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Hellali R, Chelly Dagdia Z, Ktaish A, Zeitouni K, Annane D. Corticosteroid sensitivity detection in sepsis patients using a personalized data mining approach: A clinical investigation. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 245:108017. [PMID: 38241801 DOI: 10.1016/j.cmpb.2024.108017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/29/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND AND OBJECTIVE Sepsis is a life-threatening disease with high mortality, incidence, and morbidity. Corticosteroids (CS) are a recommended treatment for sepsis, but some patients respond negatively to CS therapy. Early prediction of corticosteroid responsiveness can help intervene and reduce mortality. In this study, we aim to develop a data mining methodology for predicting CS responsiveness of septic patients. METHODS We used data from a randomized controlled trial called APROCCHSS, which recruited 1241 septis patients to study the effectiveness of corticotherapy. We conducted a thorough study of multiple machine learning models to select the most efficient prediction model, called "signature". We evaluated the performance of the signature using precision, sensitivity, and specificity values. RESULTS We found that Logistic Regression was the best model with an AUC of 72%. We conducted further experiments to examine the impact of additional features and the model's generalizability to different groups of patients. We also performed a statistical analysis to analyze the effect of the treatment at the individual level and on the population as a whole. CONCLUSIONS Our data mining methodology can accurately predict cortico-sensitivity or resistance in septis patients. The signature has been deployed into the Assistance Publique - Hôpitaux de Paris (APHP) information system as a web service, taking patient information as input and providing a prediction of cortico-sensitivity or resistance. Early prediction of corticosteroid responsiveness can help clinicians intervene promptly and improve patient outcomes.
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Affiliation(s)
- Rahma Hellali
- Université Paris-Saclay, UVSQ, DAVID, Paris, France.
| | - Zaineb Chelly Dagdia
- Université Paris-Saclay, UVSQ, DAVID, Paris, France; Université de Tunis, Institut supérieur de gestion de Tunis, LARODEC, Tunis, Tunisia
| | | | | | - Djillali Annane
- Réanimation medico-chirurgicale, hôpital Raymond-Poincaré, AP-HP, Garches, France
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Myska V, Genzor S, Mezina A, Burget R, Mizera J, Stybnar M, Kolarik M, Sova M, Dutta MK. Artificial-Intelligence-Driven Algorithms for Predicting Response to Corticosteroid Treatment in Patients with Post-Acute COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13101755. [PMID: 37238239 DOI: 10.3390/diagnostics13101755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Pulmonary fibrosis is one of the most severe long-term consequences of COVID-19. Corticosteroid treatment increases the chances of recovery; unfortunately, it can also have side effects. Therefore, we aimed to develop prediction models for a personalized selection of patients benefiting from corticotherapy. The experiment utilized various algorithms, including Logistic Regression, k-NN, Decision Tree, XGBoost, Random Forest, SVM, MLP, AdaBoost, and LGBM. In addition easily human-interpretable model is presented. All algorithms were trained on a dataset consisting of a total of 281 patients. Every patient conducted an examination at the start and three months after the post-COVID treatment. The examination comprised a physical examination, blood tests, functional lung tests, and an assessment of health state based on X-ray and HRCT. The Decision tree algorithm achieved balanced accuracy (BA) of 73.52%, ROC-AUC of 74.69%, and 71.70% F1 score. Other algorithms achieving high accuracy included Random Forest (BA 70.00%, ROC-AUC 70.62%, 67.92% F1 score) and AdaBoost (BA 70.37%, ROC-AUC 63.58%, 70.18% F1 score). The experiments prove that information obtained during the initiation of the post-COVID-19 treatment can be used to predict whether the patient will benefit from corticotherapy. The presented predictive models can be used by clinicians to make personalized treatment decisions.
