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Yousef H, Malagurski Tortei B, Castiglione F. Predicting multiple sclerosis disease progression and outcomes with machine learning and MRI-based biomarkers: a review. J Neurol 2024:10.1007/s00415-024-12651-3. [PMID: 39266777 DOI: 10.1007/s00415-024-12651-3] [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: 05/08/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 09/14/2024]
Abstract
Multiple sclerosis (MS) is a demyelinating neurological disorder with a highly heterogeneous clinical presentation and course of progression. Disease-modifying therapies are the only available treatment, as there is no known cure for the disease. Careful selection of suitable therapies is necessary, as they can be accompanied by serious risks and adverse effects such as infection. Magnetic resonance imaging (MRI) plays a central role in the diagnosis and management of MS, though MRI lesions have displayed only moderate associations with MS clinical outcomes, known as the clinico-radiological paradox. With the advent of machine learning (ML) in healthcare, the predictive power of MRI can be improved by leveraging both traditional and advanced ML algorithms capable of analyzing increasingly complex patterns within neuroimaging data. The purpose of this review was to examine the application of MRI-based ML for prediction of MS disease progression. Studies were divided into five main categories: predicting the conversion of clinically isolated syndrome to MS, cognitive outcome, EDSS-related disability, motor disability and disease activity. The performance of ML models is discussed along with highlighting the influential MRI-derived biomarkers. Overall, MRI-based ML presents a promising avenue for MS prognosis. However, integration of imaging biomarkers with other multimodal patient data shows great potential for advancing personalized healthcare approaches in MS.
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Affiliation(s)
- Hibba Yousef
- Technology Innovation Institute, Biotechnology Research Center, P.O.Box: 9639, Masdar City, Abu Dhabi, United Arab Emirates.
| | - Brigitta Malagurski Tortei
- Technology Innovation Institute, Biotechnology Research Center, P.O.Box: 9639, Masdar City, Abu Dhabi, United Arab Emirates
| | - Filippo Castiglione
- Technology Innovation Institute, Biotechnology Research Center, P.O.Box: 9639, Masdar City, Abu Dhabi, United Arab Emirates
- Institute for Applied Computing (IAC), National Research Council of Italy, Rome, Italy
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2
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Pilehvari S, Morgan Y, Peng W. An analytical review on the use of artificial intelligence and machine learning in diagnosis, prediction, and risk factor analysis of multiple sclerosis. Mult Scler Relat Disord 2024; 89:105761. [PMID: 39018642 DOI: 10.1016/j.msard.2024.105761] [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: 09/14/2023] [Revised: 06/19/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024]
Abstract
Medical research offers potential for disease prediction, like Multiple Sclerosis (MS). This neurological disorder damages nerve cell sheaths, with treatments focusing on symptom relief. Manual MS detection is time-consuming and error prone. Though MS lesion detection has been studied, limited attention has been paid to clinical analysis and computational risk factor prediction. Artificial intelligence (AI) techniques and Machine Learning (ML) methods offer accurate and effective alternatives to mapping MS progression. However, there are challenges in accessing clinical data and interdisciplinary collaboration. By analyzing 103 papers, we recognize the trends, strengths and weaknesses of AI, ML, and statistical methods applied to MS diagnosis. AI/ML-based approaches are suggested to identify MS risk factors, select significant MS features, and improve the diagnostic accuracy, such as Rule-based Fuzzy Logic (RBFL), Adaptive Fuzzy Inference System (ANFIS), Artificial Neural Network methods (ANN), Support Vector Machine (SVM), and Bayesian Networks (BNs). Meanwhile, applications of the Expanded Disability Status Scale (EDSS) and Magnetic Resonance Imaging (MRI) can enhance MS diagnostic accuracy. By examining established risk factors like obesity, smoking, and education, some research tackled the issue of disease progression. The performance metrics varied across different aspects of MS studies: Diagnosis: Sensitivity ranged from 60 % to 98 %, specificity from 60 % to 98 %, and accuracy from 61 % to 97 %. Prediction: Sensitivity ranged from 76 % to 98 %, specificity from 65 % to 98 %, and accuracy from 62 % to 99 %. Segmentation: Accuracy ranged up to 96.7 %. Classification: Sensitivity ranged from 78 % to 97.34 %, specificity from 65 % to 99.32 %, and accuracy from 71 % to 97.94 %. Furthermore, the literature shows that combining techniques can improve efficiency, exploiting their strengths for better overall performance.
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Affiliation(s)
- Shima Pilehvari
- University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Yasser Morgan
- University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Wei Peng
- University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada.
