part of healthcare systems. Digital transformation in health care requires the active involvement of patients as the central part of healthcare interventions. In the case of chronic health conditions, such as inflammatory bowel disease (IBD), it is believed that the adoption of new digital tools helps to maintain and extend the health and care of patients, optimizing the course of the treatment of the disease. The study goal was to undertake a literature review associating the use of chatbot technology with IBD patients' health care. This study intends to support digital product developments, mainly chatbot for IBD or other chronic diseases. The work was carried out through two literature review phases. The first one was based on a systematic approach and the second was a scoping review focused only on Frontiers Journals. This review followed a planned protocol for search and selection strategy that was created by a research team discussion. Chatbot technology for chronic disease self-management can have high acceptance and usability levels. The more interaction with a chatbot, the more patients are able to increase their self-care practice, but there is a challenge. The chatbot ontology to personalize the communication still needed to have strong guidelines helping other researchers to define which Electronic Medical Records (EMRs) should be used in the chatbots to improve the user satisfaction, engagement, and dialog quality. The literature review showed us both evidence and success of these tools in other health disorders. Some of them revealed a huge potential for conversational agents as a part of digital health interventions.
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Affiliation(s)
- Cláudia Pernencar
- ICNOVA—NOVA Institute of Communication, NOVA School of Social Sciences and Humanities, Universidade NOVA de Lisboa, Lisbon, Portugal
- LIDA—Arts and Design Research Lab, Polytechnic Institute of Leiria, Leiria, Portugal
- *Correspondence: Cláudia Pernencar
| | - Inga Saboia
- UFC Virtual, Federal University of Ceará, Fortaleza, Brazil
- DigiMedia—Department of Communication and Art, University of Aveiro, Aveiro, Portugal
| | - Joana Carmo Dias
- COMEGI—Research Center on Organizations, Markets and Industrial Management, Lisbon, Portugal
- UNIDCOM/IADE—Design and Communication Research Centre, Lisbon, Portugal
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16
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Stidham RW, Takenaka K. Artificial Intelligence for Disease Assessment in Inflammatory Bowel Disease: How Will it Change Our Practice? Gastroenterology 2022; 162:1493-1506. [PMID: 34995537 PMCID: PMC8997186 DOI: 10.1053/j.gastro.2021.12.238] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Artificial intelligence (AI) has arrived and it will directly impact how we assess, monitor, and manage inflammatory bowel disease (IBD). Advances in the machine learning methodologies that power AI have produced astounding results for replicating expert judgment and predicting clinical outcomes, particularly in the analysis of imaging. This review will cover general concepts for AI in IBD, with descriptions of common machine learning methods, including decision trees and neural networks. Applications of AI in IBD will cover recent achievements in endoscopic image interpretation and scoring, new capabilities for cross-sectional image analysis, natural language processing for automated understanding of clinical text, and progress in AI-powered clinical decision support tools. In addition to detailing current evidence supporting the capabilities of AI for replicating expert clinical judgment, speculative commentary on how AI may advance concepts of disease activity assessment, care pathways, and pathophysiologic mechanisms of IBD will be addressed.
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Affiliation(s)
- Ryan W. Stidham
- Division of Gastroenterology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Kento Takenaka
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
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17
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Brooks-Warburton J, Ashton J, Dhar A, Tham T, Allen PB, Hoque S, Lovat LB, Sebastian S. Artificial intelligence and inflammatory bowel disease: practicalities and future prospects. Frontline Gastroenterol 2021; 13:325-331. [PMID: 35722596 PMCID: PMC9186028 DOI: 10.1136/flgastro-2021-102003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/16/2021] [Indexed: 02/04/2023] Open
Abstract
Artificial intelligence (AI) is an emerging technology predicted to have significant applications in healthcare. This review highlights AI applications that impact the patient journey in inflammatory bowel disease (IBD), from genomics to endoscopic applications in disease classification, stratification and self-monitoring to risk stratification for personalised management. We discuss the practical AI applications currently in use while giving a balanced view of concerns and pitfalls and look to the future with the potential of where AI can provide significant value to the care of the patient with IBD.
