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Chakrabarty N, Mahajan A. Imaging Analytics using Artificial Intelligence in Oncology: A Comprehensive Review. Clin Oncol (R Coll Radiol) 2024; 36:498-513. [PMID: 37806795 DOI: 10.1016/j.clon.2023.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The present era has seen a surge in artificial intelligence-related research in oncology, mainly using deep learning, because of powerful computer hardware, improved algorithms and the availability of large amounts of data from open-source domains and the use of transfer learning. Here we discuss the multifaceted role of deep learning in cancer care, ranging from risk stratification, the screening and diagnosis of cancer, to the prediction of genomic mutations, treatment response and survival outcome prediction, through the use of convolutional neural networks. Another role of artificial intelligence is in the generation of automated radiology reports, which is a boon in high-volume centres to minimise report turnaround time. Although a validated and deployable deep-learning model for clinical use is still in its infancy, there is ongoing research to overcome the barriers for its universal implementation and we also delve into this aspect. We also briefly describe the role of radiomics in oncoimaging. Artificial intelligence can provide answers pertaining to cancer management at baseline imaging, saving cost and time. Imaging biobanks, which are repositories of anonymised images, are also briefly described. We also discuss the commercialisation and ethical issues pertaining to artificial intelligence. The latest generation generalist artificial intelligence model is also briefly described at the end of the article. We believe this article will not only enrich knowledge, but also promote research acumen in the minds of readers to take oncoimaging to another level using artificial intelligence and also work towards clinical translation of such research.
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Affiliation(s)
- N Chakrabarty
- Department of Radiodiagnosis, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Parel, Mumbai, Maharashtra, India.
| | - A Mahajan
- The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK.
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2
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Rönn T, Perfilyev A, Oskolkov N, Ling C. Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets. Sci Rep 2024; 14:14637. [PMID: 38918439 PMCID: PMC11199577 DOI: 10.1038/s41598-024-64846-3] [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: 12/14/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Type 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple layers of biomedical information, such as different Omics, may allow more accurate understanding of complex diseases such as T2D. Our aim was to explore and use Machine Learning to integrate multiple sources of biological/molecular information (multiOmics), in our case RNA-sequening, DNA methylation, SNP and phenotypic data from islet donors with T2D and non-diabetic controls. We exploited Machine Learning to perform multiOmics integration of DNA methylation, expression, SNPs, and phenotypes from pancreatic islets of 110 individuals, with ~ 30% being T2D cases. DNA methylation was analyzed using Infinium MethylationEPIC array, expression was analyzed using RNA-sequencing, and SNPs were analyzed using HumanOmniExpress arrays. Supervised linear multiOmics integration via DIABLO based on Partial Least Squares (PLS) achieved an accuracy of 91 ± 15% of T2D prediction with an area under the curve of 0.96 ± 0.08 on the test dataset after cross-validation. Biomarkers identified by this multiOmics integration, including SACS and TXNIP DNA methylation, OPRD1 and RHOT1 expression and a SNP annotated to ANO1, provide novel insights into the interplay between different biological mechanisms contributing to T2D. This Machine Learning approach of multiOmics cross-sectional data from human pancreatic islets achieved a promising accuracy of T2D prediction, which may potentially find broad applications in clinical diagnostics. In addition, it delivered novel candidate biomarkers for T2D and links between them across the different Omics.
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Affiliation(s)
- Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Sölvegatan 35, 223 62, Lund, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Lund University, 205 02, Malmö, Sweden.
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Birdal O, İpek E, Saygı M, Doğan R, Pay L, Tanboğa IH. Cluster analysis of clinical, angiographic, and laboratory parameters in patients with ST-segment elevation myocardial infarction. Lipids Health Dis 2024; 23:166. [PMID: 38835073 DOI: 10.1186/s12944-024-02128-7] [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: 01/07/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
INTRODUCTION ST-segment elevation myocardial infarction (STEMI) represents the most harmful clinical manifestation of coronary artery disease. Risk assessment plays a beneficial role in determining both the treatment approach and the appropriate time for discharge. Hierarchical agglomerative clustering (HAC), a machine learning algorithm, is an innovative approach employed for the categorization of patients with comparable clinical and laboratory features. The aim of the present study was to investigate the role of HAC in categorizing STEMI patients and to compare the results of these patients. METHODS A total of 3205 patients who were diagnosed with STEMI at the university hospital emergency clinic between 2015 and 2023 were included in the study. The patients were divided into 2 different phenotypic disease clusters using the HAC method, and their outcomes were compared. RESULTS In the present study, a total of 3205 STEMI patients were included; 2731 patients were in cluster 1, and 474 patients were in cluster 2. Mortality was observed in 147 (5.4%) patients in cluster 1 and 108 (23%) patients in cluster 2 (chi-square P value < 0.01). Survival analysis revealed that patients in cluster 2 had a significantly greater risk of death than patients in cluster 1 did (log-rank P < 0.001). After adjustment for age and sex in the Cox proportional hazards model, cluster 2 exhibited a notably greater risk of death than did cluster 1 (HR = 3.51, 95% CI = 2.71-4.54; P < 0.001). CONCLUSION Our study showed that the HAC method may be a potential tool for predicting one-month mortality in STEMI patients.
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Affiliation(s)
- Oğuzhan Birdal
- Department of Cardiology, Ataturk University, Erzurum, 25240, Turkey.
| | - Emrah İpek
- Department of First Aid and Emergency, Health Services Vocational School, Nisantasi University, Istanbul, 34360, Turkey
| | - Mehmet Saygı
- Department of Cardiology, Hisar Intercontinental Hospital, Istanbul, 34764, Turkey
| | - Remziye Doğan
- Department of Cardiology, Hisar Intercontinental Hospital, Istanbul, 34764, Turkey
| | - Levent Pay
- Department of Cardiology, Ardahan State Hospital, Ardahan, 75000, Turkey
| | - Ibrahim Halil Tanboğa
- Department of Cardiology and Biostatistics, Nisantasi University, Istanbul, 34360, Turkey
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Mesquita F, Bernardino J, Henriques J, Raposo JF, Ribeiro RT, Paredes S. Machine learning techniques to predict the risk of developing diabetic nephropathy: a literature review. J Diabetes Metab Disord 2024; 23:825-839. [PMID: 38932857 PMCID: PMC11196462 DOI: 10.1007/s40200-023-01357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/20/2023] [Indexed: 06/28/2024]
Abstract
Purpose Diabetes is a major public health challenge with widespread prevalence, often leading to complications such as Diabetic Nephropathy (DN)-a chronic condition that progressively impairs kidney function. In this context, it is important to evaluate if Machine learning models can exploit the inherent temporal factor in clinical data to predict the risk of developing DN faster and more accurately than current clinical models. Methods Three different databases were used for this literature review: Scopus, Web of Science, and PubMed. Only articles written in English and published between January 2015 and December 2022 were included. Results We included 11 studies, from which we discuss a number of algorithms capable of extracting knowledge from clinical data, incorporating dynamic aspects in patient assessment, and exploring their evolution over time. We also present a comparison of the different approaches, their performance, advantages, disadvantages, interpretation, and the value that the time factor can bring to a more successful prediction of diabetic nephropathy. Conclusion Our analysis showed that some studies ignored the temporal factor, while others partially exploited it. Greater use of the temporal aspect inherent in Electronic Health Records (EHR) data, together with the integration of omics data, could lead to the development of more reliable and powerful predictive models.
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Affiliation(s)
- F. Mesquita
- Polytechnic Institute of Coimbra, Coimbra Institute of Engineering, Rua Pedro Nunes - Quinta da Nora, 3030-199 Coimbra, Portugal
| | - J. Bernardino
- Polytechnic Institute of Coimbra, Coimbra Institute of Engineering, Rua Pedro Nunes - Quinta da Nora, 3030-199 Coimbra, Portugal
- Center for Informatics and Systems of University of Coimbra, University of Coimbra, Pólo II, 3030-290 Coimbra, Portugal
| | - J. Henriques
- Center for Informatics and Systems of University of Coimbra, University of Coimbra, Pólo II, 3030-290 Coimbra, Portugal
| | - JF. Raposo
- Education and Research Center, APDP Diabetes Portugal, Rua Do Salitre 118-120, 1250-203 Lisbon, Portugal
| | - RT. Ribeiro
- Education and Research Center, APDP Diabetes Portugal, Rua Do Salitre 118-120, 1250-203 Lisbon, Portugal
| | - S. Paredes
- Polytechnic Institute of Coimbra, Coimbra Institute of Engineering, Rua Pedro Nunes - Quinta da Nora, 3030-199 Coimbra, Portugal
- Center for Informatics and Systems of University of Coimbra, University of Coimbra, Pólo II, 3030-290 Coimbra, Portugal
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Steinfeldt J, Wild B, Buergel T, Pietzner M, Upmeier Zu Belzen J, Vauvelle A, Hegselmann S, Denaxas S, Hemingway H, Langenberg C, Landmesser U, Deanfield J, Eils R. Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats. Nat Commun 2024; 15:4257. [PMID: 38763986 PMCID: PMC11102902 DOI: 10.1038/s41467-024-48568-8] [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: 11/17/2023] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
The COVID-19 pandemic exposed a global deficiency of systematic, data-driven guidance to identify high-risk individuals. Here, we illustrate the utility of routinely recorded medical history to predict the risk for 1883 diseases across clinical specialties and support the rapid response to emerging health threats such as COVID-19. We developed a neural network to learn from health records of 502,460 UK Biobank. Importantly, we observed discriminative improvements over basic demographic predictors for 1774 (94.3%) endpoints. After transferring the unmodified risk models to the All of US cohort, we replicated these improvements for 1347 (89.8%) of 1500 investigated endpoints, demonstrating generalizability across healthcare systems and historically underrepresented groups. Ultimately, we showed how this approach could have been used to identify individuals vulnerable to severe COVID-19. Our study demonstrates the potential of medical history to support guidance for emerging pandemics by systematically estimating risk for thousands of diseases at once at minimal cost.
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Affiliation(s)
- Jakob Steinfeldt
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Klinik/Centrum, Charitéplatz 1, 10117, Berlin, Germany
- Computational Medicine, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
- Friede Springer Cardiovascular Prevention Center@Charite, Charite - University Medicine Berlin, Berlin, Germany
- Institute of Cardiovascular Sciences, University College London, London, UK
| | - Benjamin Wild
- Center for Digital Health, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
| | - Thore Buergel
- Institute of Cardiovascular Sciences, University College London, London, UK
- Center for Digital Health, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
| | - Maik Pietzner
- Computational Medicine, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Precision Health University Research Institute, Queen Mary University of London and Barts NHS Trust, London, UK
| | - Julius Upmeier Zu Belzen
- Center for Digital Health, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
| | - Andre Vauvelle
- Institute of Health Informatics, University College London, London, UK
| | - Stefan Hegselmann
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Massachusetts, USA
- Pattern Recognition and Image Analysis Lab, University of Münster, Münster, Germany
| | - Spiros Denaxas
- Institute of Health Informatics, University College London, London, UK
- British Heart Foundation Data Science Centre, London, UK
- Health Data Research UK, London, UK
- National Institute for Health Research, Biomedical Research Centre at University College London Hospitals National Institute for Health Research, Biomedical Research Centre, London, UK
| | - Harry Hemingway
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, London, UK
- National Institute for Health Research, Biomedical Research Centre at University College London Hospitals National Institute for Health Research, Biomedical Research Centre, London, UK
| | - Claudia Langenberg
- Computational Medicine, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Precision Health University Research Institute, Queen Mary University of London and Barts NHS Trust, London, UK
| | - Ulf Landmesser
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Klinik/Centrum, Charitéplatz 1, 10117, Berlin, Germany
- Friede Springer Cardiovascular Prevention Center@Charite, Charite - University Medicine Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Berlin, Germany
| | - John Deanfield
- Institute of Cardiovascular Sciences, University College London, London, UK
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health (BIH), Charite - University Medicine Berlin, Berlin, Germany.
- Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany.
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Wang H, Alanis N, Haygood L, Swoboda TK, Hoot N, Phillips D, Knowles H, Stinson SA, Mehta P, Sambamoorthi U. Using natural language processing in emergency medicine health service research: A systematic review and meta-analysis. Acad Emerg Med 2024. [PMID: 38757352 DOI: 10.1111/acem.14937] [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: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVES Natural language processing (NLP) represents one of the adjunct technologies within artificial intelligence and machine learning, creating structure out of unstructured data. This study aims to assess the performance of employing NLP to identify and categorize unstructured data within the emergency medicine (EM) setting. METHODS We systematically searched publications related to EM research and NLP across databases including MEDLINE, Embase, Scopus, CENTRAL, and ProQuest Dissertations & Theses Global. Independent reviewers screened, reviewed, and evaluated article quality and bias. NLP usage was categorized into syndromic surveillance, radiologic interpretation, and identification of specific diseases/events/syndromes, with respective sensitivity analysis reported. Performance metrics for NLP usage were calculated and the overall area under the summary of receiver operating characteristic curve (SROC) was determined. RESULTS A total of 27 studies underwent meta-analysis. Findings indicated an overall mean sensitivity (recall) of 82%-87%, specificity of 95%, with the area under the SROC at 0.96 (95% CI 0.94-0.98). Optimal performance using NLP was observed in radiologic interpretation, demonstrating an overall mean sensitivity of 93% and specificity of 96%. CONCLUSIONS Our analysis revealed a generally favorable performance accuracy in using NLP within EM research, particularly in the realm of radiologic interpretation. Consequently, we advocate for the adoption of NLP-based research to augment EM health care management.