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Noteboom S, Seiler M, Chien C, Rane RP, Barkhof F, Strijbis EMM, Paul F, Schoonheim MM, Ritter K. Evaluation of machine learning-based classification of clinical impairment and prediction of clinical worsening in multiple sclerosis. J Neurol 2024; 271:5577-5589. [PMID: 38909341 PMCID: PMC11319410 DOI: 10.1007/s00415-024-12507-w] [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: 02/29/2024] [Revised: 06/01/2024] [Accepted: 06/09/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Robust predictive models of clinical impairment and worsening in multiple sclerosis (MS) are needed to identify patients at risk and optimize treatment strategies. OBJECTIVE To evaluate whether machine learning (ML) methods can classify clinical impairment and predict worsening in people with MS (pwMS) and, if so, which combination of clinical and magnetic resonance imaging (MRI) features and ML algorithm is optimal. METHODS We used baseline clinical and structural MRI data from two MS cohorts (Berlin: n = 125, Amsterdam: n = 330) to evaluate the capability of five ML models in classifying clinical impairment at baseline and predicting future clinical worsening over a follow-up of 2 and 5 years. Clinical worsening was defined by increases in the Expanded Disability Status Scale (EDSS), Timed 25-Foot Walk Test (T25FW), 9-Hole Peg Test (9HPT), or Symbol Digit Modalities Test (SDMT). Different combinations of clinical and volumetric MRI measures were systematically assessed in predicting clinical outcomes. ML models were evaluated using Monte Carlo cross-validation, area under the curve (AUC), and permutation testing to assess significance. RESULTS The ML models significantly determined clinical impairment at baseline for the Amsterdam cohort, but did not reach significance for predicting clinical worsening over a follow-up of 2 and 5 years. High disability (EDSS ≥ 4) was best determined by a support vector machine (SVM) classifier using clinical and global MRI volumes (AUC = 0.83 ± 0.07, p = 0.015). Impaired cognition (SDMT Z-score ≤ -1.5) was best determined by a SVM using regional MRI volumes (thalamus, ventricles, lesions, and hippocampus), reaching an AUC of 0.73 ± 0.04 (p = 0.008). CONCLUSION ML models could aid in classifying pwMS with clinical impairment and identify relevant biomarkers, but prediction of clinical worsening is an unmet need.
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Affiliation(s)
- Samantha Noteboom
- MS Center Amsterdam, Anatomy and Neurosciences, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands.
| | - Moritz Seiler
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience Berlin, Berlin, Germany
| | - Claudia Chien
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Roshan P Rane
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience Berlin, Berlin, Germany
| | - Frederik Barkhof
- MS Center Amsterdam, Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
- Centre for Medical Image Computing, Queen Square Institute of Neurology, University College London, London, UK
| | - Eva M M Strijbis
- MS Center Amsterdam, Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Friedemann Paul
- Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Menno M Schoonheim
- MS Center Amsterdam, Anatomy and Neurosciences, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
| | - Kerstin Ritter
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience Berlin, Berlin, Germany
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Mayfield JD, Murtagh R, Ciotti J, Robertson D, Naqa IE. Time-Dependent Deep Learning Prediction of Multiple Sclerosis Disability. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024:10.1007/s10278-024-01031-y. [PMID: 38871944 DOI: 10.1007/s10278-024-01031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 06/15/2024]
Abstract
The majority of deep learning models in medical image analysis concentrate on single snapshot timepoint circumstances, such as the identification of current pathology on a given image or volume. This is often in contrast to the diagnostic methodology in radiology where presumed pathologic findings are correlated to prior studies and subsequent changes over time. For multiple sclerosis (MS), the current body of literature describes various forms of lesion segmentation with few studies analyzing disability progression over time. For the purpose of longitudinal time-dependent analysis, we propose a combinatorial analysis of a video vision transformer (ViViT) benchmarked against traditional recurrent neural network of Convolutional Neural Network-Long Short-Term Memory (CNN-LSTM) architectures and a hybrid Vision Transformer-LSTM (ViT-LSTM) to predict long-term disability based upon the Extended Disability Severity Score (EDSS). The patient cohort was procured from a two-site institution with 703 patients' multisequence, contrast-enhanced MRIs of the cervical spine between the years 2002 and 2023. Following a competitive performance analysis, a VGG-16-based CNN-LSTM was compared to ViViT with an ablation analysis to determine time-dependency of the models. The VGG16-LSTM predicted trinary classification of EDSS score in 6 years with 0.74 AUC versus the ViViT with 0.84 AUC (p-value < 0.001 per 5 × 2 cross-validation F-test) on an 80:20 hold-out testing split. However, the VGG16-LSTM outperformed ViViT when patients with only 2 years of MRIs (n = 94) (0.75 AUC versus 0.72 AUC, respectively). Exact EDSS classification was investigated for both models using both classification and regression strategies but showed collectively worse performance. Our experimental results demonstrate the ability of time-dependent deep learning models to predict disability in MS using trinary stratification of disability, mimicking clinical practice. Further work includes external validation and subsequent observational clinical trials.
