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Alessandri S, Ratto ML, Rabellino S, Piacenti G, Contaldo SG, Pernice S, Beccuti M, Calogero RA, Alessandri L. CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. BMC Bioinformatics 2024; 25:110. [PMID: 38475691 DOI: 10.1186/s12859-024-05695-9] [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: 03/14/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged. RESULTS CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices.
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Affiliation(s)
| | - Maria L Ratto
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Sergio Rabellino
- Department of Computer Science, University of Torino, Turin, Italy
| | - Gabriele Piacenti
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | | | - Simone Pernice
- Department of Computer Science, University of Torino, Turin, Italy
| | - Marco Beccuti
- Department of Computer Science, University of Torino, Turin, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy.
| | - Luca Alessandri
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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Hodges A, Skarphol A, Strand MA. A call to develop opioid risk assessment programs for implementation in the pharmacy setting. J Am Pharm Assoc (2003) 2024; 64:350-354. [PMID: 37866627 DOI: 10.1016/j.japh.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
The United States persists in combatting the opioid epidemic. Collectively, researchers should be in search of evidence-based solutions. One such could be an appropriate screening tool to determine a patient's risk of opioid misuse. The screening tool should be transparent, provide high specificity, be validated across a variety of healthcare settings, and be a guided clinical decision-making tool to avoid weaponizing an opioid risk score. We should shift our focus from the number of opioid prescriptions dispensed to appropriateness of each prescription. We should be aware of utilizing non-opioid therapy options. In addition, healthcare providers should be knowledgeable of opioid misuse resources in their area to avoid practicing defensively, while instead concentrating their efforts on patients' best interests. The patients' dignity should be upheld through empathetic care from healthcare providers. We need to reduce the stigma surrounding opioid use, and ensure patient safety with one, cohesive, validated, opioid risk assessment tool.
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Orlenko A, Freda PJ, Ghosh A, Choi H, Matsumoto N, Bright TJ, Walker CT, Obafemi-Ajayi T, Moore JH. Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024; 29:359-373. [PMID: 38160292 PMCID: PMC11250986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
This work demonstrates the use of cluster analysis in detecting fair and unbiased novel discoveries. Given a sample population of elective spinal fusion patients, we identify two overarching subgroups driven by insurance type. The Medicare group, associated with lower socioeconomic status, exhibited an over-representation of negative risk factors. The findings provide a compelling depiction of the interwoven socioeconomic and racial disparities present within the healthcare system, highlighting their consequential effects on health inequalities. The results are intended to guide design of fair and precise machine learning models based on intentional integration of population stratification.
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Affiliation(s)
- Alena Orlenko
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, California, USA*These authors contributed equally to the paper
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Borchert RJ, Azevedo T, Badhwar A, Bernal J, Betts M, Bruffaerts R, Burkhart MC, Dewachter I, Gellersen HM, Low A, Lourida I, Machado L, Madan CR, Malpetti M, Mejia J, Michopoulou S, Muñoz-Neira C, Pepys J, Peres M, Phillips V, Ramanan S, Tamburin S, Tantiangco HM, Thakur L, Tomassini A, Vipin A, Tang E, Newby D, Ranson JM, Llewellyn DJ, Veldsman M, Rittman T. Artificial intelligence for diagnostic and prognostic neuroimaging in dementia: A systematic review. Alzheimers Dement 2023; 19:5885-5904. [PMID: 37563912 DOI: 10.1002/alz.13412] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Artificial intelligence (AI) and neuroimaging offer new opportunities for diagnosis and prognosis of dementia. METHODS We systematically reviewed studies reporting AI for neuroimaging in diagnosis and/or prognosis of cognitive neurodegenerative diseases. RESULTS A total of 255 studies were identified. Most studies relied on the Alzheimer's Disease Neuroimaging Initiative dataset. Algorithmic classifiers were the most commonly used AI method (48%) and discriminative models performed best for differentiating Alzheimer's disease from controls. The accuracy of algorithms varied with the patient cohort, imaging modalities, and stratifiers used. Few studies performed validation in an independent cohort. DISCUSSION The literature has several methodological limitations including lack of sufficient algorithm development descriptions and standard definitions. We make recommendations to improve model validation including addressing key clinical questions, providing sufficient description of AI methods and validating findings in independent datasets. Collaborative approaches between experts in AI and medicine will help achieve the promising potential of AI tools in practice. HIGHLIGHTS There has been a rapid expansion in the use of machine learning for diagnosis and prognosis in neurodegenerative disease Most studies (71%) relied on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset with no other individual dataset used more than five times There has been a recent rise in the use of more complex discriminative models (e.g., neural networks) that performed better than other classifiers for classification of AD vs healthy controls We make recommendations to address methodological considerations, addressing key clinical questions, and validation We also make recommendations for the field more broadly to standardize outcome measures, address gaps in the literature, and monitor sources of bias.