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Affiliation(s)
- Hao Wang
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Naomi Alanis
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Laura Haygood
- Health Sciences Librarian for Public Health, Brown University, Providence, Rhode Island, USA
| | - Thomas K Swoboda
- Department of Emergency Medicine, The Valley Health System, Touro University Nevada School of Osteopathic Medicine, Las Vegas, Nevada, USA
| | - Nathan Hoot
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Daniel Phillips
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Heidi Knowles
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Sara Ann Stinson
- Mary Couts Burnett Library, Burnett School of Medicine at Texas Christian University, Fort Worth, Texas, USA
| | - Prachi Mehta
- Department of Emergency Medicine, JPS Health Network, Fort Worth, Texas, USA
| | - Usha Sambamoorthi
- College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
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Pamplin JC, Remondelli MH, Thota D, Trapier J, Davis WT, Fisher N, Kwon P, Quinn MT. Revolutionizing Combat Casualty Care: The Power of Digital Twins in Optimizing Casualty Care Through Passive Data Collection. Mil Med 2024:usae249. [PMID: 38743585 DOI: 10.1093/milmed/usae249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/13/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
The potential impact of large-scale combat operations and multidomain operations against peer adversaries poses significant challenges to the Military Health System including large volumes of critically ill and injured casualties, prolonged care times in austere care contexts, limited movement, contested logistics, and denied communications. These challenges contribute to the probability of higher casualty mortality and risk that casualty care hinders commanders' forward momentum or opportunities for overmatch on the battlefield. Novel technical solutions and associated concepts of operation that fundamentally change the delivery of casualty care are necessary to achieve desired medical outcomes that include maximizing Warfighter battle-readiness, minimizing return-to-duty time, optimizing medical evacuation that clears casualties from the battlefield while minimizing casualty morbidity and mortality, and minimizing resource consumption across the care continuum. These novel solutions promise to "automate" certain aspects of casualty care at the level of the individual caregiver and the system level, to unburden our limited number of providers to do more and make better (data-driven) decisions. In this commentary, we describe concepts of casualty digital twins-virtual representations of a casualty's physical journey through the roles of care-and how they, combined with passive data collection about casualty status, caregiver actions, and real-time resource use, can lead to human-machine teaming and increasing automation of casualty care across the care continuum while maintaining or improving outcomes. Our path to combat casualty care automation starts with mapping and modeling the context of casualty care in realistic environments through passive data collection of large amounts of unstructured data to inform machine learning models. These context-aware models will be matched with patient physiology models to create casualty digital twins that better predict casualty needs and resources required and ultimately inform and accelerate decision-making across the continuum of care. We will draw from the experience of the automotive industry as an exemplar for achieving automation in health care and inculcate automation as a mechanism for optimizing the casualty care survival chain.
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Affiliation(s)
- Jeremy C Pamplin
- The Telemedicine and Advanced Technology Research Center, Frederick, MD, 21702 USA
- Department of Medicine, Department of Emergency and Operational Medicine, The Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Mason H Remondelli
- School of Medicine, The Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Darshan Thota
- The Joint Trauma System, Joint Base San Antonio, TX 78234, USA
| | - Jeremy Trapier
- The Telemedicine and Advanced Technology Research Center, Frederick, MD, 21702 USA
| | - William T Davis
- School of Medicine, The Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- United States Air Force En route Care Research Center/59th MDW/ST, JBSA-Fort Sam Houston, TX 78234, USA
| | - Nathan Fisher
- The Telemedicine and Advanced Technology Research Center, Frederick, MD, 21702 USA
| | - Paul Kwon
- Program Executive Office for Simulation, Training and Instrumentation, Orlando, FL 32826, USA
| | - Matthew T Quinn
- The Telemedicine and Advanced Technology Research Center, Frederick, MD, 21702 USA
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Sena J, Mostafiz MT, Zhang J, Davidson AE, Bandyopadhyay S, Nerella S, Ren Y, Ozrazgat-Baslanti T, Shickel B, Loftus T, Schwartz WR, Bihorac A, Rashidi P. Wearable sensors in patient acuity assessment in critical care. Front Neurol 2024; 15:1386728. [PMID: 38784909 PMCID: PMC11112699 DOI: 10.3389/fneur.2024.1386728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
Acuity assessments are vital for timely interventions and fair resource allocation in critical care settings. Conventional acuity scoring systems heavily depend on subjective patient assessments, leaving room for implicit bias and errors. These assessments are often manual, time-consuming, intermittent, and challenging to interpret accurately, especially for healthcare providers. This risk of bias and error is likely most pronounced in time-constrained and high-stakes environments, such as critical care settings. Furthermore, such scores do not incorporate other information, such as patients' mobility level, which can indicate recovery or deterioration in the intensive care unit (ICU), especially at a granular level. We hypothesized that wearable sensor data could assist in assessing patient acuity granularly, especially in conjunction with clinical data from electronic health records (EHR). In this prospective study, we evaluated the impact of integrating mobility data collected from wrist-worn accelerometers with clinical data obtained from EHR for estimating acuity. Accelerometry data were collected from 87 patients wearing accelerometers on their wrists in an academic hospital setting. The data was evaluated using five deep neural network models: VGG, ResNet, MobileNet, SqueezeNet, and a custom Transformer network. These models outperformed a rule-based clinical score (Sequential Organ Failure Assessment, SOFA) used as a baseline when predicting acuity state (for ground truth we labeled as unstable patients if they needed life-supporting therapies, and as stable otherwise), particularly regarding the precision, sensitivity, and F1 score. The results demonstrate that integrating accelerometer data with demographics and clinical variables improves predictive performance compared to traditional scoring systems in healthcare. Deep learning models consistently outperformed the SOFA score baseline across various scenarios, showing notable enhancements in metrics such as the area under the receiver operating characteristic (ROC) Curve (AUC), precision, sensitivity, specificity, and F1 score. The most comprehensive scenario, leveraging accelerometer, demographics, and clinical data, achieved the highest AUC of 0.73, compared to 0.53 when using SOFA score as the baseline, with significant improvements in precision (0.80 vs. 0.23), specificity (0.79 vs. 0.73), and F1 score (0.77 vs. 0.66). This study demonstrates a novel approach beyond the simplistic differentiation between stable and unstable conditions. By incorporating mobility and comprehensive patient information, we distinguish between these states in critically ill patients and capture essential nuances in physiology and functional status. Unlike rudimentary definitions, such as equating low blood pressure with instability, our methodology delves deeper, offering a more holistic understanding and potentially valuable insights for acuity assessment.
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Affiliation(s)
- Jessica Sena
- Department of Computer Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Mohammad Tahsin Mostafiz
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, United States
| | - Jiaqing Zhang
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, United States
| | - Andrea E. Davidson
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
| | | | - Subhash Nerella
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Yuanfang Ren
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
| | - Tezcan Ozrazgat-Baslanti
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
| | - Benjamin Shickel
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Tyler Loftus
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, United States
| | | | - Azra Bihorac
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
| | - Parisa Rashidi
- Intelligent Clinical Care Center, University of Florida, Gainesville, FL, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
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Watkins WS, Hernandez EJ, Miller TA, Blue NR, Zimmerman R, Griffiths ER, Frise E, Bernstein D, Boskovski MT, Brueckner M, Chung WK, Gaynor JW, Gelb BD, Goldmuntz E, Gruber PJ, Newburger JW, Roberts AE, Morton SU, Mayer JE, Seidman CE, Seidman JG, Shen Y, Wagner M, Yost HJ, Yandell M, Tristani-Firouzi M. Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306784. [PMID: 38746151 PMCID: PMC11092705 DOI: 10.1101/2024.05.03.24306784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
While genome sequencing has transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.
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10
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Zhu F, Zhang XY, Cheng Z, Liu CL. Revisiting Confidence Estimation: Towards Reliable Failure Prediction. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2024; 46:3370-3387. [PMID: 38090830 DOI: 10.1109/tpami.2023.3342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Reliable confidence estimation is a challenging yet fundamental requirement in many risk-sensitive applications. However, modern deep neural networks are often overconfident for their incorrect predictions, i.e., misclassified samples from known classes, and out-of-distribution (OOD) samples from unknown classes. In recent years, many confidence calibration and OOD detection methods have been developed. In this paper, we find a general, widely existing but actually-neglected phenomenon that most confidence estimation methods are harmful for detecting misclassification errors. We investigate this problem and reveal that popular calibration and OOD detection methods often lead to worse confidence separation between correctly classified and misclassified examples, making it difficult to decide whether to trust a prediction or not. Finally, we propose to enlarge the confidence gap by finding flat minima, which yields state-of-the-art failure prediction performance under various settings including balanced, long-tailed, and covariate-shift classification scenarios. Our study not only provides a strong baseline for reliable confidence estimation but also acts as a bridge between understanding calibration, OOD detection, and failure prediction.
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Li Y, Yang AY, Marelli A, Li Y. MixEHR-SurG: A joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records. J Biomed Inform 2024; 153:104638. [PMID: 38631461 DOI: 10.1016/j.jbi.2024.104638] [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: 12/20/2023] [Revised: 03/07/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
Survival models can help medical practitioners to evaluate the prognostic importance of clinical variables to patient outcomes such as mortality or hospital readmission and subsequently design personalized treatment regimes. Electronic Health Records (EHRs) hold the promise for large-scale survival analysis based on systematically recorded clinical features for each patient. However, existing survival models either do not scale to high dimensional and multi-modal EHR data or are difficult to interpret. In this study, we present a supervised topic model called MixEHR-SurG to simultaneously integrate heterogeneous EHR data and model survival hazard. Our contributions are three-folds: (1) integrating EHR topic inference with Cox proportional hazards likelihood; (2) integrating patient-specific topic hyperparameters using the PheCode concepts such that each topic can be identified with exactly one PheCode-associated phenotype; (3) multi-modal survival topic inference. This leads to a highly interpretable survival topic model that can infer PheCode-specific phenotype topics associated with patient mortality. We evaluated MixEHR-SurG using a simulated dataset and two real-world EHR datasets: the Quebec Congenital Heart Disease (CHD) data consisting of 8211 subjects with 75,187 outpatient claim records of 1767 unique ICD codes; the MIMIC-III consisting of 1458 subjects with multi-modal EHR records. Compared to the baselines, MixEHR-SurG achieved a superior dynamic AUROC for mortality prediction, with a mean AUROC score of 0.89 in the simulation dataset and a mean AUROC of 0.645 on the CHD dataset. Qualitatively, MixEHR-SurG associates severe cardiac conditions with high mortality risk among the CHD patients after the first heart failure hospitalization and critical brain injuries with increased mortality among the MIMIC-III patients after their ICU discharge. Together, the integration of the Cox proportional hazards model and EHR topic inference in MixEHR-SurG not only leads to competitive mortality prediction but also meaningful phenotype topics for in-depth survival analysis. The software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-SurG.
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Affiliation(s)
- Yixuan Li
- Department of Mathematics and Statistics, McGill University, Montreal, Canada; Mila - Quebec AI institute, Montreal, Canada
| | - Archer Y Yang
- Department of Mathematics and Statistics, McGill University, Montreal, Canada; Mila - Quebec AI institute, Montreal, Canada; School of Computer Science, McGill University, Montreal, Canada.
| | - Ariane Marelli
- McGill Adult Unit for Congenital Heart Disease (MAUDE Unit), McGill University of Health Centre, Montreal, Canada.
| | - Yue Li
- Mila - Quebec AI institute, Montreal, Canada; School of Computer Science, McGill University, Montreal, Canada.
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Hammoud M, Douglas S, Darmach M, Alawneh S, Sanyal S, Kanbour Y. Evaluating the Diagnostic Performance of Symptom Checkers: Clinical Vignette Study. JMIR AI 2024; 3:e46875. [PMID: 38875676 PMCID: PMC11091811 DOI: 10.2196/46875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 03/02/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Medical self-diagnostic tools (or symptom checkers) are becoming an integral part of digital health and our daily lives, whereby patients are increasingly using them to identify the underlying causes of their symptoms. As such, it is essential to rigorously investigate and comprehensively report the diagnostic performance of symptom checkers using standard clinical and scientific approaches. OBJECTIVE This study aims to evaluate and report the accuracies of a few known and new symptom checkers using a standard and transparent methodology, which allows the scientific community to cross-validate and reproduce the reported results, a step much needed in health informatics. METHODS We propose a 4-stage experimentation methodology that capitalizes on the standard clinical vignette approach to evaluate 6 symptom checkers. To this end, we developed and peer-reviewed 400 vignettes, each approved by at least 5 out of 7 independent and experienced primary care physicians. To establish a frame of reference and interpret the results of symptom checkers accordingly, we further compared the best-performing symptom checker against 3 primary care physicians with an average experience of 16.6 (SD 9.42) years. To measure accuracy, we used 7 standard metrics, including M1 as a measure of a symptom checker's or a physician's ability to return a vignette's main diagnosis at the top of their differential list, F1-score as a trade-off measure between recall and precision, and Normalized Discounted Cumulative Gain (NDCG) as a measure of a differential list's ranking quality, among others. RESULTS The diagnostic accuracies of the 6 tested symptom checkers vary significantly. For instance, the differences in the M1, F1-score, and NDCG results between the best-performing and worst-performing symptom checkers or ranges were 65.3%, 39.2%, and 74.2%, respectively. The same was observed among the participating human physicians, whereby the M1, F1-score, and NDCG ranges were 22.8%, 15.3%, and 21.3%, respectively. When compared against each other, physicians outperformed the best-performing symptom checker by an average of 1.2% using F1-score, whereas the best-performing symptom checker outperformed physicians by averages of 10.2% and 25.1% using M1 and NDCG, respectively. CONCLUSIONS The performance variation between symptom checkers is substantial, suggesting that symptom checkers cannot be treated as a single entity. On a different note, the best-performing symptom checker was an artificial intelligence (AI)-based one, shedding light on the promise of AI in improving the diagnostic capabilities of symptom checkers, especially as AI keeps advancing exponentially.