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Affiliation(s)
- Vojtech Myska
- Department of Telecommunications, Faculty of Electrical Engineering and Communications, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Samuel Genzor
- Department of Respiratory Medicine, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, I. P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Anzhelika Mezina
- Department of Telecommunications, Faculty of Electrical Engineering and Communications, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Radim Burget
- Department of Telecommunications, Faculty of Electrical Engineering and Communications, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Jan Mizera
- Department of Respiratory Medicine, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, I. P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Michal Stybnar
- Czech National e-Health Center, University Hospital Olomouc, I. P. Pavlova 6, 779 00 Olomouc, Czech Republic
| | - Martin Kolarik
- Department of Telecommunications, Faculty of Electrical Engineering and Communications, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Milan Sova
- Department of Respiratory Diseases and Tuberculosis, University Hospital Brno and Faculty of Medicine and Dentistry, Masaryk University Brno, Jihlavska 340/20, 625 00 Brno, Czech Republic
| | - Malay Kishore Dutta
- Centre for Advanced Studies, Dr. A. P. J. Abdul Kalam Technical University, Jankipuram Vistar, Lucknow 226021, India
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Zhong JY, Fischer NL. Commentary: The desire of medical students to integrate artificial intelligence into medical education: An opinion article. Front Digit Health 2023; 5:1151390. [PMID: 37090065 PMCID: PMC10117773 DOI: 10.3389/fdgth.2023.1151390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Affiliation(s)
- Jimmy Y. Zhong
- Science of Learning in Education Centre (SoLEC), Office of Education Research, National Institute of Education, Nanyang Technological University, Singapore, Singapore
- Center for Advanced Brain Imaging (CABI), Georgia Institute of Technology, Atlanta, GA, United States
- Correspondence: Jimmy Y. Zhong
| | - Nastassja L. Fischer
- Centre for Research and Development in Learning (CRADLE), Nanyang Technological University, Singapore, Singapore
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4
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Dalal S, Onyema EM, Malik A. Hybrid XGBoost model with hyperparameter tuning for prediction of liver disease with better accuracy. World J Gastroenterol 2022; 28:6551-6563. [PMID: 36569269 PMCID: PMC9782838 DOI: 10.3748/wjg.v28.i46.6551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 11/21/2022] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND Liver disease indicates any pathology that can harm or destroy the liver or prevent it from normal functioning. The global community has recently witnessed an increase in the mortality rate due to liver disease. This could be attributed to many factors, among which are human habits, awareness issues, poor healthcare, and late detection. To curb the growing threats from liver disease, early detection is critical to help reduce the risks and improve treatment outcome. Emerging technologies such as machine learning, as shown in this study, could be deployed to assist in enhancing its prediction and treatment.
AIM To present a more efficient system for timely prediction of liver disease using a hybrid eXtreme Gradient Boosting model with hyperparameter tuning with a view to assist in early detection, diagnosis, and reduction of risks and mortality associated with the disease.
METHODS The dataset used in this study consisted of 416 people with liver problems and 167 with no such history. The data were collected from the state of Andhra Pradesh, India, through https://www.kaggle.com/datasets/uciml/indian-liver-patient-records. The population was divided into two sets depending on the disease state of the patient. This binary information was recorded in the attribute "is_patient".
RESULTS The results indicated that the chi-square automated interaction detection and classification and regression trees models achieved an accuracy level of 71.36% and 73.24%, respectively, which was much better than the conventional method. The proposed solution would assist patients and physicians in tackling the problem of liver disease and ensuring that cases are detected early to prevent it from developing into cirrhosis (scarring) and to enhance the survival of patients. The study showed the potential of machine learning in health care, especially as it concerns disease prediction and monitoring.
CONCLUSION This study contributed to the knowledge of machine learning application to health and to the efforts toward combating the problem of liver disease. However, relevant authorities have to invest more into machine learning research and other health technologies to maximize their potential.