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Affiliation(s)
- Robin J Borchert
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Department of Radiology, University of Cambridge, Cambridge, UK
| | - Tiago Azevedo
- Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - AmanPreet Badhwar
- Department of Pharmacology and Physiology, University of Montreal, Montreal, Canada
- Centre de recherche de l'Institut Universitaire de Gériatrie (CRIUGM), Montreal, Canada
| | - Jose Bernal
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Matthew Betts
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
- Center for Behavioral Brain Sciences, University of Magdeburg, Magdeburg, Germany
| | - Rose Bruffaerts
- Computational Neurology, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | | | - Ilse Dewachter
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Helena M Gellersen
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Audrey Low
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | - Luiza Machado
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maura Malpetti
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jhony Mejia
- Department of Biomedical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Sofia Michopoulou
- Imaging Physics, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Carlos Muñoz-Neira
- Research into Memory, Brain sciences and dementia Group (ReMemBr Group), Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Artificial Intelligence & Computational Neuroscience Group (AICN Group), Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Jack Pepys
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Marion Peres
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Siddharth Ramanan
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | | | - Lokendra Thakur
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, UK
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alessandro Tomassini
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | | | - Eugene Tang
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Danielle Newby
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- Alan Turing Institute, London, UK
| | - Michele Veldsman
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - Timothy Rittman
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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Oduoye MO, Javed B, Gupta N, Valentina Sih CM. Algorithmic bias and research integrity; the role of nonhuman authors in shaping scientific knowledge with respect to artificial intelligence: a perspective. Int J Surg 2023; 109:2987-2990. [PMID: 37318857 PMCID: PMC10583945 DOI: 10.1097/js9.0000000000000552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Artificial intelligence technologies were developed to assist authors in bettering the organization and caliber of their published papers, which are both growing in quantity and sophistication. Even though the usage of artificial intelligence tools in particular ChatGPT's natural language processing systems has been shown to be beneficial in research, there are still concerns about accuracy, responsibility, and transparency when it comes to the norms regarding authorship credit and contributions. Genomic algorithms quickly examine large amounts of genetic data to identify potential disease-causing mutations. By analyzing millions of medications for potential therapeutic benefits, they can quickly and relatively economically find novel approaches to treatment. Researchers from several fields can collaborate on difficult tasks with the assistance of nonhuman writers, promoting interdisciplinary research. Sadly, there are a number of significant disadvantages associated with employing nonhuman authors, including the potential for algorithmic prejudice. Biased data may be reinforced by the algorithm since machine learning algorithms can only be as objective as the data they are trained on. It is overdue that scholars bring forth basic moral concerns in the fight against algorithmic prejudice. Overall, even if the use of nonhuman authors has the potential to significantly improve scientific research, it is crucial for scientists to be aware of these drawbacks and take precautions to avoid bias and limits. To provide accurate and objective results, algorithms must be carefully designed and implemented, and researchers need to be mindful of the larger ethical ramifications of their usage.
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Affiliation(s)
- Malik Olatunde Oduoye
- College of Medical Sciences, Ahmadu Bello University Teaching Hospital, Shika, Kaduna State, Nigeria
- Department of Medical Research, Medical Research Circle, Bukavu, Democratic Republic of Congo
| | - Binish Javed
- Department of Medical Research, Medical Research Circle, Bukavu, Democratic Republic of Congo
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Nikhil Gupta
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Manohar Lohia Hospital, New Delhi, India
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Wang C, Liu S, Yang H, Guo J, Wu Y, Liu J. Ethical Considerations of Using ChatGPT in Health Care. J Med Internet Res 2023; 25:e48009. [PMID: 37566454 PMCID: PMC10457697 DOI: 10.2196/48009] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/05/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
ChatGPT has promising applications in health care, but potential ethical issues need to be addressed proactively to prevent harm. ChatGPT presents potential ethical challenges from legal, humanistic, algorithmic, and informational perspectives. Legal ethics concerns arise from the unclear allocation of responsibility when patient harm occurs and from potential breaches of patient privacy due to data collection. Clear rules and legal boundaries are needed to properly allocate liability and protect users. Humanistic ethics concerns arise from the potential disruption of the physician-patient relationship, humanistic care, and issues of integrity. Overreliance on artificial intelligence (AI) can undermine compassion and erode trust. Transparency and disclosure of AI-generated content are critical to maintaining integrity. Algorithmic ethics raise concerns about algorithmic bias, responsibility, transparency and explainability, as well as validation and evaluation. Information ethics include data bias, validity, and effectiveness. Biased training data can lead to biased output, and overreliance on ChatGPT can reduce patient adherence and encourage self-diagnosis. Ensuring the accuracy, reliability, and validity of ChatGPT-generated content requires rigorous validation and ongoing updates based on clinical practice. To navigate the evolving ethical landscape of AI, AI in health care must adhere to the strictest ethical standards. Through comprehensive ethical guidelines, health care professionals can ensure the responsible use of ChatGPT, promote accurate and reliable information exchange, protect patient privacy, and empower patients to make informed decisions about their health care.