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Chen JL, Stumpe MC, Cohen E. Evolving From Discrete Molecular Data Integrations to Actionable Molecular Insights Within the Electronic Health Record. JCO Clin Cancer Inform 2024; 8:e2400011. [PMID: 38603638 DOI: 10.1200/cci.24.00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/13/2024] Open
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Thakkar A, Gupta A, De Sousa A. Artificial intelligence in positive mental health: a narrative review. Front Digit Health 2024; 6:1280235. [PMID: 38562663 PMCID: PMC10982476 DOI: 10.3389/fdgth.2024.1280235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
The paper reviews the entire spectrum of Artificial Intelligence (AI) in mental health and its positive role in mental health. AI has a huge number of promises to offer mental health care and this paper looks at multiple facets of the same. The paper first defines AI and its scope in the area of mental health. It then looks at various facets of AI like machine learning, supervised machine learning and unsupervised machine learning and other facets of AI. The role of AI in various psychiatric disorders like neurodegenerative disorders, intellectual disability and seizures are discussed along with the role of AI in awareness, diagnosis and intervention in mental health disorders. The role of AI in positive emotional regulation and its impact in schizophrenia, autism spectrum disorders and mood disorders is also highlighted. The article also discusses the limitations of AI based approaches and the need for AI based approaches in mental health to be culturally aware, with structured flexible algorithms and an awareness of biases that can arise in AI. The ethical issues that may arise with the use of AI in mental health are also visited.
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Yao X, Jiang X, Luo H, Liang H, Ye X, Wei Y, Cong S. MOCAT: multi-omics integration with auxiliary classifiers enhanced autoencoder. BioData Min 2024; 17:9. [PMID: 38444019 PMCID: PMC10916109 DOI: 10.1186/s13040-024-00360-6] [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: 12/21/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Integrating multi-omics data is emerging as a critical approach in enhancing our understanding of complex diseases. Innovative computational methods capable of managing high-dimensional and heterogeneous datasets are required to unlock the full potential of such rich and diverse data. METHODS We propose a Multi-Omics integration framework with auxiliary Classifiers-enhanced AuToencoders (MOCAT) to utilize intra- and inter-omics information comprehensively. Additionally, attention mechanisms with confidence learning are incorporated for enhanced feature representation and trustworthy prediction. RESULTS Extensive experiments were conducted on four benchmark datasets to evaluate the effectiveness of our proposed model, including BRCA, ROSMAP, LGG, and KIPAN. Our model significantly improved most evaluation measurements and consistently surpassed the state-of-the-art methods. Ablation studies showed that the auxiliary classifiers significantly boosted classification accuracy in the ROSMAP and LGG datasets. Moreover, the attention mechanisms and confidence evaluation block contributed to improvements in the predictive accuracy and generalizability of our model. CONCLUSIONS The proposed framework exhibits superior performance in disease classification and biomarker discovery, establishing itself as a robust and versatile tool for analyzing multi-layer biological data. This study highlights the significance of elaborated designed deep learning methodologies in dissecting complex disease phenotypes and improving the accuracy of disease predictions.
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Affiliation(s)
- Xiaohui Yao
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Xiaohan Jiang
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
| | - Haoran Luo
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Hong Liang
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Xiufen Ye
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Yanhui Wei
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China
| | - Shan Cong
- Qingdao Innovation and Development Center, Harbin Engineering University, 1777 Sansha Rd, Qingdao, 266000, Shandong, China.
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, 145 Nantong St, Harbin, 150001, Heilongjiang, China.
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Oss Boll H, Amirahmadi A, Ghazani MM, Morais WOD, Freitas EPD, Soliman A, Etminani F, Byttner S, Recamonde-Mendoza M. Graph neural networks for clinical risk prediction based on electronic health records: A survey. J Biomed Inform 2024; 151:104616. [PMID: 38423267 DOI: 10.1016/j.jbi.2024.104616] [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: 09/22/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE This study aims to comprehensively review the use of graph neural networks (GNNs) for clinical risk prediction based on electronic health records (EHRs). The primary goal is to provide an overview of the state-of-the-art of this subject, highlighting ongoing research efforts and identifying existing challenges in developing effective GNNs for improved prediction of clinical risks. METHODS A search was conducted in the Scopus, PubMed, ACM Digital Library, and Embase databases to identify relevant English-language papers that used GNNs for clinical risk prediction based on EHR data. The study includes original research papers published between January 2009 and May 2023. RESULTS Following the initial screening process, 50 articles were included in the data collection. A significant increase in publications from 2020 was observed, with most selected papers focusing on diagnosis prediction (n = 36). The study revealed that the graph attention network (GAT) (n = 19) was the most prevalent architecture, and MIMIC-III (n = 23) was the most common data resource. CONCLUSION GNNs are relevant tools for predicting clinical risk by accounting for the relational aspects among medical events and entities and managing large volumes of EHR data. Future studies in this area may address challenges such as EHR data heterogeneity, multimodality, and model interpretability, aiming to develop more holistic GNN models that can produce more accurate predictions, be effectively implemented in clinical settings, and ultimately improve patient care.
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Affiliation(s)
- Heloísa Oss Boll
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, 91501-970, RS, Brazil; School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden.
| | - Ali Amirahmadi
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Mirfarid Musavian Ghazani
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Wagner Ourique de Morais
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Edison Pignaton de Freitas
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, 91501-970, RS, Brazil
| | - Amira Soliman
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Farzaneh Etminani
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Stefan Byttner
- School of Information Technology, Halmstad University, Kristian IV:s väg 3, Halmstad, 301 18, Sweden
| | - Mariana Recamonde-Mendoza
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, 91501-970, RS, Brazil; Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Av. Protásio Alves, 211, Bloco C, Porto Alegre, 90035-903, RS, Brazil
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Atcı ŞY, Güneş A, Zontul M, Arslan Z. Identifying Diabetic Retinopathy in the Human Eye: A Hybrid Approach Based on a Computer-Aided Diagnosis System Combined with Deep Learning. Tomography 2024; 10:215-230. [PMID: 38393285 PMCID: PMC10892594 DOI: 10.3390/tomography10020017] [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: 12/15/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Diagnosing and screening for diabetic retinopathy is a well-known issue in the biomedical field. A component of computer-aided diagnosis that has advanced significantly over the past few years as a result of the development and effectiveness of deep learning is the use of medical imagery from a patient's eye to identify the damage caused to blood vessels. Issues with unbalanced datasets, incorrect annotations, a lack of sample images, and improper performance evaluation measures have negatively impacted the performance of deep learning models. Using three benchmark datasets of diabetic retinopathy, we conducted a detailed comparison study comparing various state-of-the-art approaches to address the effect caused by class imbalance, with precision scores of 93%, 89%, 81%, 76%, and 96%, respectively, for normal, mild, moderate, severe, and DR phases. The analyses of the hybrid modeling, including CNN analysis and SHAP model derivation results, are compared at the end of the paper, and ideal hybrid modeling strategies for deep learning classification models for automated DR detection are identified.
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Affiliation(s)
- Şükran Yaman Atcı
- Department of Computer Engineering, İstanbul Aydın University, Istanbul 34295, Turkey; (A.G.); (Z.A.)
| | - Ali Güneş
- Department of Computer Engineering, İstanbul Aydın University, Istanbul 34295, Turkey; (A.G.); (Z.A.)
| | - Metin Zontul
- Department of Computer Engineering, Sivas University of Science and Technology, Sivas 58140, Turkey;
| | - Zafer Arslan
- Department of Computer Engineering, İstanbul Aydın University, Istanbul 34295, Turkey; (A.G.); (Z.A.)
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Aamir A, Iqbal A, Jawed F, Ashfaque F, Hafsa H, Anas Z, Oduoye MO, Basit A, Ahmed S, Abdul Rauf S, Khan M, Mansoor T. Exploring the current and prospective role of artificial intelligence in disease diagnosis. Ann Med Surg (Lond) 2024; 86:943-949. [PMID: 38333305 PMCID: PMC10849462 DOI: 10.1097/ms9.0000000000001700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/28/2023] [Indexed: 02/10/2024] Open
Abstract
Artificial intelligence (AI) refers to the simulation of human intelligence processes by machines, especially computer systems, providing assistance in a variety of patient care and health systems. The aim of this review is to contribute valuable insights to the ongoing discourse on the transformative potential of AI in healthcare, providing a nuanced understanding of its current applications, future possibilities, and associated challenges. The authors conducted a literature search on the current role of AI in disease diagnosis and its possible future applications using PubMed, Google Scholar, and ResearchGate within 10 years. Our investigation revealed that AI, encompassing machine-learning and deep-learning techniques, has become integral to healthcare, facilitating immediate access to evidence-based guidelines, the latest medical literature, and tools for generating differential diagnoses. However, our research also acknowledges the limitations of current AI methodologies in disease diagnosis and explores uncertainties and obstacles associated with the complete integration of AI into clinical practice. This review has highlighted the critical significance of integrating AI into the medical healthcare framework and meticulously examined the evolutionary trajectory of healthcare-oriented AI from its inception, delving into the current state of development and projecting the extent of reliance on AI in the future. The authors have found that central to this study is the exploration of how the strategic integration of AI can accelerate the diagnostic process, heighten diagnostic accuracy, and enhance overall operational efficiency, concurrently relieving the burdens faced by healthcare practitioners.
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Affiliation(s)
- Ali Aamir
- Department of Medicine, Dow University of Health Sciences
| | - Arham Iqbal
- Department of Medicine, Dow International Medical College, Karachi, Pakistan
| | - Fareeha Jawed
- Department of Medicine, Dow University of Health Sciences
| | - Faiza Ashfaque
- Department of Medicine, Dow University of Health Sciences
| | - Hafiza Hafsa
- Department of Medicine, Dow University of Health Sciences
| | - Zahra Anas
- Department of Medicine, Dow University of Health Sciences
| | - Malik Olatunde Oduoye
- Department of Research, Medical Research Circle, Bukavu, Democratic Republic of Congo
| | - Abdul Basit
- Department of Medicine, Dow University of Health Sciences
| | - Shaheer Ahmed
- Department of Medicine, Dow University of Health Sciences
| | | | - Mushkbar Khan
- Liaquat National Hospital and Medical College, Pakistan
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Liu Q, Tian Y, Zhou T, Lyu K, Wang Z, Zheng Y, Liu Y, Ren J, Li J. An Explainable and Personalized Cognitive Reasoning Model Based on Knowledge Graph: Toward Decision Making for General Practice. IEEE J Biomed Health Inform 2024; 28:707-718. [PMID: 37669206 DOI: 10.1109/jbhi.2023.3312154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
General practice plays a prominent role in primary health care (PHC). However, evidence has shown that the quality of PHC is still unsatisfactory, and the accuracy of clinical diagnosis and treatment must be improved in China. Decision making tools based on artificial intelligence can help general practitioners diagnose diseases, but most existing research is not sufficiently scalable and explainable. An explainable and personalized cognitive reasoning model based on knowledge graph (CRKG) proposed in this article can provide personalized diagnosis, perform decision making in general practice, and simulate the mode of thinking of human beings utilizing patients' electronic health records (EHRs) and knowledge graph. Taking abdominal diseases as the application point, an abdominal disease knowledge graph is first constructed in a semiautomated manner. Then, the CRKG designed referring to dual process theory in cognitive science involves the update strategy of global graph representations and reasoning on a personal cognitive graph by adopting the idea of graph neural networks and attention mechanisms. For the diagnosis of diseases in general practice, the CRKG outperforms all the baselines with a precision@1 of 0.7873, recall@10 of 0.9020 and hits@10 of 0.9340. Additionally, the visualization of the reasoning process for each visit of a patient based on the knowledge graph enhances clinicians' comprehension and contributes to explainability. This study is of great importance for the exploration and application of decision making based on EHRs and knowledge graph.