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Affiliation(s)
- John D Mayfield
- USF Health Department of Radiology, 2 Tampa General Circle, STC 6103, Tampa, FL, 33612, USA.
| | - Ryan Murtagh
- USF Health Department of Radiology, 2 Tampa General Circle, STC 6103, Tampa, FL, 33612, USA
| | - John Ciotti
- Department of Neurology, University of South Florida, Morsani College of Medicine, USF Multiple Sclerosis Center, 13330 USF Laurel Drive, Tampa, FL, 33612, USA
| | - Derrick Robertson
- Department of Neurology, James A. Haley VA Medical Center, 13000 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Issam El Naqa
- University of South Florida, College of Engineering, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
- H. Lee Moffitt Cancer Center Department of Machine Learning, Tampa, FL, 33612, USA
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Begum N, Rahman MM, Omar Faruk M. Machine learning prediction of nutritional status among pregnant women in Bangladesh: Evidence from Bangladesh demographic and health survey 2017-18. PLoS One 2024; 19:e0304389. [PMID: 38820295 PMCID: PMC11142495 DOI: 10.1371/journal.pone.0304389] [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: 01/24/2024] [Accepted: 05/12/2024] [Indexed: 06/02/2024] Open
Abstract
AIM Malnutrition in pregnant women significantly affects both mother and child health. This research aims to identify the best machine learning (ML) techniques for predicting the nutritional status of pregnant women in Bangladesh and detect the most essential features based on the best-performed algorithm. METHODS This study used retrospective cross-sectional data from the Bangladeshi Demographic and Health Survey 2017-18. Different feature transformations and machine learning classifiers were applied to find the best transformation and classification model. RESULTS This investigation found that robust scaling outperformed all feature transformation methods. The result shows that the Random Forest algorithm with robust scaling outperforms all other machine learning algorithms with 74.75% accuracy, 57.91% kappa statistics, 73.36% precision, 73.08% recall, and 73.09% f1 score. In addition, the Random Forest algorithm had the highest precision (76.76%) and f1 score (71.71%) for predicting the underweight class, as well as an expected precision of 82.01% and f1 score of 83.78% for the overweight/obese class when compared to other algorithms with a robust scaling method. The respondent's age, wealth index, region, husband's education level, husband's age, and occupation were crucial features for predicting the nutritional status of pregnant women in Bangladesh. CONCLUSION The proposed classifier could help predict the expected outcome and reduce the burden of malnutrition among pregnant women in Bangladesh.
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Affiliation(s)
- Najma Begum
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Mohammad Omar Faruk
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
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Rasouli S, Dakkali MS, Azarbad R, Ghazvini A, Asani M, Mirzaasgari Z, Arish M. Predicting the conversion from clinically isolated syndrome to multiple sclerosis: An explainable machine learning approach. Mult Scler Relat Disord 2024; 86:105614. [PMID: 38642495 DOI: 10.1016/j.msard.2024.105614] [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: 12/03/2023] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/22/2024]
Abstract
INTRODUCTION Predicting the conversion of clinically isolated syndrome (CIS) to clinically definite multiple sclerosis (CDMS) is critical to personalizing treatment planning and benefits for patients. The aim of this study is to develop an explainable machine learning (ML) model for predicting this conversion based on demographic, clinical, and imaging data. METHOD The ML model, Extreme Gradient Boosting (XGBoost), was employed on the public dataset of 273 Mexican mestizo CIS patients with 10-year follow-up. The data was divided into a training set for cross-validation and feature selection, and a holdout test set for final testing. Feature importance was determined using the SHapley Additive Explanations library (SHAP). Then, two experiments were conducted to optimize the model's performance by selectively adding variables and selecting the most contributive variables for the final model. RESULTS Nine variables including age, gender, schooling, motor symptoms, infratentorial and periventricular lesion at imaging, oligoclonal band in cerebrospinal fluid, lesion and symptoms types were significant. The model achieved an accuracy of 83.6 %, AUC of 91.8 %, sensitivity of 83.9 %, and specificity of 83.4 % in cross-validation. In the final testing, the model achieved an accuracy of 78.3 %, AUC of 85.8 %, sensitivity of 75 %, and specificity of 81.1 %. Finally, a web-based demo of the model was created for testing purposes. CONCLUSION The model, focusing on feature selection and interpretability, effectively stratifies risk for treatment decisions and disability prevention in MS patients. It provides a numerical risk estimate for CDMS conversion, enhancing transparency in clinical decision-making and aiding in patient care.