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Affiliation(s)
- Changyu Wang
- Department of Medical Informatics, West China Medical School, Sichuan University, Chengdu, China
- West China College of Stomatology, Sichuan University, Chengdu, China
| | - Siru Liu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Hao Yang
- Information Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiulin Guo
- Information Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxuan Wu
- Department of Medical Informatics, West China Medical School, Sichuan University, Chengdu, China
| | - Jialin Liu
- Department of Medical Informatics, West China Medical School, Sichuan University, Chengdu, China
- Information Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Otolaryngology-Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
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Berbís MA, Paulano Godino F, Royuela del Val J, Alcalá Mata L, Luna A. Clinical impact of artificial intelligence-based solutions on imaging of the pancreas and liver. World J Gastroenterol 2023; 29:1427-1445. [PMID: 36998424 PMCID: PMC10044858 DOI: 10.3748/wjg.v29.i9.1427] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/13/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Artificial intelligence (AI) has experienced substantial progress over the last ten years in many fields of application, including healthcare. In hepatology and pancreatology, major attention to date has been paid to its application to the assisted or even automated interpretation of radiological images, where AI can generate accurate and reproducible imaging diagnosis, reducing the physicians’ workload. AI can provide automatic or semi-automatic segmentation and registration of the liver and pancreatic glands and lesions. Furthermore, using radiomics, AI can introduce new quantitative information which is not visible to the human eye to radiological reports. AI has been applied in the detection and characterization of focal lesions and diffuse diseases of the liver and pancreas, such as neoplasms, chronic hepatic disease, or acute or chronic pancreatitis, among others. These solutions have been applied to different imaging techniques commonly used to diagnose liver and pancreatic diseases, such as ultrasound, endoscopic ultrasonography, computerized tomography (CT), magnetic resonance imaging, and positron emission tomography/CT. However, AI is also applied in this context to many other relevant steps involved in a comprehensive clinical scenario to manage a gastroenterological patient. AI can also be applied to choose the most convenient test prescription, to improve image quality or accelerate its acquisition, and to predict patient prognosis and treatment response. In this review, we summarize the current evidence on the application of AI to hepatic and pancreatic radiology, not only in regard to the interpretation of images, but also to all the steps involved in the radiological workflow in a broader sense. Lastly, we discuss the challenges and future directions of the clinical application of AI methods.
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Affiliation(s)
- M Alvaro Berbís
- Department of Radiology, HT Médica, San Juan de Dios Hospital, Córdoba 14960, Spain
- Faculty of Medicine, Autonomous University of Madrid, Madrid 28049, Spain
| | | | | | - Lidia Alcalá Mata
- Department of Radiology, HT Médica, Clínica las Nieves, Jaén 23007, Spain
| | - Antonio Luna
- Department of Radiology, HT Médica, Clínica las Nieves, Jaén 23007, Spain
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Bricout J, Greer J, Fields N, Xu L, Tamplain P, Doelling K, Sharma B. The "humane in the loop": Inclusive research design and policy approaches to foster capacity building assistive technologies in the COVID-19 era. Assist Technol 2022; 34:644-652. [PMID: 34048326 DOI: 10.1080/10400435.2021.1930282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic is emerging as a driver of greater reliance on wireless technologies, including intelligent assistive technologies, such as robots and artificial intelligence. We must integrate the humane "into the loop" of human-AT interactions to realize the full potential of wireless inclusion for people with disabilities and older adults. Embedding ethics into these new technologies is critical and requires a co-design approach, with end users participating throughout. Developing humane AT begins with a participatory, user-centered design embedded in an iterative co-creation process, and guided by an ethos prioritizing beneficence, user autonomy and agency. To gain insight into plausible AT development pathways ("futures"), we use scenario planning as a tool to articulate themes in the research literature. Four plausible scenarios are developed and compared to identify one as a desired "humane" future for AT development. Policy and practice recommendations derived from this scenario, and their implications for the role of AT in the advancement of human potential are explored.
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Affiliation(s)
- John Bricout
- School of Social Work, University of Minnesota, Twin Cities, Minnesota, USA
| | | | - Noelle Fields
- School of Social Work, University of Texas at Arlington
| | - Ling Xu
- School of Social Work, University of Texas at Arlington
| | | | - Kris Doelling
- School of Social Work, University of Texas at Arlington
| | - Bonita Sharma
- School of Social Work, University of Texas at San Antonio
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Zhou Z, Huang C, Fu P, Huang H, Zhang Q, Wu X, Yu Q, Sun Y. Prediction of in-hospital hypokalemia using machine learning and first hospitalization day records in patients with traumatic brain injury. CNS Neurosci Ther 2022; 29:181-191. [PMID: 36258296 PMCID: PMC9804086 DOI: 10.1111/cns.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 02/06/2023] Open
Abstract
AIMS Hypokalemia is a common complication following traumatic brain injury, which may complicate treatment and lead to unfavorable outcomes. Identifying patients at risk of hypokalemia on the first day of admission helps to implement prophylactic treatment, reduce complications, and improve prognosis. METHODS This multicenter retrospective study was performed between January 2017 and December 2020 using the electronic medical records of patients admitted due to traumatic brain injury. A propensity score matching approach was adopted with a ratio of 1:1 to overcome overfitting and data imbalance during subgroup analyses. Five machine learning algorithms were applied to generate a best-performed prediction model for in-hospital hypokalemia. The internal fivefold cross-validation and external validation were performed to demonstrate the interpretability and generalizability. RESULTS A total of 4445 TBI patients were recruited for analysis and model generation. Hypokalemia occurred in 46.55% of recruited patients and the incidences of mild, moderate, and severe hypokalemia were 32.06%, 12.69%, and 1.80%, respectively. Hypokalemia was associated with increased mortality, while severe hypokalemia cast greater impacts. The logistic regression algorithm had the best performance in predicting decreased serum potassium and moderate-to-severe hypokalemia, with an AUC of 0.73 ± 0.011 and 0.74 ± 0.019, respectively. The prediction model was further verified using two external datasets, including our previous published data and the open-assessed Medical Information Mart for Intensive Care database. Linearized calibration curves showed no statistical difference (p > 0.05) with perfect predictions. CONCLUSIONS The occurrence of hypokalemia following traumatic brain injury can be predicted by first hospitalization day records and machine learning algorithms. The logistic regression algorithm showed an optimal predicting performance verified by both internal and external validation.