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20
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Marelli AJ, Li C, Liu A, Nguyen H, Moroz H, Brophy JM, Guo L, Buckeridge DL, Tang J, Yang AY, Li Y. Machine Learning Informed Diagnosis for Congenital Heart Disease in Large Claims Data Source. JACC. ADVANCES 2024; 3:100801. [PMID: 38939385 PMCID: PMC11198709 DOI: 10.1016/j.jacadv.2023.100801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 08/10/2023] [Accepted: 10/20/2023] [Indexed: 06/29/2024]
Abstract
Background With an increasing interest in using large claims databases in medical practice and research, it is a meaningful and essential step to efficiently identify patients with the disease of interest. Objectives This study aims to establish a machine learning (ML) approach to identify patients with congenital heart disease (CHD) in large claims databases. Methods We harnessed data from the Quebec claims and hospitalization databases from 1983 to 2000. The study included 19,187 patients. Of them, 3,784 were labeled as true CHD patients using a clinician developed algorithm with manual audits considered as the gold standards. To establish an accurate ML-empowered automated CHD classification system, we evaluated ML methods including Gradient Boosting Decision Tree, Support Vector Machine, Decision tree, and compared them to regularized logistic regression. The Area Under the Precision Recall Curve was used as the evaluation metric. External validation was conducted with an updated data set to 2010 with different subjects. Results Among the ML methods we evaluated, Gradient Boosting Decision Tree led the performance in identifying true CHD patients with 99.3% Area Under the Precision Recall Curve, 98.0% for sensitivity, and 99.7% for specificity. External validation returned similar statistics on model performance. Conclusions This study shows that a tedious and time-consuming clinical inspection for CHD patient identification can be replaced by an extremely efficient ML algorithm in large claims database. Our findings demonstrate that ML methods can be used to automate complicated algorithms to identify patients with complex diseases.
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Affiliation(s)
- Ariane J. Marelli
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - Chao Li
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - Aihua Liu
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - Hanh Nguyen
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - Harry Moroz
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - James M. Brophy
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Québec, Canada
| | - Liming Guo
- McGill University Health Centre, McGill Adult Unit for Congenital Heart Disease Excellence, Montreal, Québec, Canada
| | - David L. Buckeridge
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Québec, Canada
| | - Jian Tang
- Department of Decision Sciences HEC, Université de Montréal, Montreal, Québec, Canada
| | - Archer Y. Yang
- Department of Mathematics and Statistics, McGill University, Montreal, Québec, Canada
| | - Yue Li
- School of Computer Science, McGill University, Montreal, Québec, Canada
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Bali V, Turzhitsky V, Schelfhout J, Paudel M, Hulbert E, Peterson-Brandt J, Hertzberg J, Kelly NR, Patel RH. Machine learning to identify chronic cough from administrative claims data. Sci Rep 2024; 14:2449. [PMID: 38291064 PMCID: PMC10828499 DOI: 10.1038/s41598-024-51522-9] [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: 02/02/2023] [Accepted: 01/06/2024] [Indexed: 02/01/2024] Open
Abstract
Accurate identification of patient populations is an essential component of clinical research, especially for medical conditions such as chronic cough that are inconsistently defined and diagnosed. We aimed to develop and compare machine learning models to identify chronic cough from medical and pharmacy claims data. In this retrospective observational study, we compared 3 machine learning algorithms based on XG Boost, logistic regression, and neural network approaches using a large claims and electronic health record database. Of the 327,423 patients who met the study criteria, 4,818 had chronic cough based on linked claims-electronic health record data. The XG Boost model showed the best performance, achieving a Receiver-Operator Characteristic Area Under the Curve (ROC-AUC) of 0.916. We selected a cutoff that favors a high positive predictive value (PPV) to minimize false positives, resulting in a sensitivity, specificity, PPV, and negative predictive value of 18.0%, 99.6%, 38.7%, and 98.8%, respectively on the held-out testing set (n = 82,262). Logistic regression and neural network models achieved slightly lower ROC-AUCs of 0.907 and 0.838, respectively. The XG Boost and logistic regression models maintained their robust performance in subgroups of individuals with higher rates of chronic cough. Machine learning algorithms are one way of identifying conditions that are not coded in medical records, and can help identify individuals with chronic cough from claims data with a high degree of classification value.
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Affiliation(s)
- Vishal Bali
- Center for Observational and Real-World Evidence (CORE), Merck & Co, Rahway, NJ, USA.
| | - Vladimir Turzhitsky
- Center for Observational and Real-World Evidence (CORE), Merck & Co, Rahway, NJ, USA
| | - Jonathan Schelfhout
- Center for Observational and Real-World Evidence (CORE), Merck & Co, Rahway, NJ, USA
| | - Misti Paudel
- Health Economics and Outcomes Research (HEOR), Optum Insight, Eden Prairie, MN, USA
| | - Erin Hulbert
- Health Economics and Outcomes Research (HEOR), Optum Insight, Eden Prairie, MN, USA
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Wang L, Wang X, Liao KP, Cai T. Semisupervised transfer learning for evaluation of model classification performance. Biometrics 2024; 80:ujae002. [PMID: 38465982 PMCID: PMC10926267 DOI: 10.1093/biomtc/ujae002] [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: 11/18/2022] [Revised: 12/17/2023] [Accepted: 01/17/2024] [Indexed: 03/12/2024]
Abstract
In many modern machine learning applications, changes in covariate distributions and difficulty in acquiring outcome information have posed challenges to robust model training and evaluation. Numerous transfer learning methods have been developed to robustly adapt the model itself to some unlabeled target populations using existing labeled data in a source population. However, there is a paucity of literature on transferring performance metrics, especially receiver operating characteristic (ROC) parameters, of a trained model. In this paper, we aim to evaluate the performance of a trained binary classifier on unlabeled target population based on ROC analysis. We proposed Semisupervised Transfer lEarning of Accuracy Measures (STEAM), an efficient three-step estimation procedure that employs (1) double-index modeling to construct calibrated density ratio weights and (2) robust imputation to leverage the large amount of unlabeled data to improve estimation efficiency. We establish the consistency and asymptotic normality of the proposed estimator under the correct specification of either the density ratio model or the outcome model. We also correct for potential overfitting bias in the estimators in finite samples with cross-validation. We compare our proposed estimators to existing methods and show reductions in bias and gains in efficiency through simulations. We illustrate the practical utility of the proposed method on evaluating prediction performance of a phenotyping model for rheumatoid arthritis (RA) on a temporally evolving EHR cohort.
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Affiliation(s)
- Linshanshan Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - Xuan Wang
- Division of Biostatistics, Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, United States
| | - Katherine P Liao
- Division of Rheumatology, Brigham and Women’s Hospital, Boston, MA 02115, United States
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
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23
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Wen J, Hou J, Bonzel CL, Zhao Y, Castro VM, Gainer VS, Weisenfeld D, Cai T, Ho YL, Panickan VA, Costa L, Hong C, Gaziano JM, Liao KP, Lu J, Cho K, Cai T. LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. PATTERNS (NEW YORK, N.Y.) 2024; 5:100906. [PMID: 38264714 PMCID: PMC10801250 DOI: 10.1016/j.patter.2023.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 01/25/2024]
Abstract
Electronic health record (EHR) data are increasingly used to support real-world evidence studies but are limited by the lack of precise timings of clinical events. Here, we propose a label-efficient incident phenotyping (LATTE) algorithm to accurately annotate the timing of clinical events from longitudinal EHR data. By leveraging the pre-trained semantic embeddings, LATTE selects predictive features and compresses their information into longitudinal visit embeddings through visit attention learning. LATTE models the sequential dependency between the target event and visit embeddings to derive the timings. To improve label efficiency, LATTE constructs longitudinal silver-standard labels from unlabeled patients to perform semi-supervised training. LATTE is evaluated on the onset of type 2 diabetes, heart failure, and relapses of multiple sclerosis. LATTE consistently achieves substantial improvements over benchmark methods while providing high prediction interpretability. The event timings are shown to help discover risk factors of heart failure among patients with rheumatoid arthritis.
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Affiliation(s)
- Jun Wen
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Jue Hou
- University of Minnesota, Minneapolis, MN, USA
| | - Clara-Lea Bonzel
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | | | | | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, USA
- Mass General Brigham, Boston, MA, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Vidul A. Panickan
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | - J. Michael Gaziano
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Katherine P. Liao
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Junwei Lu
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Tianxi Cai
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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24
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Soares Dias Portela A, Saxena V, Rosenn E, Wang SH, Masieri S, Palmieri J, Pasinetti GM. Role of Artificial Intelligence in Multinomial Decisions and Preventative Nutrition in Alzheimer's Disease. Mol Nutr Food Res 2024:e2300605. [PMID: 38175857 DOI: 10.1002/mnfr.202300605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Alzheimer's disease (AD) affects 50 million people worldwide, an increase of 35 million since 2015, and it is known for memory loss and cognitive decline. Considering the morbidity associated with AD, it is important to explore lifestyle elements influencing the chances of developing AD, with special emphasis on nutritional aspects. This review will first discuss how dietary factors have an impact in AD development and the possible role of Artificial Intelligence (AI) and Machine Learning (ML) in preventative care of AD patients through nutrition. The Mediterranean-DASH diets provide individuals with many nutrient benefits which assists the prevention of neurodegeneration by having neuroprotective roles. Lack of micronutrients, protein-energy, and polyunsaturated fatty acids increase the chance of cognitive decline, loss of memory, and synaptic dysfunction among others. ML software has the ability to design models of algorithms from data introduced to present practical solutions that are accessible and easy to use. It can give predictions for a precise medicine approach to evaluate individuals as a whole. There is no doubt the future of nutritional science lies on customizing diets for individuals to reduce dementia risk factors, maintain overall health and brain function.
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Affiliation(s)
| | - Vrinda Saxena
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Eric Rosenn
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Shu-Han Wang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Sibilla Masieri
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Joshua Palmieri
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Giulio Maria Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
- Geriatrics Research, Education and Clinical Center, JJ Peters VA Medical Center, Bronx, NY, 10468, USA
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25
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de Sonnaville ESV, Vermeule J, Oostra K, Knoester H, van Woensel JBM, Allouch SB, Oosterlaan J, Kӧnigs M. Predicting long-term neurocognitive outcome after pediatric intensive care unit admission for bronchiolitis-preliminary exploration of the potential of machine learning. Eur J Pediatr 2024; 183:471-482. [PMID: 37930398 PMCID: PMC10857960 DOI: 10.1007/s00431-023-05307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
PURPOSE For successful prevention and intervention, it is important to unravel the complex constellation of factors that affect neurocognitive functioning after pediatric intensive care unit (PICU) admission. This study aims (1) to elucidate the potential relevance of patient and PICU-related characteristics for long-term adverse neurocognitive outcome after PICU admission for bronchiolitis, and (2) to perform a preliminary exploration of the potential of machine learning as compared to linear regression to improve neurocognitive outcome prediction in a relatively small sample of children after PICU admission. METHODS This cross-sectional observational study investigated 65 children aged 6-12 years with previous PICU admission for bronchiolitis (age ≤ 1 year). They were compared to demographically comparable healthy peers (n = 76) on neurocognitive functioning. Patient and PICU-related characteristics used for the prediction models were as follows: demographic characteristics, perinatal and disease parameters, laboratory results, and intervention characteristics, including hourly validated mechanical ventilation parameters. Neurocognitive outcome was measured by intelligence and computerized neurocognitive testing. Prediction models were developed for each of the neurocognitive outcomes using Regression Trees, k-Nearest Neighbors, and conventional linear regression analysis. RESULTS The patient group had lower intelligence than the control group (p < .001, d = -0.59) and poorer performance in neurocognitive functions, i.e., speed and attention (p = .03, d = -0.41) and verbal memory (p < .001, d = -0.60). Lower intelligence was predicted by lower birth weight and lower socioeconomic status (R2 = 25.9%). Poorer performance on the speed and attention domain was predicted by younger age at follow-up (R2 = 53.5%). Poorer verbal memory was predicted by lower birth weight, younger age at follow-up, and greater exposure to acidotic events (R2 = 50.6%). The machine learning models did not reveal added value in terms of model performance as compared to linear regression. CONCLUSION The findings of this study suggest that in children with previous PICU admission for bronchiolitis, (1) lower birth weight, younger age at follow-up, and lower socioeconomic status are associated with poorer neurocognitive outcome; and (2) greater exposure to acidotic events during PICU admission is associated with poorer verbal memory outcome. The findings of this study provide no evidence for the added value of machine learning models as compared to linear regression analysis in the prediction of long-term neurocognitive outcome in a relatively small sample of children. WHAT IS KNOWN • Adverse neurocognitive outcomes are described in PICU survivors, which are known to interfere with development in other major domains of functioning, such as mental health, academic achievement, and socioeconomic success, highlighting neurocognition as an important outcome after PICU admission. • Machine learning is a rapidly growing field of artificial intelligence that is increasingly applied in health care settings, with great potential to capture the complexity of outcome prediction. WHAT IS NEW • This study shows that lower birth weight, lower socioeconomic status, and greater exposure to acidotic events during PICU admission for bronchiolitis are associated with poorer long-term neurocognitive outcome after PICU admission. Results provide no evidence for the added value of machine learning models in a relatively small sample of children. • As bronchiolitis seldom manifests neurologically, the relation between acidotic events and neurocognitive outcome may reflect either potentially harmful effects of acidosis itself or related processes such as hypercapnia or hypoxic and/or ischemic events during PICU admission. This study further highlights the importance of structured follow-up to monitor long-term outcome of children after PICU admission.