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Affiliation(s)
- Surjeet Dalal
- Department of CSE, Amity University, Gurugram 122413, Haryana, India
| | - Edeh Michael Onyema
- Department of Mathematics and Computer Science, Coal City University, Enugu 400102, Nigeria
| | - Amit Malik
- Department of CSE, SRM University, Delhi-NCR, Sonipat 131001, Haryana, India
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Oh SH, Lee SJ, Park J. Effective data-driven precision medicine by cluster-applied deep reinforcement learning. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.109877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Ramón A, Zaragozá M, Torres AM, Cascón J, Blasco P, Milara J, Mateo J. Application of Machine Learning in Hospitalized Patients with Severe COVID-19 Treated with Tocilizumab. J Clin Med 2022; 11:jcm11164729. [PMID: 36012968 PMCID: PMC9410189 DOI: 10.3390/jcm11164729] [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: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Among the IL-6 inhibitors, tocilizumab is the most widely used therapeutic option in patients with SARS-CoV-2-associated severe respiratory failure (SRF). The aim of our study was to provide evidence on predictors of poor outcome in patients with COVID-19 treated with tocilizumab, using machine learning (ML) techniques. We conducted a retrospective study, analyzing the clinical, laboratory and sociodemographic data of patients admitted for severe COVID-19 with SRF, treated with tocilizumab. The extreme gradient boost (XGB) method had the highest balanced accuracy (93.16%). The factors associated with a worse outcome of tocilizumab use in terms of mortality were: baseline situation at the start of tocilizumab treatment requiring invasive mechanical ventilation (IMV), elevated ferritin, lactate dehydrogenase (LDH) and glutamate-pyruvate transaminase (GPT), lymphopenia, and low PaFi [ratio between arterial oxygen pressure and inspired oxygen fraction (PaO2/FiO2)] values. The factors associated with a worse outcome of tocilizumab use in terms of hospital stay were: baseline situation at the start of tocilizumab treatment requiring IMV or supplemental oxygen, elevated levels of ferritin, glutamate-oxaloacetate transaminase (GOT), GPT, C-reactive protein (CRP), LDH, lymphopenia, and low PaFi values. In our study focused on patients with severe COVID-19 treated with tocilizumab, the factors that were weighted most strongly in predicting worse clinical outcome were baseline status at the start of tocilizumab treatment requiring IMV and hyperferritinemia.
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Affiliation(s)
- Antonio Ramón
- Department of Pharmacy, General University Hospital, 46014 Valencia, Spain
| | - Marta Zaragozá
- Department of Pharmacy, General University Hospital, 46014 Valencia, Spain
| | - Ana María Torres
- Institute of Technology, University of Castilla-La Mancha, 16002 Cuenca, Spain
| | - Joaquín Cascón
- Institute of Technology, University of Castilla-La Mancha, 16002 Cuenca, Spain
| | - Pilar Blasco
- Department of Pharmacy, General University Hospital, 46014 Valencia, Spain
| | - Javier Milara
- Department of Pharmacy, General University Hospital, 46014 Valencia, Spain
- Department of Pharmacology, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain
- Centre for Biomedical Research Network on Respiratory Diseases (CIBERES), Health Institute Carlos III, 28029 Madrid, Spain
- Correspondence:
| | - Jorge Mateo
- Institute of Technology, University of Castilla-La Mancha, 16002 Cuenca, Spain
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Niranjan V, Setlur AS, Karunakaran C, Uttarkar A, Kumar KM, Skariyachan S. Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2. Struct Chem 2022; 33:1585-1608. [PMID: 35938064 PMCID: PMC9346052 DOI: 10.1007/s11224-022-02020-z] [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: 04/18/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022]
Abstract
The unprecedented outbreak of the severe acute respiratory syndrome (SARS) Coronavirus-2, across the globe, triggered a worldwide uproar in the search for immediate treatment strategies. With no specific drug and not much data available, alternative approaches such as drug repurposing came to the limelight. To date, extensive research on the repositioning of drugs has led to the identification of numerous drugs against various important protein targets of the coronavirus strains, with hopes of the drugs working against the major variants of concerns (alpha, beta, gamma, delta, omicron) of the virus. Advancements in computational sciences have led to improved scope of repurposing via techniques such as structure-based approaches including molecular docking, molecular dynamic simulations and quantitative structure activity relationships, network-based approaches, and artificial intelligence-based approaches with other core machine and deep learning algorithms. This review highlights the various approaches to repurposing drugs from a computational biological perspective, with various mechanisms of action of the drugs against some of the major protein targets of SARS-CoV-2. Additionally, clinical trials data on potential COVID-19 repurposed drugs are also highlighted with stress on the major SARS-CoV-2 targets and the structural effect of variants on these targets. The interaction modelling of some important repurposed drugs has also been elucidated. Furthermore, the merits and demerits of drug repurposing are also discussed, with a focus on the scope and applications of the latest advancements in repurposing.