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Affiliation(s)
- Zhengyu Zhou
- Department of Anesthesia, Huashan HospitalFudan UniversityShanghaiChina
| | - Chiungwei Huang
- Health Consultation and Physical Examination Center, Zhongshan HospitalFudan UniversityShanghaiChina,Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Pengfei Fu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Hong Huang
- Information Center, Huashan HospitalFudan UniversityShanghaiChina
| | - Qi Zhang
- Information Center, Huashan HospitalFudan UniversityShanghaiChina
| | - Xuehai Wu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiChina,National Center for Neurological DisordersShanghaiChina,Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghaiChina,Neurosurgical Institute of Fudan UniversityShanghaiChina,Shanghai Clinical Medical Center of NeurosurgeryShanghaiChina
| | - Qiong Yu
- Department of Anesthesia, Huashan HospitalFudan UniversityShanghaiChina
| | - Yirui Sun
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiChina,National Center for Neurological DisordersShanghaiChina,Shanghai Key Laboratory of Brain Function Restoration and Neural RegenerationShanghaiChina,Neurosurgical Institute of Fudan UniversityShanghaiChina,Shanghai Clinical Medical Center of NeurosurgeryShanghaiChina
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Johann to Berens P, Schivre G, Theune M, Peter J, Sall SO, Mutterer J, Barneche F, Bourbousse C, Molinier J. Advanced Image Analysis Methods for Automated Segmentation of Subnuclear Chromatin Domains. EPIGENOMES 2022; 6:epigenomes6040034. [PMID: 36278680 PMCID: PMC9624336 DOI: 10.3390/epigenomes6040034] [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: 06/28/2022] [Revised: 09/19/2022] [Accepted: 10/01/2022] [Indexed: 11/07/2022] Open
Abstract
The combination of ever-increasing microscopy resolution with cytogenetical tools allows for detailed analyses of nuclear functional partitioning. However, the need for reliable qualitative and quantitative methodologies to detect and interpret chromatin sub-nuclear organization dynamics is crucial to decipher the underlying molecular processes. Having access to properly automated tools for accurate and fast recognition of complex nuclear structures remains an important issue. Cognitive biases associated with human-based curation or decisions for object segmentation tend to introduce variability and noise into image analysis. Here, we report the development of two complementary segmentation methods, one semi-automated (iCRAQ) and one based on deep learning (Nucl.Eye.D), and their evaluation using a collection of A. thaliana nuclei with contrasted or poorly defined chromatin compartmentalization. Both methods allow for fast, robust and sensitive detection as well as for quantification of subtle nucleus features. Based on these developments, we highlight advantages of semi-automated and deep learning-based analyses applied to plant cytogenetics.
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Affiliation(s)
| | - Geoffrey Schivre
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
- Université Paris-Saclay, 91190 Orsay, France
| | - Marius Theune
- FB 10 / Molekulare Pflanzenphysiologie, Bioenergetik in Photoautotrophen, Universität Kassel, 34127 Kassel, Germany
| | - Jackson Peter
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
| | | | - Jérôme Mutterer
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
| | - Fredy Barneche
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
| | - Clara Bourbousse
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
- Correspondence: (C.B.); (J.M.)
| | - Jean Molinier
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
- Correspondence: (C.B.); (J.M.)
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Hammouda N, Neyra JA. Can Artificial Intelligence Assist in Delivering Continuous Renal Replacement Therapy? Adv Chronic Kidney Dis 2022; 29:439-449. [PMID: 36253027 PMCID: PMC9586461 DOI: 10.1053/j.ackd.2022.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 01/25/2023]
Abstract
Continuous renal replacement therapy (CRRT) is widely utilized to support critically ill patients with acute kidney injury. Artificial intelligence (AI) has the potential to enhance CRRT delivery, but evidence is limited. We reviewed existing literature on the utilization of AI in CRRT with the objective of identifying current gaps in evidence and research considerations. We conducted a scoping review focusing on the development or use of AI-based tools in patients receiving CRRT. Ten papers were identified; 6 of 10 (60%) published in 2021, and 6 of 10 (60%) focused on machine learning models to augment CRRT delivery. All innovations were in the design/early validation phase of development. Primary research interests focused on early indicators of CRRT need, prognostication of mortality and kidney recovery, and identification of risk factors for mortality. Secondary research priorities included dynamic CRRT monitoring, predicting CRRT-related complications, and automated data pooling for point-of-care analysis. Literature gaps included prospective validation and implementation, biases ascertainment, and evaluation of AI-generated health care disparities. Research on AI applications to enhance CRRT delivery has grown exponentially in the last years, but the field remains premature. There is a need to evaluate how these applications could enhance bedside decision-making capacity and assist structure and processes of CRRT delivery.
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Affiliation(s)
- Nada Hammouda
- Department of Applied Clinical Research, University of Texas, Southwestern, Dallas, TX
| | - Javier A Neyra
- Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL.