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Affiliation(s)
- Eleonore S V de Sonnaville
- Department of Pediatric Intensive Care, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Emma Children's Hospital Amsterdam UMC Follow Me program & Emma Neuroscience Group, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands.
| | - Jacob Vermeule
- University of Amsterdam, Informatics Institute, Science Park 904, Amsterdam, The Netherlands
| | - Kjeld Oostra
- University of Amsterdam, Informatics Institute, Science Park 904, Amsterdam, The Netherlands
| | - Hennie Knoester
- Department of Pediatric Intensive Care, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Job B M van Woensel
- Department of Pediatric Intensive Care, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Somaya Ben Allouch
- University of Amsterdam, Informatics Institute, Science Park 904, Amsterdam, The Netherlands
| | - Jaap Oosterlaan
- Emma Children's Hospital Amsterdam UMC Follow Me program & Emma Neuroscience Group, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Marsh Kӧnigs
- Emma Children's Hospital Amsterdam UMC Follow Me program & Emma Neuroscience Group, Emma Children's Hospital, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
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Khosravi M, Zare Z, Mojtabaeian SM, Izadi R. Artificial Intelligence and Decision-Making in Healthcare: A Thematic Analysis of a Systematic Review of Reviews. Health Serv Res Manag Epidemiol 2024; 11:23333928241234863. [PMID: 38449840 PMCID: PMC10916499 DOI: 10.1177/23333928241234863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024] Open
Abstract
Introduction The use of artificial intelligence (AI), which can emulate human intelligence and enhance clinical results, has grown in healthcare decision-making due to the digitalization effects and the COVID-19 pandemic. The purpose of this study was to determine the scope of applications of AI tools in the decision-making process in healthcare service delivery networks. Materials and methods This study used a qualitative method to conduct a systematic review of the existing reviews. Review articles published between 2000 and 2024 in English-language were searched in PubMed, Scopus, ProQuest, and Cochrane databases. The CASP (Critical Appraisal Skills Programme) Checklist for Systematic Reviews was used to evaluate the quality of the articles. Based on the eligibility criteria, the final articles were selected and the data extraction was done independently by 2 authors. Finally, the thematic analysis approach was used to analyze the data extracted from the selected articles. Results Of the 14 219 identified records, 18 review articles were eligible and included in the analysis, which covered the findings of 669 other articles. The quality assessment score of all reviewed articles was high. And, the thematic analysis of the data identified 3 main themes including clinical decision-making, organizational decision-making, and shared decision-making; which originated from 8 subthemes. Conclusions This study revealed that AI tools have been applied in various aspects of healthcare decision-making. The use of AI can improve the quality, efficiency, and effectiveness of healthcare services by providing accurate, timely, and personalized information to support decision-making. Further research is needed to explore the best practices and standards for implementing AI in healthcare decision-making.
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Affiliation(s)
- Mohsen Khosravi
- Department of Health Care Management, School of Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Zare
- Department of Health Care Management, School of Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Morteza Mojtabaeian
- Department of Healthcare Economics, School of Management and Medical Informatics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reyhane Izadi
- Department of Health Care Management, School of Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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27
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Avtanski D, Hadzi-Petrushev N, Josifovska S, Mladenov M, Reddy V. Emerging technologies in adipose tissue research. Adipocyte 2023; 12:2248673. [PMID: 37599422 PMCID: PMC10443968 DOI: 10.1080/21623945.2023.2248673] [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: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
Technologies are transforming the understanding of adipose tissue as a complex and dynamic tissue that plays a critical role in energy homoeostasis and metabolic health. This mini-review provides a brief overview of the potential impact of novel technologies in biomedical research and aims to identify areas where these technologies can make the most significant contribution to adipose tissue research. It discusses the impact of cutting-edge technologies such as single-cell sequencing, multi-omics analyses, spatial transcriptomics, live imaging, 3D tissue engineering, microbiome analysis, in vivo imaging, and artificial intelligence/machine learning. As these technologies continue to evolve, we can expect them to play an increasingly important role in advancing our understanding of adipose tissue and improving the treatment of related diseases.
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Affiliation(s)
- Dimiter Avtanski
- Friedman Diabetes Institute, Lenox Hill Hospital, New York, NY, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Nikola Hadzi-Petrushev
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Slavica Josifovska
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Mitko Mladenov
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Varun Reddy
- New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, USA
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Yang Z, Mitra A, Liu W, Berlowitz D, Yu H. TransformEHR: transformer-based encoder-decoder generative model to enhance prediction of disease outcomes using electronic health records. Nat Commun 2023; 14:7857. [PMID: 38030638 PMCID: PMC10687211 DOI: 10.1038/s41467-023-43715-z] [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: 05/03/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
Deep learning transformer-based models using longitudinal electronic health records (EHRs) have shown a great success in prediction of clinical diseases or outcomes. Pretraining on a large dataset can help such models map the input space better and boost their performance on relevant tasks through finetuning with limited data. In this study, we present TransformEHR, a generative encoder-decoder model with transformer that is pretrained using a new pretraining objective-predicting all diseases and outcomes of a patient at a future visit from previous visits. TransformEHR's encoder-decoder framework, paired with the novel pretraining objective, helps it achieve the new state-of-the-art performance on multiple clinical prediction tasks. Comparing with the previous model, TransformEHR improves area under the precision-recall curve by 2% (p < 0.001) for pancreatic cancer onset and by 24% (p = 0.007) for intentional self-harm in patients with post-traumatic stress disorder. The high performance in predicting intentional self-harm shows the potential of TransformEHR in building effective clinical intervention systems. TransformEHR is also generalizable and can be easily finetuned for clinical prediction tasks with limited data.
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Affiliation(s)
- Zhichao Yang
- College of Information and Computer Science, University of Massachusetts Amherst, Amherst, MA, USA
| | - Avijit Mitra
- College of Information and Computer Science, University of Massachusetts Amherst, Amherst, MA, USA
| | - Weisong Liu
- School of Computer & Information Sciences, University of Massachusetts Lowell, Lowell, MA, USA
- Center for Healthcare Organization and Implementation Research, VA Bedford Health Care System, Bedford, MA, USA
| | - Dan Berlowitz
- Center for Healthcare Organization and Implementation Research, VA Bedford Health Care System, Bedford, MA, USA
- Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
| | - Hong Yu
- College of Information and Computer Science, University of Massachusetts Amherst, Amherst, MA, USA.
- School of Computer & Information Sciences, University of Massachusetts Lowell, Lowell, MA, USA.
- Center for Healthcare Organization and Implementation Research, VA Bedford Health Care System, Bedford, MA, USA.
- Center for Biomedical and Health Research in Data Sciences, University of Massachusetts Lowell, Lowell, MA, USA.
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Keszthelyi D, Gaudet-Blavignac C, Bjelogrlic M, Lovis C. Patient Information Summarization in Clinical Settings: Scoping Review. JMIR Med Inform 2023; 11:e44639. [PMID: 38015588 DOI: 10.2196/44639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/15/2023] [Accepted: 07/25/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Information overflow, a common problem in the present clinical environment, can be mitigated by summarizing clinical data. Although there are several solutions for clinical summarization, there is a lack of a complete overview of the research relevant to this field. OBJECTIVE This study aims to identify state-of-the-art solutions for clinical summarization, to analyze their capabilities, and to identify their properties. METHODS A scoping review of articles published between 2005 and 2022 was conducted. With a clinical focus, PubMed and Web of Science were queried to find an initial set of reports, later extended by articles found through a chain of citations. The included reports were analyzed to answer the questions of where, what, and how medical information is summarized; whether summarization conserves temporality, uncertainty, and medical pertinence; and how the propositions are evaluated and deployed. To answer how information is summarized, methods were compared through a new framework "collect-synthesize-communicate" referring to information gathering from data, its synthesis, and communication to the end user. RESULTS Overall, 128 articles were included, representing various medical fields. Exclusively structured data were used as input in 46.1% (59/128) of papers, text in 41.4% (53/128) of articles, and both in 10.2% (13/128) of papers. Using the proposed framework, 42.2% (54/128) of the records contributed to information collection, 27.3% (35/128) contributed to information synthesis, and 46.1% (59/128) presented solutions for summary communication. Numerous summarization approaches have been presented, including extractive (n=13) and abstractive summarization (n=19); topic modeling (n=5); summary specification (n=11); concept and relation extraction (n=30); visual design considerations (n=59); and complete pipelines (n=7) using information extraction, synthesis, and communication. Graphical displays (n=53), short texts (n=41), static reports (n=7), and problem-oriented views (n=7) were the most common types in terms of summary communication. Although temporality and uncertainty information were usually not conserved in most studies (74/128, 57.8% and 113/128, 88.3%, respectively), some studies presented solutions to treat this information. Overall, 115 (89.8%) articles showed results of an evaluation, and methods included evaluations with human participants (median 15, IQR 24 participants): measurements in experiments with human participants (n=31), real situations (n=8), and usability studies (n=28). Methods without human involvement included intrinsic evaluation (n=24), performance on a proxy (n=10), or domain-specific tasks (n=11). Overall, 11 (8.6%) reports described a system deployed in clinical settings. CONCLUSIONS The scientific literature contains many propositions for summarizing patient information but reports very few comparisons of these proposals. This work proposes to compare these algorithms through how they conserve essential aspects of clinical information and through the "collect-synthesize-communicate" framework. We found that current propositions usually address these 3 steps only partially. Moreover, they conserve and use temporality, uncertainty, and pertinent medical aspects to varying extents, and solutions are often preliminary.
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Affiliation(s)
- Daniel Keszthelyi
- Division of Medical Information Sciences, University Hospitals of Geneva, Geneva, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland
| | - Christophe Gaudet-Blavignac
- Division of Medical Information Sciences, University Hospitals of Geneva, Geneva, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland
| | - Mina Bjelogrlic
- Division of Medical Information Sciences, University Hospitals of Geneva, Geneva, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland
| | - Christian Lovis
- Division of Medical Information Sciences, University Hospitals of Geneva, Geneva, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland
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Love CS. "Just the Facts Ma'am": Moral and Ethical Considerations for Artificial Intelligence in Medicine and its Potential to Impact Patient Autonomy and Hope. LINACRE QUARTERLY 2023; 90:375-394. [PMID: 37974568 PMCID: PMC10638968 DOI: 10.1177/00243639231162431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Applying machine-based learning and synthetic cognition, commonly referred to as artificial intelligence (AI), to medicine intimates prescient knowledge. The ability of these algorithms to potentially unlock secrets held within vast data sets makes them invaluable to healthcare. Complex computer algorithms are routinely used to enhance diagnoses in fields like oncology, cardiology, and neurology. These algorithms have found utility in making healthcare decisions that are often complicated by seemingly endless relationships between exogenous and endogenous variables. They have also found utility in the allocation of limited healthcare resources and the management of end-of-life issues. With the increase in computing power and the ability to test a virtually unlimited number of relationships, scientists and engineers have the unprecedented ability to increase the prognostic confidence that comes from complex data analysis. While these systems present exciting opportunities for the democratization and precision of healthcare, their use raises important moral and ethical considerations around Christian concepts of autonomy and hope. The purpose of this essay is to explore some of the practical limitations associated with AI in medicine and discuss some of the potential theological implications that machine-generated diagnoses may present. Specifically, this article examines how these systems may disrupt the patient and healthcare provider relationship emblematic of Christ's healing mission. Finally, this article seeks to offer insights that might help in the development of a more robust ethical framework for the application of these systems in the future.
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Woodman RJ, Mangoni AA. A comprehensive review of machine learning algorithms and their application in geriatric medicine: present and future. Aging Clin Exp Res 2023; 35:2363-2397. [PMID: 37682491 PMCID: PMC10627901 DOI: 10.1007/s40520-023-02552-2] [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: 06/13/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
The increasing access to health data worldwide is driving a resurgence in machine learning research, including data-hungry deep learning algorithms. More computationally efficient algorithms now offer unique opportunities to enhance diagnosis, risk stratification, and individualised approaches to patient management. Such opportunities are particularly relevant for the management of older patients, a group that is characterised by complex multimorbidity patterns and significant interindividual variability in homeostatic capacity, organ function, and response to treatment. Clinical tools that utilise machine learning algorithms to determine the optimal choice of treatment are slowly gaining the necessary approval from governing bodies and being implemented into healthcare, with significant implications for virtually all medical disciplines during the next phase of digital medicine. Beyond obtaining regulatory approval, a crucial element in implementing these tools is the trust and support of the people that use them. In this context, an increased understanding by clinicians of artificial intelligence and machine learning algorithms provides an appreciation of the possible benefits, risks, and uncertainties, and improves the chances for successful adoption. This review provides a broad taxonomy of machine learning algorithms, followed by a more detailed description of each algorithm class, their purpose and capabilities, and examples of their applications, particularly in geriatric medicine. Additional focus is given on the clinical implications and challenges involved in relying on devices with reduced interpretability and the progress made in counteracting the latter via the development of explainable machine learning.