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Affiliation(s)
- Johanne Brooks-Warburton
- Department of Clinical Pharmacology and Biological Sciences, University of Hertfordshire, Hatfield, UK,Gastroenterology Department, Lister Hospital, Stevenage, UK
| | - James Ashton
- Paediatric Gastroenterology, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Anjan Dhar
- Gastroenterology, County Durham & Darlington NHS Foundation Trust, Bishop Auckland, UK
| | - Tony Tham
- Department of Gastroenterology, Ulster Hospital, Dundonald, UK
| | - Patrick B Allen
- Department of Gastroenterology, Ulster Hospital, Dundonald, UK
| | - Sami Hoque
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Laurence B Lovat
- Division of Surgery & Interventional Science, University College London, London, UK
| | - Shaji Sebastian
- Department of Gastroenterology, Hull University Teaching Hospitals NHS Trust, Hull, UK,Hull York Medical School, Hull, UK
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18
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Lee H, Kang J, Yeo J. Medical Specialty Recommendations by an Artificial Intelligence Chatbot on a Smartphone: Development and Deployment. J Med Internet Res 2021; 23:e27460. [PMID: 33882012 PMCID: PMC8104000 DOI: 10.2196/27460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/03/2021] [Accepted: 04/17/2021] [Indexed: 01/22/2023] Open
Abstract
Background The COVID-19 pandemic has limited daily activities and even contact between patients and primary care providers. This makes it more difficult to provide adequate primary care services, which include connecting patients to an appropriate medical specialist. A smartphone-compatible artificial intelligence (AI) chatbot that classifies patients’ symptoms and recommends the appropriate medical specialty could provide a valuable solution. Objective In order to establish a contactless method of recommending the appropriate medical specialty, this study aimed to construct a deep learning–based natural language processing (NLP) pipeline and to develop an AI chatbot that can be used on a smartphone. Methods We collected 118,008 sentences containing information on symptoms with labels (medical specialty), conducted data cleansing, and finally constructed a pipeline of 51,134 sentences for this study. Several deep learning models, including 4 different long short-term memory (LSTM) models with or without attention and with or without a pretrained FastText embedding layer, as well as bidirectional encoder representations from transformers for NLP, were trained and validated using a randomly selected test data set. The performance of the models was evaluated on the basis of the precision, recall, F1-score, and area under the receiver operating characteristic curve (AUC). An AI chatbot was also designed to make it easy for patients to use this specialty recommendation system. We used an open-source framework called “Alpha” to develop our AI chatbot. This takes the form of a web-based app with a frontend chat interface capable of conversing in text and a backend cloud-based server application to handle data collection, process the data with a deep learning model, and offer the medical specialty recommendation in a responsive web that is compatible with both desktops and smartphones. Results The bidirectional encoder representations from transformers model yielded the best performance, with an AUC of 0.964 and F1-score of 0.768, followed by LSTM model with embedding vectors, with an AUC of 0.965 and F1-score of 0.739. Considering the limitations of computing resources and the wide availability of smartphones, the LSTM model with embedding vectors trained on our data set was adopted for our AI chatbot service. We also deployed an Alpha version of the AI chatbot to be executed on both desktops and smartphones. Conclusions With the increasing need for telemedicine during the current COVID-19 pandemic, an AI chatbot with a deep learning–based NLP model that can recommend a medical specialty to patients through their smartphones would be exceedingly useful. This chatbot allows patients to identify the proper medical specialist in a rapid and contactless manner, based on their symptoms, thus potentially supporting both patients and primary care providers.
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Affiliation(s)
- Hyeonhoon Lee
- Department of Clinical Korean Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Jaehyun Kang
- Department of Computer Science, Yonsei University, Seoul, Republic of Korea
| | - Jonghyeon Yeo
- School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea
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19
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McKillop M, South BR, Preininger A, Mason M, Jackson GP. Leveraging conversational technology to answer common COVID-19 questions. J Am Med Inform Assoc 2021; 28:850-855. [PMID: 33517402 PMCID: PMC7798957 DOI: 10.1093/jamia/ocaa316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/17/2020] [Accepted: 11/28/2020] [Indexed: 11/13/2022] Open
Abstract
The rapidly evolving science about the Coronavirus Disease 2019 (COVID-19) pandemic created unprecedented health information needs and dramatic changes in policies globally. We describe a platform, Watson Assistant (WA), which has been used to develop conversational agents to deliver COVID-19 related information. We characterized the diverse use cases and implementations during the early pandemic and measured adoption through a number of users, messages sent, and conversational turns (ie, pairs of interactions between users and agents). Thirty-seven institutions in 9 countries deployed COVID-19 conversational agents with WA between March 30 and August 10, 2020, including 24 governmental agencies, 7 employers, 5 provider organizations, and 1 health plan. Over 6.8 million messages were delivered through the platform. The mean number of conversational turns per session ranged between 1.9 and 3.5. Our experience demonstrates that conversational technologies can be rapidly deployed for pandemic response and are adopted globally by a wide range of users.