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Besculides M, Mazumdar M, Phlegar S, Freeman R, Wilson S, Joshi H, Kia A, Gorbenko K. Implementing a Machine Learning Screening Tool for Malnutrition: Insights from Qualitative Research Applicable to Other ML-Based CDSS (Preprint). JMIR Form Res 2022. [PMID: 37440303 PMCID: PMC10375393 DOI: 10.2196/42262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Machine learning (ML)-based clinical decision support systems (CDSS) are popular in clinical practice settings but are often criticized for being limited in usability, interpretability, and effectiveness. Evaluating the implementation of ML-based CDSS is critical to ensure CDSS is acceptable and useful to clinicians and helps them deliver high-quality health care. Malnutrition is a common and underdiagnosed condition among hospital patients, which can have serious adverse impacts. Early identification and treatment of malnutrition are important. OBJECTIVE This study aims to evaluate the implementation of an ML tool, Malnutrition Universal Screening Tool (MUST)-Plus, that predicts hospital patients at high risk for malnutrition and identify best implementation practices applicable to this and other ML-based CDSS. METHODS We conducted a qualitative postimplementation evaluation using in-depth interviews with registered dietitians (RDs) who use MUST-Plus output in their everyday work. After coding the data, we mapped emergent themes onto select domains of the nonadoption, abandonment, scale-up, spread, and sustainability (NASSS) framework. RESULTS We interviewed 17 of the 24 RDs approached (71%), representing 37% of those who use MUST-Plus output. Several themes emerged: (1) enhancements to the tool were made to improve accuracy and usability; (2) MUST-Plus helped identify patients that would not otherwise be seen; perceived usefulness was highest in the original site; (3) perceived accuracy varied by respondent and site; (4) RDs valued autonomy in prioritizing patients; (5) depth of tool understanding varied by hospital and level; (6) MUST-Plus was integrated into workflows and electronic health records; and (7) RDs expressed a desire to eventually have 1 automated screener. CONCLUSIONS Our findings suggest that continuous involvement of stakeholders at new sites given staff turnover is vital to ensure buy-in. Qualitative research can help identify the potential bias of ML tools and should be widely used to ensure health equity. Ongoing collaboration among CDSS developers, data scientists, and clinical providers may help refine CDSS for optimal use and improve the acceptability of CDSS in the clinical context.
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Tejavibulya L, Rolison M, Gao S, Liang Q, Peterson H, Dadashkarimi J, Farruggia MC, Hahn CA, Noble S, Lichenstein SD, Pollatou A, Dufford AJ, Scheinost D. Predicting the future of neuroimaging predictive models in mental health. Mol Psychiatry 2022; 27:3129-3137. [PMID: 35697759 PMCID: PMC9708554 DOI: 10.1038/s41380-022-01635-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 12/11/2022]
Abstract
Predictive modeling using neuroimaging data has the potential to improve our understanding of the neurobiology underlying psychiatric disorders and putatively information interventions. Accordingly, there is a plethora of literature reviewing published studies, the mathematics underlying machine learning, and the best practices for using these approaches. As our knowledge of mental health and machine learning continue to evolve, we instead aim to look forward and "predict" topics that we believe will be important in current and future studies. Some of the most discussed topics in machine learning, such as bias and fairness, the handling of dirty data, and interpretable models, may be less familiar to the broader community using neuroimaging-based predictive modeling in psychiatry. In a similar vein, transdiagnostic research and targeting brain-based features for psychiatric intervention are modern topics in psychiatry that predictive models are well-suited to tackle. In this work, we target an audience who is a researcher familiar with the fundamental procedures of machine learning and who wishes to increase their knowledge of ongoing topics in the field. We aim to accelerate the utility and applications of neuroimaging-based predictive models for psychiatric research by highlighting and considering these topics. Furthermore, though not a focus, these ideas generalize to neuroimaging-based predictive modeling in other clinical neurosciences and predictive modeling with different data types (e.g., digital health data).
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Affiliation(s)
- Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA.
| | - Max Rolison
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Siyuan Gao
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | - Qinghao Liang
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | - Hannah Peterson
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Javid Dadashkarimi
- Department of Computer Science, Yale School of Engineering and Applied Science, New Haven, CT, USA
| | - Michael C Farruggia
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA
| | - C Alice Hahn
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Noble
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | | | - Angeliki Pollatou
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexander J Dufford
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT, USA
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
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14
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Rashidi HH, Pepper J, Howard T, Klein K, May L, Albahra S, Phinney B, Salemi MR, Tran NK. Comparative performance of two automated machine learning platforms for COVID-19 detection by MALDI-TOF-MS. PLoS One 2022; 17:e0263954. [PMID: 35905092 PMCID: PMC9337631 DOI: 10.1371/journal.pone.0263954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/25/2022] [Indexed: 11/19/2022] Open
Abstract
The 2019 novel coronavirus infectious disease (COVID-19) pandemic has resulted in an unsustainable need for diagnostic tests. Currently, molecular tests are the accepted standard for the detection of SARS-CoV-2. Mass spectrometry (MS) enhanced by machine learning (ML) has recently been postulated to serve as a rapid, high-throughput, and low-cost alternative to molecular methods. Automated ML is a novel approach that could move mass spectrometry techniques beyond the confines of traditional laboratory settings. However, it remains unknown how different automated ML platforms perform for COVID-19 MS analysis. To this end, the goal of our study is to compare algorithms produced by two commercial automated ML platforms (Platforms A and B). Our study consisted of MS data derived from 361 subjects with molecular confirmation of COVID-19 status including SARS-CoV-2 variants. The top optimized ML model with respect to positive percent agreement (PPA) within Platforms A and B exhibited an accuracy of 94.9%, PPA of 100%, negative percent agreement (NPA) of 93%, and an accuracy of 91.8%, PPA of 100%, and NPA of 89%, respectively. These results illustrate the MS method's robustness against SARS-CoV-2 variants and highlight similarities and differences in automated ML platforms in producing optimal predictive algorithms for a given dataset.