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Affiliation(s)
- Richard J Woodman
- Centre of Epidemiology and Biostatistics, College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
| | - Arduino A Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Department of Clinical Pharmacology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA, Australia
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Mann H, Bar Hillel A, Lev-Tzion R, Greenfeld S, Kariv R, Lederman N, Matz E, Dotan I, Turner D, Lerner B. Medical concept embedding of real-valued electronic health records with application to inflammatory bowel disease. Artif Intell Med 2023; 145:102684. [PMID: 37925213 DOI: 10.1016/j.artmed.2023.102684] [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: 09/12/2022] [Revised: 08/23/2023] [Accepted: 10/06/2023] [Indexed: 11/06/2023]
Abstract
Deep learning approaches are gradually being applied to electronic health record (EHR) data, but they fail to incorporate medical diagnosis codes and real-valued laboratory tests into a single input sequence for temporal modeling. Therefore, the modeling misses the existing medical interrelations among codes and lab test results that should be exploited to promote early disease detection. To find connections between past diagnoses, represented by medical codes, and real-valued laboratory tests, in order to exploit the full potential of the EHR in medical diagnosis, we present a novel method to embed the two sources of data into a recurrent neural network. Experimenting with a database of Crohn's disease (CD), a type of inflammatory bowel disease, patients and their controls (~1:2.2), we show that the introduction of lab test results improves the network's predictive performance more than the introduction of past diagnoses but also, surprisingly, more than when both are combined. In addition, using bootstrapping, we generalize the analysis of the imbalanced database to a medical condition that simulates real-life prevalence of a high-risk CD group of first-degree relatives with results that make our embedding method ready to screen this group in the population.
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Affiliation(s)
- Hanan Mann
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Israel
| | - Aharon Bar Hillel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Israel
| | - Raffi Lev-Tzion
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | | | | | | | - Eran Matz
- Leumit Health Services, Tel Aviv, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva, and the Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Boaz Lerner
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Israel.
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Wickersham M, Bartelo N, Kulm S, Liu Y, Zhang Y, Elemento O. USING MACHINE LEARNING METHODS TO ASSESS THE RISK OF ALCOHOL MISUSE IN OLDER ADULTS. RESEARCH SQUARE 2023:rs.3.rs-3154584. [PMID: 37886491 PMCID: PMC10602059 DOI: 10.21203/rs.3.rs-3154584/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The population of older adults, defined in this study as those 50 years of age or older, continues to increase every year. Substance misuse, particularly alcohol misuse, is often neglected in these individuals. To better identify older adults who might not be properly assessed for alcohol misuse, we have derived a risk assessment tool using patients from the United Kingdom Biobank (UKB), which was validated on patients in the Weill Cornell Medicine (WCM) electronic health record (EHR). The model and tooling created stratifies the risk of alcohol misuse in older adults using 10 features that are commonly found in most EHR systems. We found that the area under the receiver operating curve (AUROC) to correctly predict alcohol misuse in older adults for the UKB and WCM models were 0.84 and 0.78, respectively. We further show that of those who self-identified as having ongoing alcohol misuse in the UKB cohort, only 12.5% of these patients had any alcohol-related F.10 ICD-10 code. Extending this to the WCM cohort, we forecast that 7,838 out of 12,360 older adults with no F.10 ICD-10 code (63.4%) may be missed as having alcohol misuse in the EHR. Overall, this study importantly prioritizes the health of older adults by being able to predict alcohol misuse in an understudied population.
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Affiliation(s)
- Matthew Wickersham
- Weill-Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, New York, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States
| | - Nicholas Bartelo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States
| | - Scott Kulm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States
| | - Yifan Liu
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, United States
| | - Yiye Zhang
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, United States
- Department of Emergency Medicine, Weill Cornell Medicine, New York, New York, United States
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, United States
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [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: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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Berge GT, Granmo OC, Tveit TO, Ruthjersen AL, Sharma J. Combining unsupervised, supervised and rule-based learning: the case of detecting patient allergies in electronic health records. BMC Med Inform Decis Mak 2023; 23:188. [PMID: 37723446 PMCID: PMC10507898 DOI: 10.1186/s12911-023-02271-8] [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: 07/01/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Data mining of electronic health records (EHRs) has a huge potential for improving clinical decision support and to help healthcare deliver precision medicine. Unfortunately, the rule-based and machine learning-based approaches used for natural language processing (NLP) in healthcare today all struggle with various shortcomings related to performance, efficiency, or transparency. METHODS In this paper, we address these issues by presenting a novel method for NLP that implements unsupervised learning of word embeddings, semi-supervised learning for simplified and accelerated clinical vocabulary and concept building, and deterministic rules for fine-grained control of information extraction. The clinical language is automatically learnt, and vocabulary, concepts, and rules supporting a variety of NLP downstream tasks can further be built with only minimal manual feature engineering and tagging required from clinical experts. Together, these steps create an open processing pipeline that gradually refines the data in a transparent way, which greatly improves the interpretable nature of our method. Data transformations are thus made transparent and predictions interpretable, which is imperative for healthcare. The combined method also has other advantages, like potentially being language independent, demanding few domain resources for maintenance, and able to cover misspellings, abbreviations, and acronyms. To test and evaluate the combined method, we have developed a clinical decision support system (CDSS) named Information System for Clinical Concept Searching (ICCS) that implements the method for clinical concept tagging, extraction, and classification. RESULTS In empirical studies the method shows high performance (recall 92.6%, precision 88.8%, F-measure 90.7%), and has demonstrated its value to clinical practice. Here we employ a real-life EHR-derived dataset to evaluate the method's performance on the task of classification (i.e., detecting patient allergies) against a range of common supervised learning algorithms. The combined method achieves state-of-the-art performance compared to the alternative methods we evaluate. We also perform a qualitative analysis of common word embedding methods on the task of word similarity to examine their potential for supporting automatic feature engineering for clinical NLP tasks. CONCLUSIONS Based on the promising results, we suggest more research should be aimed at exploiting the inherent synergies between unsupervised, supervised, and rule-based paradigms for clinical NLP.
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Affiliation(s)
- Geir Thore Berge
- Department of Information Systems, University of Agder, Kristiansand, Norway
- Department of Technology and eHealth, Sørlandet Hospital Trust, Kristiansand, Norway
| | | | - Tor Oddbjørn Tveit
- Department of Technology and eHealth, Sørlandet Hospital Trust, Kristiansand, Norway
- Department of Anesthesia and Intensive Care, Sørlandet Hospital Trust, Kristiansand, Norway
| | - Anna Linda Ruthjersen
- Department of Technology and eHealth, Sørlandet Hospital Trust, Kristiansand, Norway
| | - Jivitesh Sharma
- Department of Technology and eHealth, Sørlandet Hospital Trust, Kristiansand, Norway.
- Department of ICT, University of Agder, Grimstad, Norway.
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Forrest IS, O’Neal AJ, Pedra JHF, Do R. Cholesterol Contributes to Risk, Severity, and Machine Learning-Driven Diagnosis of Lyme Disease. Clin Infect Dis 2023; 77:839-847. [PMID: 37227948 PMCID: PMC10506776 DOI: 10.1093/cid/ciad307] [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: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Lyme disease is the most prevalent vector-borne disease in the US, yet its host factors are poorly understood and diagnostic tests are limited. We evaluated patients in a large health system to uncover cholesterol's role in the susceptibility, severity, and machine learning-based diagnosis of Lyme disease. METHODS A longitudinal health system cohort comprised 1 019 175 individuals with electronic health record data and 50 329 with linked genetic data. Associations of blood cholesterol level, cholesterol genetic scores comprising common genetic variants, and burden of rare loss-of-function (LoF) variants in cholesterol metabolism genes with Lyme disease were investigated. A portable machine learning model was constructed and tested to predict Lyme disease using routine lipid and clinical measurements. RESULTS There were 3832 cases of Lyme disease. Increasing cholesterol was associated with greater risk of Lyme disease and hypercholesterolemia was more prevalent in Lyme disease cases than in controls. Cholesterol genetic scores and rare LoF variants in CD36 and LDLR were associated with Lyme disease risk. Serological profiling of cases revealed parallel trajectories of rising cholesterol and immunoglobulin levels over the disease course, including marked increases in individuals with LoF variants and high cholesterol genetic scores. The machine learning model predicted Lyme disease solely using routine lipid panel, blood count, and metabolic measurements. CONCLUSIONS These results demonstrate the value of large-scale genetic and clinical data to reveal host factors underlying infectious disease biology, risk, and prognosis and the potential for their clinical translation to machine learning diagnostics that do not need specialized assays.
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Affiliation(s)
- Iain S Forrest
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anya J O’Neal
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Joao H F Pedra
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Garcia Valencia OA, Thongprayoon C, Jadlowiec CC, Mao SA, Miao J, Cheungpasitporn W. Enhancing Kidney Transplant Care through the Integration of Chatbot. Healthcare (Basel) 2023; 11:2518. [PMID: 37761715 PMCID: PMC10530762 DOI: 10.3390/healthcare11182518] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Kidney transplantation is a critical treatment option for end-stage kidney disease patients, offering improved quality of life and increased survival rates. However, the complexities of kidney transplant care necessitate continuous advancements in decision making, patient communication, and operational efficiency. This article explores the potential integration of a sophisticated chatbot, an AI-powered conversational agent, to enhance kidney transplant practice and potentially improve patient outcomes. Chatbots and generative AI have shown promising applications in various domains, including healthcare, by simulating human-like interactions and generating contextually appropriate responses. Noteworthy AI models like ChatGPT by OpenAI, BingChat by Microsoft, and Bard AI by Google exhibit significant potential in supporting evidence-based research and healthcare decision making. The integration of chatbots in kidney transplant care may offer transformative possibilities. As a clinical decision support tool, it could provide healthcare professionals with real-time access to medical literature and guidelines, potentially enabling informed decision making and improved knowledge dissemination. Additionally, the chatbot has the potential to facilitate patient education by offering personalized and understandable information, addressing queries, and providing guidance on post-transplant care. Furthermore, under clinician or transplant pharmacist supervision, it has the potential to support post-transplant care and medication management by analyzing patient data, which may lead to tailored recommendations on dosages, monitoring schedules, and potential drug interactions. However, to fully ascertain its effectiveness and safety in these roles, further studies and validation are required. Its integration with existing clinical decision support systems may enhance risk stratification and treatment planning, contributing to more informed and efficient decision making in kidney transplant care. Given the importance of ethical considerations and bias mitigation in AI integration, future studies may evaluate long-term patient outcomes, cost-effectiveness, user experience, and the generalizability of chatbot recommendations. By addressing these factors and potentially leveraging AI capabilities, the integration of chatbots in kidney transplant care holds promise for potentially improving patient outcomes, enhancing decision making, and fostering the equitable and responsible use of AI in healthcare.
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Affiliation(s)
- Oscar A. Garcia Valencia
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (O.A.G.V.); (C.T.)
| | - Charat Thongprayoon
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (O.A.G.V.); (C.T.)
| | - Caroline C. Jadlowiec
- Division of Transplant Surgery, Department of Surgery, Mayo Clinic, Phoenix, AZ 85054, USA;
| | - Shennen A. Mao
- Division of Transplant Surgery, Department of Transplantation, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jing Miao
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (O.A.G.V.); (C.T.)
| | - Wisit Cheungpasitporn
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (O.A.G.V.); (C.T.)
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Lee JM, Hauskrecht M. Personalized event prediction for Electronic Health Records. Artif Intell Med 2023; 143:102620. [PMID: 37673563 PMCID: PMC10503594 DOI: 10.1016/j.artmed.2023.102620] [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: 05/11/2022] [Revised: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 09/08/2023]
Abstract
Clinical event sequences consist of hundreds of clinical events that represent records of patient care in time. Developing accurate predictive models of such sequences is of a great importance for supporting a variety of models for interpreting/classifying the current patient condition, or predicting adverse clinical events and outcomes, all aimed to improve patient care. One important challenge of learning predictive models of clinical sequences is their patient-specific variability. Based on underlying clinical conditions, each patient's sequence may consist of different sets of clinical events (observations, lab results, medications, procedures). Hence, simple population-wide models learned from event sequences for many different patients may not accurately predict patient-specific dynamics of event sequences and their differences. To address the problem, we propose and investigate multiple new event sequence prediction models and methods that let us better adjust the prediction for individual patients and their specific conditions. The methods developed in this work pursue refinement of population-wide models to subpopulations, self-adaptation, and a meta-level model switching that is able to adaptively select the model with the best chance to support the immediate prediction. We analyze and test the performance of these models on clinical event sequences of patients in MIMIC-III database.
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Affiliation(s)
- Jeong Min Lee
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Milos Hauskrecht
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA.
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Yu A, Zhong Y, Feng X, Wei Y. Quantile regression for nonignorable missing data with its application of analyzing electronic medical records. Biometrics 2023; 79:2036-2049. [PMID: 35861675 DOI: 10.1111/biom.13723] [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: 11/18/2021] [Accepted: 07/15/2022] [Indexed: 11/27/2022]
Abstract
Over the past decade, there has been growing enthusiasm for using electronic medical records (EMRs) for biomedical research. Quantile regression estimates distributional associations, providing unique insights into the intricacies and heterogeneity of the EMR data. However, the widespread nonignorable missing observations in EMR often obscure the true associations and challenge its potential for robust biomedical discoveries. We propose a novel method to estimate the covariate effects in the presence of nonignorable missing responses under quantile regression. This method imposes no parametric specifications on response distributions, which subtly uses implicit distributions induced by the corresponding quantile regression models. We show that the proposed estimator is consistent and asymptotically normal. We also provide an efficient algorithm to obtain the proposed estimate and a randomly weighted bootstrap approach for statistical inferences. Numerical studies, including an empirical analysis of real-world EMR data, are used to assess the proposed method's finite-sample performance compared to existing literature.