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Affiliation(s)
- Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka India
| | | | | | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka India
| | - Kalavathi Murugan Kumar
- Department of Bioinformatics, Pondicherry University, Chinna Kalapet, Kalapet, Puducherry, Tamil Nadu India
| | - Sinosh Skariyachan
- Department of Microbiology, St. Pius X College, Rajapuram, Kasaragod, Kerala India
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Mandadi S, Pulluru H, Annie F. Comparative outcomes of combined corticosteroid and remdesivir therapy with corticosteroid monotherapy in ventilated COVID-19 patients. PLoS One 2022; 17:e0264301. [PMID: 35196344 PMCID: PMC8865672 DOI: 10.1371/journal.pone.0264301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Abstract
Remdesivir (RDV) reduces time to clinical improvement in hospitalized COVID -19 patients requiring supplemental oxygen. Dexamethasone improves survival in those requiring oxygen support. Data is lacking on the efficacy of combination therapy in patients on mechanical ventilation. We analyzed for comparative outcomes between Corticosteroid (CS) therapy with combined Corticosteroid and Remdesivir (CS-RDV) therapy. We conducted an observational cohort study of patients aged 18 to 90 with COVID-19 requiring ventilatory support using TriNetX (COVID-19 Research Network) between January 20, 2020, and February 9, 2021. We compared patients who received at least 48 hours of CS-RDV combination therapy to CS monotherapy. The primary outcome was 28-day all-cause mortality rates in propensity-matched (PSM) cohorts. Secondary outcomes were Length of Stay (LOS), Secondary Bacterial Infections (SBI), and MRSA (Methicillin-Resistant Staphylococcus aureus), and Pseudomonas infections. We used univariate and multivariate Cox proportional hazards models and stratified log-rank tests. Of 388 patients included, 91 (23.5%) received CS-RDV therapy, and 297 (76.5%) received CS monotherapy. After propensity score matching, with 74 patients in each cohort, all-cause mortality was 36.4% and 29.7% in the CS-RDV and CS therapy, respectively (P = 0.38). We used a Kaplan-Meier with a log-rank test on follow up period (P = 0.23), and a Hazards Ratio model (P = 0.26). SBI incidence was higher in the CS group (13.5% vs. 35.1%, P = 0.02) with a similar LOS (13.4 days vs. 13.4 days, P = 1.00) and similar incidence of MRSA/Pseudomonas infections (13.5% vs. 13.5%, P = 1.00) in both the groups. Therefore, CS-RDV therapy is non-inferior to CS therapy in reducing 28-day all-cause in-hospital mortality but associated with a significant decrease in the incidence of SBI in critically ill COVID-19 patients.
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Affiliation(s)
- Subhadra Mandadi
- Department of Infectious Diseases, Charleston Area Medical Center, Charleston, West Virginia, United States of America
- * E-mail:
| | - Harish Pulluru
- Department of Hospital Medicine, Charleston Area Medical Center, Charleston, West Virginia, United States of America
| | - Frank Annie
- Charleston Area Medical Center Health Education and Research Institute, Charleston, West Virginia, United States of America
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Wang Z, Xu Z, He D, Chan S. Deep logarithmic neural network for Internet intrusion detection. Soft comput 2021. [DOI: 10.1007/s00500-021-05987-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Rubin GD. CT Diagnosis of COVID-19: A View through the PICOTS Lens. Radiology 2021; 301:E375-E377. [PMID: 34184939 PMCID: PMC8267780 DOI: 10.1148/radiol.2021211454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Geoffrey D Rubin
- University of Arizona Medical Center - University Campus - Department of Radiology 1501 N. Campbell Ave. Tucson Arizona 85724-5128 United States
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Maron JL. Personalizing Therapies and Targeting Treatment Strategies Through Pharmacogenomics and Artificial Intelligence. Clin Ther 2021; 43:793-794. [PMID: 34052008 DOI: 10.1016/j.clinthera.2021.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Jill L Maron
- Departments of Pediatrics and Obstetrics & Gynecology, Mother Infant Research Institute, Tufts Medical Center, Boston, Massachusetts
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