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Affiliation(s)
- Hooman H. Rashidi
- Robert. J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - John Pepper
- Spectra Pass LLC & Allegiant Airlines, Las Vegas, Nevada, United States of America
| | - Taylor Howard
- Dept. of Pathology and Laboratory Medicine, UC Davis, Davis, California, United States of America
| | - Karina Klein
- Dept. of Emergency Medicine, UC Davis, Davis, California, United States of America
| | - Larissa May
- Dept. of Emergency Medicine, UC Davis, Davis, California, United States of America
| | - Samer Albahra
- Robert. J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Brett Phinney
- Proteomics Core, UC Davis, Davis, California, United States of America
| | | | - Nam K. Tran
- Dept. of Pathology and Laboratory Medicine, UC Davis, Davis, California, United States of America
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15
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Exponential growth of systematic reviews assessing artificial intelligence studies in medicine: challenges and opportunities. Syst Rev 2022; 11:132. [PMID: 35761303 PMCID: PMC9238033 DOI: 10.1186/s13643-022-01984-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
The evidence-based medicine (EBM) movement is stepping up its efforts to assess medical artificial intelligence (AI) and data science studies. Since 2017, there has been a marked increase in the number of published systematic reviews that assess medical AI studies. Increasingly, data from observational studies are used in systematic reviews of medical AI studies. Assessment of risk of bias is especially important in medical AI studies to detect possible "AI bias".
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16
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Epstein R, Lee V, Mohr R, Zankich VR. The Answer Bot Effect (ABE): A powerful new form of influence made possible by intelligent personal assistants and search engines. PLoS One 2022; 17:e0268081. [PMID: 35648736 PMCID: PMC9159602 DOI: 10.1371/journal.pone.0268081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
We introduce and quantify a relatively new form of influence: the Answer Bot Effect (ABE). In a 2015 report in PNAS, researchers demonstrated the power that biased search results have to shift opinions and voting preferences without people’s knowledge–by up to 80% in some demographic groups. They labeled this phenomenon the Search Engine Manipulation Effect (SEME), speculating that its power derives from the high level of trust people have in algorithmically-generated content. We now describe three experiments with a total of 1,736 US participants conducted to determine to what extent giving users “the answer”–either via an answer box at the top of a page of search results or via a vocal reply to a question posed to an intelligent personal assistant (IPA)–might also impact opinions and votes. Participants were first given basic information about two candidates running for prime minister of Australia (this, in order to assure that participants were “undecided”), then asked questions about their voting preferences, then given answers to questions they posed about the candidates–either with answer boxes or with vocal answers on an Alexa simulator–and then asked again about their voting preferences. The experiments were controlled, randomized, double-blind, and counterbalanced. Experiments 1 and 2 demonstrated that answer boxes can shift voting preferences by as much as 38.6% and that the appearance of an answer box can reduce search times and clicks on search results. Experiment 3 demonstrated that even a single question-and-answer interaction on an IPA can shift voting preferences by more than 40%. Multiple questions posed to an IPA leading to answers that all have the same bias can shift voting preferences by more than 65%. Simple masking procedures still produced large opinion shifts while reducing awareness of bias to close to zero. ABE poses a serious threat to both democracy and human autonomy because (a) it produces large shifts in opinions and voting preferences with little or no user awareness, (b) it is an ephemeral form of influence that leaves no paper trail, and (c) worldwide, it is controlled almost exclusively by just four American tech companies. ABE will become a greater threat as people increasingly rely on IPAs for answers.
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Affiliation(s)
- Robert Epstein
- American Institute for Behavioral Research and Technology, Vista, California, United States of America
- * E-mail:
| | - Vivian Lee
- American Institute for Behavioral Research and Technology, Vista, California, United States of America
| | - Roger Mohr
- American Institute for Behavioral Research and Technology, Vista, California, United States of America
| | - Vanessa R. Zankich
- American Institute for Behavioral Research and Technology, Vista, California, United States of America
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17
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Lee J, Yang S, Holland-Hall C, Sezgin E, Gill M, Linwood S, Huang Y, Hoffman J. Prevalence of Sensitive Terms in Clinical Notes: observational study using natural language processing techniques (Preprint). JMIR Med Inform 2022; 10:e38482. [PMID: 35687381 PMCID: PMC9233261 DOI: 10.2196/38482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background Objective Methods Results Conclusions
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Affiliation(s)
- Jennifer Lee
- Nationwide Children's Hospital, Columbus, OH, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Samuel Yang
- Nationwide Children's Hospital, Columbus, OH, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Cynthia Holland-Hall
- Nationwide Children's Hospital, Columbus, OH, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Emre Sezgin
- Nationwide Children's Hospital, Columbus, OH, United States
| | - Manjot Gill
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Simon Linwood
- Nationwide Children's Hospital, Columbus, OH, United States
| | - Yungui Huang
- Nationwide Children's Hospital, Columbus, OH, United States
| | - Jeffrey Hoffman
- Nationwide Children's Hospital, Columbus, OH, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
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18
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Raclin T, Price A, Stave C, Lee E, Reddy B, Kim J, Chu L. Combining Machine Learning, Patient-Reported Outcomes and Value-Based Healthcare: Protocol for Scoping Reviews (Preprint). JMIR Res Protoc 2022; 11:e36395. [PMID: 35849426 PMCID: PMC9345029 DOI: 10.2196/36395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tyler Raclin
- Department of Anaesthesiology, Stanford School of Medicine, Stanford, CA, United States
| | - Amy Price
- Department of Anaesthesiology, Stanford School of Medicine, Stanford, CA, United States
| | - Christopher Stave
- Lane Medical Library Department, Stanford University, Stanford, CA, United States
| | - Eugenia Lee
- University of Chicago, Chicago, IL, United States
| | - Biren Reddy
- University of Chicago, Chicago, IL, United States