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Affiliation(s)
- Aiai Yu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Yujie Zhong
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Xingdong Feng
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Ying Wei
- Department of Biostatistics, Columbia University, New York, New York, USA
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Tseng YJ, Chen CJ, Chang CW. lab: an R package for generating analysis-ready data from laboratory records. PeerJ Comput Sci 2023; 9:e1528. [PMID: 37705643 PMCID: PMC10495959 DOI: 10.7717/peerj-cs.1528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/20/2023] [Indexed: 09/15/2023]
Abstract
Background Electronic health records (EHRs) play a crucial role in healthcare decision-making by giving physicians insights into disease progression and suitable treatment options. Within EHRs, laboratory test results are frequently utilized for predicting disease progression. However, processing laboratory test results often poses challenges due to variations in units and formats. In addition, leveraging the temporal information in EHRs can improve outcomes, prognoses, and diagnosis predication. Nevertheless, the irregular frequency of the data in these records necessitates data preprocessing, which can add complexity to time-series analyses. Methods To address these challenges, we developed an open-source R package that facilitates the extraction of temporal information from laboratory records. The proposed lab package generates analysis-ready time series data by segmenting the data into time-series windows and imputing missing values. Moreover, users can map local laboratory codes to the Logical Observation Identifier Names and Codes (LOINC), an international standard. This mapping allows users to incorporate additional information, such as reference ranges and related diseases. Moreover, the reference ranges provided by LOINC enable us to categorize results into normal or abnormal. Finally, the analysis-ready time series data can be further summarized using descriptive statistics and utilized to develop models using machine learning technologies. Results Using the lab package, we analyzed data from MIMIC-III, focusing on newborns with patent ductus arteriosus (PDA). We extracted time-series laboratory records and compared the differences in test results between patients with and without 30-day in-hospital mortality. We then identified significant variations in several laboratory test results 7 days after PDA diagnosis. Leveraging the time series-analysis-ready data, we trained a prediction model with the long short-term memory algorithm, achieving an area under the receiver operating characteristic curve of 0.83 for predicting 30-day in-hospital mortality in model training. These findings demonstrate the lab package's effectiveness in analyzing disease progression. Conclusions The proposed lab package simplifies and expedites the workflow involved in laboratory records extraction. This tool is particularly valuable in assisting clinical data analysts in overcoming the obstacles associated with heterogeneous and sparse laboratory records.
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Affiliation(s)
- Yi-Ju Tseng
- Department of Computer Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, United States of America
| | - Chun Ju Chen
- Department of Information Management, National Taiwan University, Taipei, Taiwan
| | - Chia Wei Chang
- Department of Computer Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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Prabhakaran S, Choong KWK, Prabhakaran S, Choy KT, Kong JC. Accuracy of deep neural learning models in the imaging prediction of pathological complete response after neoadjuvant chemoradiotherapy for locally advanced rectal cancer: a systematic review. Langenbecks Arch Surg 2023; 408:321. [PMID: 37594552 DOI: 10.1007/s00423-023-03039-4] [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: 03/18/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023]
Abstract
PURPOSE Up to 15-27% of patients achieve pathologic complete response (pCR) following neoadjuvant chemoradiotherapy (CRT) for locally advanced rectal cancer (LARC). Deep neural learning (DL) algorithms have been suggested to be a useful adjunct to allow accurate prediction of pCR and to identify patients who could potentially avoid surgery. This systematic review aims to interrogate the accuracy of DL algorithms at predicting pCR. METHODS Embase (PubMed, MEDLINE) databases and Google Scholar were searched to identify eligible English-language studies, with the search concluding in July 2022. Studies reporting on the accuracy of DL models in predicting pCR were selected for review and information pertaining to study characteristics and diagnostic measures was extracted from relevant studies. Risk of bias was evaluated using the Newcastle-Ottawa scale (NOS). RESULTS Our search yielded 85 potential publications. Nineteen full texts were reviewed, and a total of 12 articles were included in this systematic review. There were six retrospective and six prospective cohort studies. The most common DL algorithm used was the Convolutional Neural Network (CNN). Performance comparison was carried out via single modality comparison. The median performance for each best-performing algorithm was an AUC of 0.845 (range 0.71-0.99) and Accuracy of 0.85 (0.83-0.98). CONCLUSIONS There is a promising role for DL models in the prediction of pCR following neoadjuvant-CRT for LARC. Further studies are needed to provide a standardised comparison in order to allow for large-scale clinical application. PROPERO REGISTRATION PROSPERO 2021 CRD42021269904 Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021269904 .
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Affiliation(s)
- Sowmya Prabhakaran
- Department of General Surgical Specialties, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
| | | | - Swetha Prabhakaran
- Department of Colorectal Surgery, Alfred Hospital, Melbourne, Victoria, Australia
| | - Kay Tai Choy
- Department of Surgery, Austin Health, Melbourne, Victoria, Australia
| | - Joseph Ch Kong
- Department of Colorectal Surgery, Alfred Hospital, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Loscertales J, Abrisqueta-Costa P, Gutierrez A, Hernández-Rivas JÁ, Andreu-Lapiedra R, Mora A, Leiva-Farré C, López-Roda MD, Callejo-Mellén Á, Álvarez-García E, García-Marco JA. Real-World Evidence on the Clinical Characteristics and Management of Patients with Chronic Lymphocytic Leukemia in Spain Using Natural Language Processing: The SRealCLL Study. Cancers (Basel) 2023; 15:4047. [PMID: 37627075 PMCID: PMC10452602 DOI: 10.3390/cancers15164047] [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: 06/23/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The SRealCLL study aimed to obtain real-world evidence on the clinical characteristics and treatment patterns of patients with chronic lymphocytic leukemia (CLL) using natural language processing (NLP). Electronic health records (EHRs) from seven Spanish hospitals (January 2016-December 2018) were analyzed using EHRead® technology, based on NLP and machine learning. A total of 534 CLL patients were assessed. No treatment was detected in 270 (50.6%) patients (watch-and-wait, W&W). First-line (1L) treatment was identified in 230 (43.1%) patients and relapsed/refractory (2L) treatment was identified in 58 (10.9%). The median age ranged from 71 to 75 years, with a uniform male predominance (54.8-63.8%). The main comorbidities included hypertension (W&W: 35.6%; 1L: 38.3%; 2L: 39.7%), diabetes mellitus (W&W: 24.4%; 1L: 24.3%; 2L: 31%), cardiac arrhythmia (W&W: 16.7%; 1L: 17.8%; 2L: 17.2%), heart failure (W&W 16.3%, 1L 17.4%, 2L 17.2%), and dyslipidemia (W&W: 13.7%; 1L: 18.7%; 2L: 19.0%). The most common antineoplastic treatment was ibrutinib in 1L (64.8%) and 2L (62.1%), followed by bendamustine + rituximab (12.6%), obinutuzumab + chlorambucil (5.2%), rituximab + chlorambucil (4.8%), and idelalisib + rituximab (3.9%) in 1L and venetoclax (15.5%), idelalisib + rituximab (6.9%), bendamustine + rituximab (3.5%), and venetoclax + rituximab (3.5%) in 2L. This study expands the information available on patients with CLL in Spain, describing the diversity in patient characteristics and therapeutic approaches in clinical practice.
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Affiliation(s)
- Javier Loscertales
- Hematology Department, Hospital Universitario de la Princesa, Calle de Diego de León 62, 28006 Madrid, Spain;
| | - Pau Abrisqueta-Costa
- Hematology Department, Hospital Universitari Vall d’Hebron, Pg de la vall d’Hebron 199, 08035 Barcelona, Spain
| | - Antonio Gutierrez
- Hematology Department, Hospital Son Espases/IdISBa, Carretera de Valldemossa 79, 07120 Palma de Mallorca, Spain;
| | - José Ángel Hernández-Rivas
- Hematology Department, Hospital Universitario Infanta Leonor, Avda. Gran Vía del Este 80, 28031 Madrid, Spain;
| | - Rafael Andreu-Lapiedra
- Hematology Department, Hospital Universitario La Fe, Avinguda de Fernando Abril Martorell 106, 46026 Valencia, Spain;
| | - Alba Mora
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Calle de St. Antoni Maria Claret 167, 08025 Barcelona, Spain;
| | - Carolina Leiva-Farré
- Medical Department, Astrazeneca Farmacéutica Spain S.A., Calle del Puerto de Somport 21, 28050 Madrid, Spain; (C.L.-F.); (M.D.L.-R.); (Á.C.-M.); (E.Á.-G.)
| | - María Dolores López-Roda
- Medical Department, Astrazeneca Farmacéutica Spain S.A., Calle del Puerto de Somport 21, 28050 Madrid, Spain; (C.L.-F.); (M.D.L.-R.); (Á.C.-M.); (E.Á.-G.)
| | - Ángel Callejo-Mellén
- Medical Department, Astrazeneca Farmacéutica Spain S.A., Calle del Puerto de Somport 21, 28050 Madrid, Spain; (C.L.-F.); (M.D.L.-R.); (Á.C.-M.); (E.Á.-G.)
| | - Esther Álvarez-García
- Medical Department, Astrazeneca Farmacéutica Spain S.A., Calle del Puerto de Somport 21, 28050 Madrid, Spain; (C.L.-F.); (M.D.L.-R.); (Á.C.-M.); (E.Á.-G.)
| | - José Antonio García-Marco
- Hematology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Calle Joaquín Rodrigo 1, 28222 Majadahonda, Spain;
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Mamouei M, Fisher T, Rao S, Li Y, Salimi-Khorshidi G, Rahimi K. A comparative study of model-centric and data-centric approaches in the development of cardiovascular disease risk prediction models in the UK Biobank. EUROPEAN HEART JOURNAL. DIGITAL HEALTH 2023; 4:337-346. [PMID: 37538143 PMCID: PMC10393888 DOI: 10.1093/ehjdh/ztad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/01/2023] [Indexed: 08/05/2023]
Abstract
Aims A diverse set of factors influence cardiovascular diseases (CVDs), but a systematic investigation of the interplay between these determinants and the contribution of each to CVD incidence prediction is largely missing from the literature. In this study, we leverage one of the most comprehensive biobanks worldwide, the UK Biobank, to investigate the contribution of different risk factor categories to more accurate incidence predictions in the overall population, by sex, different age groups, and ethnicity. Methods and results The investigated categories include the history of medical events, behavioural factors, socioeconomic factors, environmental factors, and measurements. We included data from a cohort of 405 257 participants aged 37-73 years and trained various machine learning and deep learning models on different subsets of risk factors to predict CVD incidence. Each of the models was trained on the complete set of predictors and subsets where each category was excluded. The results were benchmarked against QRISK3. The findings highlight that (i) leveraging a more comprehensive medical history substantially improves model performance. Relative to QRISK3, the best performing models improved the discrimination by 3.78% and improved precision by 1.80%. (ii) Both model- and data-centric approaches are necessary to improve predictive performance. The benefits of using a comprehensive history of diseases were far more pronounced when a neural sequence model, BEHRT, was used. This highlights the importance of the temporality of medical events that existing clinical risk models fail to capture. (iii) Besides the history of diseases, socioeconomic factors and measurements had small but significant independent contributions to the predictive performance. Conclusion These findings emphasize the need for considering broad determinants and novel modelling approaches to enhance CVD incidence prediction.