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Affiliation(s)
| | | | | | - Mitch Mason
- IBM Watson Health, Cambridge, Massachusetts, USA
| | - Gretchen Purcell Jackson
- IBM Watson Health, Cambridge, Massachusetts, USA.,Vanderbilt University Medical Center, Nashville, Tennessee, USA
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20
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Cohen-Mekelburg S, Berry S, Stidham RW, Zhu J, Waljee AK. Clinical applications of artificial intelligence and machine learning-based methods in inflammatory bowel disease. J Gastroenterol Hepatol 2021; 36:279-285. [PMID: 33624888 PMCID: PMC8917815 DOI: 10.1111/jgh.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022]
Abstract
Our objective was to review and exemplify how selected applications of artificial intelligence (AI) might facilitate and improve inflammatory bowel disease (IBD) care and to identify gaps for future work in this field. IBD is highly complex and associated with significant variation in care and outcomes. The application of AI to IBD has the potential to reduce variation in healthcare delivery and improve quality of care. AI refers to the ability of machines to mimic human intelligence. The range of AI's ability to perform tasks that would normally require human intelligence varies from prediction to complex decision-making that more closely resembles human thought. Clinical applications of AI have been applied to study pathogenesis, diagnosis, and patient prognosis in IBD. Despite these advancements, AI in IBD is in its early development and has tremendous potential to transform future care.
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Affiliation(s)
- Shirley Cohen-Mekelburg
- Health Services Research and Development Center of Clinical Management Research and Gastroenterology Service, VA Ann Arbor
- Michigan Medicine, Department of Internal Medicine, Division of Gastroenterology and Hepatology
| | - Sameer Berry
- Michigan Medicine, Department of Internal Medicine, Division of Gastroenterology and Hepatology
| | - Ryan W Stidham
- Michigan Medicine, Department of Internal Medicine, Division of Gastroenterology and Hepatology
- Department of Computational Medicine and Bioinformatics
- Michigan Integrated Center for Health Analytics and Medical Prediction (MiCHAMP), Ann Arbor, Michigan, USA
| | - Ji Zhu
- Department of Statistics, University of Michigan
- Michigan Integrated Center for Health Analytics and Medical Prediction (MiCHAMP), Ann Arbor, Michigan, USA
| | - Akbar K Waljee
- Health Services Research and Development Center of Clinical Management Research and Gastroenterology Service, VA Ann Arbor
- Michigan Medicine, Department of Internal Medicine, Division of Gastroenterology and Hepatology
- Michigan Integrated Center for Health Analytics and Medical Prediction (MiCHAMP), Ann Arbor, Michigan, USA
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21
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Egli A, Schrenzel J, Greub G. Digital microbiology. Clin Microbiol Infect 2020; 26:1324-1331. [PMID: 32603804 PMCID: PMC7320868 DOI: 10.1016/j.cmi.2020.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Digitalization and artificial intelligence have an important impact on the way microbiology laboratories will work in the near future. Opportunities and challenges lie ahead to digitalize the microbiological workflows. Making efficient use of big data, machine learning, and artificial intelligence in clinical microbiology requires a profound understanding of data handling aspects. OBJECTIVE This review article summarizes the most important concepts of digital microbiology. The article gives microbiologists, clinicians and data scientists a viewpoint and practical examples along the diagnostic process. SOURCES We used peer-reviewed literature identified by a PubMed search for digitalization, machine learning, artificial intelligence and microbiology. CONTENT We describe the opportunities and challenges of digitalization in microbiological diagnostic processes with various examples. We also provide in this context key aspects of data structure and interoperability, as well as legal aspects. Finally, we outline the way for applications in a modern microbiology laboratory. IMPLICATIONS We predict that digitalization and the usage of machine learning will have a profound impact on the daily routine of laboratory staff. Along the analytical process, the most important steps should be identified, where digital technologies can be applied and provide a benefit. The education of all staff involved should be adapted to prepare for the advances in digital microbiology.
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Affiliation(s)
- A Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - J Schrenzel
- Laboratory of Bacteriology, University Hospitals of Geneva, Geneva, Switzerland
| | - G Greub
- Institute of Medical Microbiology, University Hospital Lausanne, Lausanne, Switzerland
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