| | - Junsung Kim
- University of Chicago, Chicago, IL, United States
| | - Larry Chu
- Department of Anaesthesiology, Stanford School of Medicine, Stanford, CA, United States
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19
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Bagge-Petersen CM, Langstrup H, Larsen JE, Frølich A. Critical user-configurations in mHealth design: How mHealth-app design practices come to bias design against chronically ill children and young people as mHealth users. Digit Health 2022; 8:20552076221109531. [PMID: 35733878 PMCID: PMC9208037 DOI: 10.1177/20552076221109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
Mobile health smartphone applications (mHealth-apps) are increasingly emerging to assist children's and young people's management of chronic conditions. However, difficulties persist in applying design approaches in mHealth projects that return apps that are useful to this group. In this article, we explore ethnographically two self-proclaimed ‘user-driven’ projects designing mHealth apps for Danish patients below the age of 18 living with, respectively, haemophilia and rheumatoid arthritis. These projects initially included the perspectives of children and young people to inform the designs, however, eventually launched the final apps for adult patients only. Through a concept of ‘critical user-configuration’, we examine the projects’ challenges with attuning the designs to children and young people and how these drove their exclusion as users of the emerging mHealth apps. Critical user-configuration draws attention to critical moments in design practices where significant shifts in user-configurations take place, shaping who can become a user. More specifically, we uncover three critical moments: where mHealth projects expand the group of prospective users; where test subjects are selected; and where data governance systems and digital health infrastructures are mobilised in the design process. Throughout these critical moments, there is a drift from user-driven to data-driven design approaches which increasingly exclude groups of users who are less datafiable – in our case children and young people. We argue that besides giving voice to minors in mHealth design processes, we need to be mindful of the design practices that become decisive for – often implicitly – who can be configured as a user.
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Affiliation(s)
- Claudia M Bagge-Petersen
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Langstrup
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob E Larsen
- Department of Applied Mathematics and Computer Science, Section for Cognitive Systems, Technical University of Denmark, Lyngby, Denmark
| | - Anne Frølich
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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20
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Akter S, McCarthy G, Sajib S, Michael K, Dwivedi YK, D’Ambra J, Shen K. Algorithmic bias in data-driven innovation in the age of AI. INTERNATIONAL JOURNAL OF INFORMATION MANAGEMENT 2021. [DOI: 10.1016/j.ijinfomgt.2021.102387] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Wang J, Li S, Yeh TN, Chakraborty R, Graham AD, Yu SX, Lin MC. Quantifying Meibomian Gland Morphology Using Artificial Intelligence. Optom Vis Sci 2021; 98:1094-1103. [PMID: 34469930 PMCID: PMC8484036 DOI: 10.1097/opx.0000000000001767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
SIGNIFICANCE Quantifying meibomian gland morphology from meibography images is used for the diagnosis, treatment, and management of meibomian gland dysfunction in clinics. A novel and automated method is described for quantifying meibomian gland morphology from meibography images. PURPOSE Meibomian gland morphological abnormality is a common clinical sign of meibomian gland dysfunction, yet there exist no automated methods that provide standard quantifications of morphological features for individual glands. This study introduces an automated artificial intelligence approach to segmenting individual meibomian gland regions in infrared meibography images and analyzing their morphological features. METHODS A total of 1443 meibography images were collected and annotated. The dataset was then divided into development and evaluation sets. The development set was used to train and tune deep learning models for segmenting glands and identifying ghost glands from images, whereas the evaluation set was used to evaluate the performance of the model. The gland segmentations were further used to analyze individual gland features, including gland local contrast, length, width, and tortuosity. RESULTS A total of 1039 meibography images (including 486 upper and 553 lower eyelids) were used for training and tuning the deep learning model, whereas the remaining 404 images (including 203 upper and 201 lower eyelids) were used for evaluations. The algorithm on average achieved 63% mean intersection over union in segmenting glands, and 84.4% sensitivity and 71.7% specificity in identifying ghost glands. Morphological features of each gland were also fed to a support vector machine for analyzing their associations with ghost glands. Analysis of model coefficients indicated that low gland local contrast was the primary indicator for ghost glands. CONCLUSIONS The proposed approach can automatically segment individual meibomian glands in infrared meibography images, identify ghost glands, and quantitatively analyze gland morphological features.
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Affiliation(s)
| | | | | | | | - Andrew D Graham
- Clinical Research Center, School of Optometry, University of California, Berkeley, Berkeley, California
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22
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Abstract
Machine learning models are built using training data, which is collected from human experience and is prone to bias. Humans demonstrate a cognitive bias in their thinking and behavior, which is ultimately reflected in the collected data. From Amazon’s hiring system, which was built using ten years of human hiring experience, to a judicial system that was trained using human judging practices, these systems all include some element of bias. The best machine learning models are said to mimic humans’ cognitive ability, and thus such models are also inclined towards bias. However, detecting and evaluating bias is a very important step for better explainable models. In this work, we aim to explain bias in learning models in relation to humans’ cognitive bias and propose a wrapper technique to detect and evaluate bias in machine learning models using an openly accessible dataset from UCI Machine Learning Repository. In the deployed dataset, the potentially biased attributes (PBAs) are gender and race. This study introduces the concept of alternation functions to swap the values of PBAs, and evaluates the impact on prediction using KL divergence. Results demonstrate females and Asians to be associated with low wages, placing some open research questions for the research community to ponder over.