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Affiliation(s)
- Mohammad Mamouei
- Corresponding author. Tel: +44 1865 617200, Fax: +44 1865 617202,
| | - Thomas Fisher
- Deep Medicine, Oxford Martin School, University of Oxford, 1st Floor, Hayes House, 75 George Street, Oxford OX1 2BQ, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Science Division, University of Oxford, Oxford, UK
| | - Shishir Rao
- Deep Medicine, Oxford Martin School, University of Oxford, 1st Floor, Hayes House, 75 George Street, Oxford OX1 2BQ, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Science Division, University of Oxford, Oxford, UK
| | - Yikuan Li
- Deep Medicine, Oxford Martin School, University of Oxford, 1st Floor, Hayes House, 75 George Street, Oxford OX1 2BQ, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Science Division, University of Oxford, Oxford, UK
| | - Ghomalreza Salimi-Khorshidi
- Deep Medicine, Oxford Martin School, University of Oxford, 1st Floor, Hayes House, 75 George Street, Oxford OX1 2BQ, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Science Division, University of Oxford, Oxford, UK
| | - Kazem Rahimi
- Deep Medicine, Oxford Martin School, University of Oxford, 1st Floor, Hayes House, 75 George Street, Oxford OX1 2BQ, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Science Division, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Amirahmadi A, Ohlsson M, Etminani K. Deep learning prediction models based on EHR trajectories: A systematic review. J Biomed Inform 2023; 144:104430. [PMID: 37380061 DOI: 10.1016/j.jbi.2023.104430] [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: 10/07/2022] [Revised: 06/08/2023] [Accepted: 06/17/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Electronic health records (EHRs) are generated at an ever-increasing rate. EHR trajectories, the temporal aspect of health records, facilitate predicting patients' future health-related risks. It enables healthcare systems to increase the quality of care through early identification and primary prevention. Deep learning techniques have shown great capacity for analyzing complex data and have been successful for prediction tasks using complex EHR trajectories. This systematic review aims to analyze recent studies to identify challenges, knowledge gaps, and ongoing research directions. METHODS For this systematic review, we searched Scopus, PubMed, IEEE Xplore, and ACM databases from Jan 2016 to April 2022 using search terms centered around EHR, deep learning, and trajectories. Then the selected papers were analyzed according to publication characteristics, objectives, and their solutions regarding existing challenges, such as the model's capacity to deal with intricate data dependencies, data insufficiency, and explainability. RESULTS After removing duplicates and out-of-scope papers, 63 papers were selected, which showed rapid growth in the number of research in recent years. Predicting all diseases in the next visit and the onset of cardiovascular diseases were the most common targets. Different contextual and non-contextual representation learning methods are employed to retrieve important information from the sequence of EHR trajectories. Recurrent neural networks and the time-aware attention mechanism for modeling long-term dependencies, self-attentions, convolutional neural networks, graphs for representing inner visit relations, and attention scores for explainability were frequently used among the reviewed publications. CONCLUSIONS This systematic review demonstrated how recent breakthroughs in deep learning methods have facilitated the modeling of EHR trajectories. Research on improving the ability of graph neural networks, attention mechanisms, and cross-modal learning to analyze intricate dependencies among EHRs has shown good progress. There is a need to increase the number of publicly available EHR trajectory datasets to allow for easier comparison among different models. Also, very few developed models can handle all aspects of EHR trajectory data.
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Affiliation(s)
- Ali Amirahmadi
- Center for Applied Intelligent Systems Research, Halmstad University, Sweden.
| | - Mattias Ohlsson
- Center for Applied Intelligent Systems Research, Halmstad University, Sweden; Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sweden
| | - Kobra Etminani
- Center for Applied Intelligent Systems Research, Halmstad University, Sweden
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Ahuja Y, Liang L, Zhou D, Huang S, Cai T. Semisupervised Calibration of Risk with Noisy Event Times (SCORNET) using electronic health record data. Biostatistics 2023; 24:760-775. [PMID: 35166342 PMCID: PMC10544799 DOI: 10.1093/biostatistics/kxac003] [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: 01/06/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 01/19/2023] Open
Abstract
Leveraging large-scale electronic health record (EHR) data to estimate survival curves for clinical events can enable more powerful risk estimation and comparative effectiveness research. However, use of EHR data is hindered by a lack of direct event time observations. Occurrence times of relevant diagnostic codes or target disease mentions in clinical notes are at best a good approximation of the true disease onset time. On the other hand, extracting precise information on the exact event time requires laborious manual chart review and is sometimes altogether infeasible due to a lack of detailed documentation. Current status labels-binary indicators of phenotype status during follow-up-are significantly more efficient and feasible to compile, enabling more precise survival curve estimation given limited resources. Existing survival analysis methods using current status labels focus almost entirely on supervised estimation, and naive incorporation of unlabeled data into these methods may lead to biased estimates. In this article, we propose Semisupervised Calibration of Risk with Noisy Event Times (SCORNET), which yields a consistent and efficient survival function estimator by leveraging a small set of current status labels and a large set of informative features. In addition to providing theoretical justification of SCORNET, we demonstrate in both simulation and real-world EHR settings that SCORNET achieves efficiency akin to the parametric Weibull regression model, while also exhibiting semi-nonparametric flexibility and relatively low empirical bias in a variety of generative settings.
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Affiliation(s)
- Yuri Ahuja
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Liang Liang
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Doudou Zhou
- Department of Statistics, University of California Davis, 1 Shields Avenue, Davis, CA 05616, USA
| | - Sicong Huang
- Department of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Tianxi Cai
- Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA and Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
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Mukherjee P, Humbert-Droz M, Chen JH, Gevaert O. SCOPE: predicting future diagnoses in office visits using electronic health records. Sci Rep 2023; 13:11005. [PMID: 37419945 PMCID: PMC10328934 DOI: 10.1038/s41598-023-38257-9] [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: 01/28/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023] Open
Abstract
We propose an interpretable and scalable model to predict likely diagnoses at an encounter based on past diagnoses and lab results. This model is intended to aid physicians in their interaction with the electronic health records (EHR). To accomplish this, we retrospectively collected and de-identified EHR data of 2,701,522 patients at Stanford Healthcare over a time period from January 2008 to December 2016. A population-based sample of patients comprising 524,198 individuals (44% M, 56% F) with multiple encounters with at least one frequently occurring diagnosis codes were chosen. A calibrated model was developed to predict ICD-10 diagnosis codes at an encounter based on the past diagnoses and lab results, using a binary relevance based multi-label modeling strategy. Logistic regression and random forests were tested as the base classifier, and several time windows were tested for aggregating the past diagnoses and labs. This modeling approach was compared to a recurrent neural network based deep learning method. The best model used random forest as the base classifier and integrated demographic features, diagnosis codes, and lab results. The best model was calibrated and its performance was comparable or better than existing methods in terms of various metrics, including a median AUROC of 0.904 (IQR [0.838, 0.954]) over 583 diseases. When predicting the first occurrence of a disease label for a patient, the median AUROC with the best model was 0.796 (IQR [0.737, 0.868]). Our modeling approach performed comparably as the tested deep learning method, outperforming it in terms of AUROC (p < 0.001) but underperforming in terms of AUPRC (p < 0.001). Interpreting the model showed that the model uses meaningful features and highlights many interesting associations among diagnoses and lab results. We conclude that the multi-label model performs comparably with RNN based deep learning model while offering simplicity and potentially superior interpretability. While the model was trained and validated on data obtained from a single institution, its simplicity, interpretability and performance makes it a promising candidate for deployment.
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Affiliation(s)
- Pritam Mukherjee
- Department of Medicine, Stanford Center for Biomedical Informatics, Stanford University, 1265 Welch Rd, Palo Alto, CA, 94305, USA
| | - Marie Humbert-Droz
- Department of Medicine, Stanford Center for Biomedical Informatics, Stanford University, 1265 Welch Rd, Palo Alto, CA, 94305, USA
| | - Jonathan H Chen
- Department of Medicine, Stanford Center for Biomedical Informatics, Stanford University, 1265 Welch Rd, Palo Alto, CA, 94305, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford Center for Biomedical Informatics, Stanford University, 1265 Welch Rd, Palo Alto, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, USA.
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Luik TT, Abu-Hanna A, van Weert HCPM, Schut MC. Early detection of colorectal cancer by leveraging Dutch primary care consultation notes with free text embeddings. Sci Rep 2023; 13:10760. [PMID: 37402757 DOI: 10.1038/s41598-023-37397-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
We aimed to assess the added predictive performance that free-text Dutch consultation notes provide in detecting colorectal cancer in primary care, in comparison to currently used models. We developed, evaluated and compared three prediction models for colorectal cancer (CRC) in a large primary care database with 60,641 patients. The prediction model with both known predictive features and free-text data (with TabTxt AUROC: 0.823) performs statistically significantly better (p < 0.05) than the other two models with only tabular (as used nowadays) and text data, respectively (AUROC Tab: 0.767; Txt: 0.797). The specificity of the two models that use demographics and known CRC features (with specificity Tab: 0.321; TabTxt: 0.335) are higher than that of the model with only free-text (specificity Txt: 0.234). The Txt and, to a lesser degree, TabTxt model are well calibrated, while the Tab model shows slight underprediction at both tails. As expected with an outcome prevalence below 0.01, all models show much uncalibrated predictions in the extreme upper tail (top 1%). Free-text consultation notes show promising results to improve the predictive performance over established prediction models that only use structured features. Clinical future implications for our CRC use case include that such improvement may help lowering the number of referrals for suspected CRC to medical specialists.
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Affiliation(s)
- Torec T Luik
- Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ameen Abu-Hanna
- Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk C P M van Weert
- Department of General Practice/Family Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn C Schut
- Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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Trottet C, Vogels T, Keitel K, Kulinkina AV, Tan R, Cobuccio L, Jaggi M, Hartley MA. Modular Clinical Decision Support Networks (MoDN)-Updatable, interpretable, and portable predictions for evolving clinical environments. PLOS DIGITAL HEALTH 2023; 2:e0000108. [PMID: 37459285 PMCID: PMC10351690 DOI: 10.1371/journal.pdig.0000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 06/12/2023] [Indexed: 07/20/2023]
Abstract
Clinical Decision Support Systems (CDSS) have the potential to improve and standardise care with probabilistic guidance. However, many CDSS deploy static, generic rule-based logic, resulting in inequitably distributed accuracy and inconsistent performance in evolving clinical environments. Data-driven models could resolve this issue by updating predictions according to the data collected. However, the size of data required necessitates collaborative learning from analogous CDSS's, which are often imperfectly interoperable (IIO) or unshareable. We propose Modular Clinical Decision Support Networks (MoDN) which allow flexible, privacy-preserving learning across IIO datasets, as well as being robust to the systematic missingness common to CDSS-derived data, while providing interpretable, continuous predictive feedback to the clinician. MoDN is a novel decision tree composed of feature-specific neural network modules that can be combined in any number or combination to make any number or combination of diagnostic predictions, updatable at each step of a consultation. The model is validated on a real-world CDSS-derived dataset, comprising 3,192 paediatric outpatients in Tanzania. MoDN significantly outperforms 'monolithic' baseline models (which take all features at once at the end of a consultation) with a mean macro F1 score across all diagnoses of 0.749 vs 0.651 for logistic regression and 0.620 for multilayer perceptron (p < 0.001). To test collaborative learning between IIO datasets, we create subsets with various percentages of feature overlap and port a MoDN model trained on one subset to another. Even with only 60% common features, fine-tuning a MoDN model on the new dataset or just making a composite model with MoDN modules matched the ideal scenario of sharing data in a perfectly interoperable setting. MoDN integrates into consultation logic by providing interpretable continuous feedback on the predictive potential of each question in a CDSS questionnaire. The modular design allows it to compartmentalise training updates to specific features and collaboratively learn between IIO datasets without sharing any data.
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Affiliation(s)
- Cécile Trottet
- Intelligent Global Health Research Group, Machine Learning and Optimization Laboratory, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Thijs Vogels
- Intelligent Global Health Research Group, Machine Learning and Optimization Laboratory, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Kristina Keitel
- Division of Pediatric Emergency Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Alexandra V. Kulinkina
- Digital Health Unit, Swiss Center for International Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Rainer Tan
- Clinical Research Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Ifakara Health Institute, Ifakara, Tanzania
- Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
| | - Ludovico Cobuccio
- Clinical Research Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Martin Jaggi
- Machine Learning and Optimization Laboratory, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Mary-Anne Hartley
- Intelligent Global Health Research Group, Machine Learning and Optimization Laboratory, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Laboratory of Intelligent Global Health Technologies, Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA
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Al-Bashabsheh E, Alaiad A, Al-Ayyoub M, Beni-Yonis O, Zitar RA, Abualigah L. Improving clinical documentation: automatic inference of ICD-10 codes from patient notes using BERT model. THE JOURNAL OF SUPERCOMPUTING 2023; 79:12766-12790. [DOI: 10.1007/s11227-023-05160-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/04/2023] [Indexed: 09/01/2023]
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50
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Hsieh YH, Hsu JC, Lin C, Lin LY. X-RIM: Extreme Recurrent Independent Mechanisms for Noise-resistant and Interpretable Stroke Risk Prediction. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083743 DOI: 10.1109/embc40787.2023.10339978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Stroke is a leading cause of mortality and long-term disability worldwide. An accurate stroke risk prediction is crucial for its early detection and prevention. Using deep learning to exploit patients' time-series electronic health records (EHRs) has been shown as a promising and efficient solution for such a prediction. Although time-series data could be more informative than a single cross-section in time, real-world time-series EHRs usually have a significantly high missing rate due to irregular patient visits. This could undermine sequential data's benefits unless a proper deep-learning model design is adopted. Furthermore, deep models have long been challenged for their interpretability, which is especially crucial for medical applications. In this study, we propose an extreme design based on the concept of recurrent independent mechanisms (RIM), termed extreme RIM (X-RIM). With no need for imputation, X-RIM utilizes the information of each input feature's temporal records through independent recurrent modules. Experiments on real-world data from the National Taiwan University Hospital showed that, in terms of the area under the precision-recall curve (AUPRC), the area under the receiver-operating characteristics curve (AUROC), and Youden Index, X-RIM (AUPRC: 0.210; AUROC: 0.764; Youden: 0.373) outperformed the classic risk score CHA2DS2-VASc (AUPRC: 0.103; AUROC: 0.650; Youden: 0.223) and other benchmarks in stroke risk prediction. Additional experiments also indicate that individual feature contributions to a prediction could be evaluated intuitively under X-RIM's independent structure to enhance interpretability.
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