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23
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Kolyshkina I, Simoff S. Interpretability of Machine Learning Solutions in Public Healthcare: The CRISP-ML Approach. Front Big Data 2021; 4:660206. [PMID: 34124652 PMCID: PMC8187858 DOI: 10.3389/fdata.2021.660206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/07/2021] [Indexed: 11/25/2022] Open
Abstract
Public healthcare has a history of cautious adoption for artificial intelligence (AI) systems. The rapid growth of data collection and linking capabilities combined with the increasing diversity of the data-driven AI techniques, including machine learning (ML), has brought both ubiquitous opportunities for data analytics projects and increased demands for the regulation and accountability of the outcomes of these projects. As a result, the area of interpretability and explainability of ML is gaining significant research momentum. While there has been some progress in the development of ML methods, the methodological side has shown limited progress. This limits the practicality of using ML in the health domain: the issues with explaining the outcomes of ML algorithms to medical practitioners and policy makers in public health has been a recognized obstacle to the broader adoption of data science approaches in this domain. This study builds on the earlier work which introduced CRISP-ML, a methodology that determines the interpretability level required by stakeholders for a successful real-world solution and then helps in achieving it. CRISP-ML was built on the strengths of CRISP-DM, addressing the gaps in handling interpretability. Its application in the Public Healthcare sector follows its successful deployment in a number of recent real-world projects across several industries and fields, including credit risk, insurance, utilities, and sport. This study elaborates on the CRISP-ML methodology on the determination, measurement, and achievement of the necessary level of interpretability of ML solutions in the Public Healthcare sector. It demonstrates how CRISP-ML addressed the problems with data diversity, the unstructured nature of data, and relatively low linkage between diverse data sets in the healthcare domain. The characteristics of the case study, used in the study, are typical for healthcare data, and CRISP-ML managed to deliver on these issues, ensuring the required level of interpretability of the ML solutions discussed in the project. The approach used ensured that interpretability requirements were met, taking into account public healthcare specifics, regulatory requirements, project stakeholders, project objectives, and data characteristics. The study concludes with the three main directions for the development of the presented cross-industry standard process.
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Affiliation(s)
| | - Simeon Simoff
- School of Computer, Data and Mathematical Sciences, Western Sydney University, Sydney, NSW, Australia
- MARCS Institute for Brain, Behaviour and Development, Western Sydney University, Sydney, NSW, Australia
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24
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Bhaskar S, Bradley S, Sakhamuri S, Moguilner S, Chattu VK, Pandya S, Schroeder S, Ray D, Banach M. Designing Futuristic Telemedicine Using Artificial Intelligence and Robotics in the COVID-19 Era. Front Public Health 2020; 8:556789. [PMID: 33224912 PMCID: PMC7667043 DOI: 10.3389/fpubh.2020.556789] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022] Open
Abstract
Technological innovations such as artificial intelligence and robotics may be of potential use in telemedicine and in building capacity to respond to future pandemics beyond the current COVID-19 era. Our international consortium of interdisciplinary experts in clinical medicine, health policy, and telemedicine have identified gaps in uptake and implementation of telemedicine or telehealth across geographics and medical specialties. This paper discusses various artificial intelligence and robotics-assisted telemedicine or telehealth applications during COVID-19 and presents an alternative artificial intelligence assisted telemedicine framework to accelerate the rapid deployment of telemedicine and improve access to quality and cost-effective healthcare. We postulate that the artificial intelligence assisted telemedicine framework would be indispensable in creating futuristic and resilient health systems that can support communities amidst pandemics.
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Affiliation(s)
- Sonu Bhaskar
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Neurovascular Imaging Laboratory & NSW Brain Clot Bank, Department of Neurology, Liverpool Hospital and South Western Sydney Local Health District, Ingham Institute for Applied Medical Research, The University of New South Wales, Sydney, NSW, Australia
| | - Sian Bradley
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- The University of New South Wales (UNSW) Medicine Sydney, South West Sydney Clinical School, Sydney, NSW, Australia
| | - Sateesh Sakhamuri
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sebastian Moguilner
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
| | - Vijay Kumar Chattu
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Shawna Pandya
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Alberta Health Services and Project PoSSUM, University of Alberta, Edmonton, AB, Canada
| | - Starr Schroeder
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Penn Medicine Lancaster General Hospital and Project PoSSUM, Lancaster, PA, United States
| | - Daniel Ray
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Farr Institute of Health Informatics, University College London (UCL) & NHS Foundation Trust, Birmingham, United Kingdom
| | - Maciej Banach
- Pandemic Health System REsilience PROGRAM (REPROGRAM) Consortium, REPROGRAM Telemedicine Study Group, Sydney, NSW, Australia
- Polish Mother's Memorial Hospital Research Institute (PMMHRI) in Lodz, Cardiovascular Research Centre, University of Zielona Gora, Zielona Gora, Poland
- Department of Hypertension, Medical University of Lodz, Łódź, Poland
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