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Affiliation(s)
- Saeid Rasouli
- School of Medicine, Five Senses Health Research Institute, Hazrat-e Rasool General Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Sedigh Dakkali
- Department of Ophthalmology, School of Medicine, Al Zahra Eye Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Reza Azarbad
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Azim Ghazvini
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdi Asani
- Department of Ophthalmology, School of Medicine, Al Zahra Eye Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zahra Mirzaasgari
- Department of Neurology, Firoozgar hospital, School of medicine, University of Medical Science, Iran
| | - Mohammed Arish
- Department of Ophthalmology, School of Medicine, Al Zahra Eye Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
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Zhang K, Lincoln JA, Jiang X, Bernstam EV, Shams S. Predicting multiple sclerosis severity with multimodal deep neural networks. BMC Med Inform Decis Mak 2023; 23:255. [PMID: 37946182 PMCID: PMC10634041 DOI: 10.1186/s12911-023-02354-6] [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: 07/17/2022] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Multiple Sclerosis (MS) is a chronic disease developed in the human brain and spinal cord, which can cause permanent damage or deterioration of the nerves. The severity of MS disease is monitored by the Expanded Disability Status Scale, composed of several functional sub-scores. Early and accurate classification of MS disease severity is critical for slowing down or preventing disease progression via applying early therapeutic intervention strategies. Recent advances in deep learning and the wide use of Electronic Health Records (EHR) create opportunities to apply data-driven and predictive modeling tools for this goal. Previous studies focusing on using single-modal machine learning and deep learning algorithms were limited in terms of prediction accuracy due to data insufficiency or model simplicity. In this paper, we proposed the idea of using patients' multimodal longitudinal and longitudinal EHR data to predict multiple sclerosis disease severity in the future. Our contribution has two main facets. First, we describe a pioneering effort to integrate structured EHR data, neuroimaging data and clinical notes to build a multi-modal deep learning framework to predict patient's MS severity. The proposed pipeline demonstrates up to 19% increase in terms of the area under the Area Under the Receiver Operating Characteristic curve (AUROC) compared to models using single-modal data. Second, the study also provides valuable insights regarding the amount useful signal embedded in each data modality with respect to MS disease prediction, which may improve data collection processes.
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Affiliation(s)
- Kai Zhang
- Department of Health Data Science and Artificial Intelligence, McWilliams School of Biomedical Informatics, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - John A Lincoln
- Department of Neurology, University of Texas Health Sciences Center, McGovern Medical School, Houston, TX, USA
| | - Xiaoqian Jiang
- Department of Health Data Science and Artificial Intelligence, McWilliams School of Biomedical Informatics, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Elmer V Bernstam
- Department of Health Data Science and Artificial Intelligence, McWilliams School of Biomedical Informatics, University of Texas Health Sciences Center at Houston, Houston, TX, USA
- Division of General Internal Medicine, Department of Internal Medicine, University of Texas Health Sciences Center, McGovern Medical School, Houston, TX, USA
| | - Shayan Shams
- Department of Health Data Science and Artificial Intelligence, McWilliams School of Biomedical Informatics, University of Texas Health Sciences Center at Houston, Houston, TX, USA.
- Department of Applied Data Science, San Jose State University, San Jose, CA, USA.
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Nashwan AJ, Alkhawaldeh IM, Shaheen N, Albalkhi I, Serag I, Sarhan K, Abujaber AA, Abd-Alrazaq A, Yassin MA. Using artificial intelligence to improve body iron quantification: A scoping review. Blood Rev 2023; 62:101133. [PMID: 37748945 DOI: 10.1016/j.blre.2023.101133] [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: 07/06/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023]
Abstract
This scoping review explores the potential of artificial intelligence (AI) in enhancing the screening, diagnosis, and monitoring of disorders related to body iron levels. A systematic search was performed to identify studies that utilize machine learning in iron-related disorders. The search revealed a wide range of machine learning algorithms used by different studies. Notably, most studies used a single data type. The studies varied in terms of sample sizes, participant ages, and geographical locations. AI's role in quantifying iron concentration is still in its early stages, yet its potential is significant. The question is whether AI-based diagnostic biomarkers can offer innovative approaches for screening, diagnosing, and monitoring of iron overload and anemia.
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Affiliation(s)
- Abdulqadir J Nashwan
- Department of Nursing, Hazm Mebaireek General Hospital, Hamad Medical Corporation, Doha, Qatar; Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.
| | | | - Nour Shaheen
- Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Ibrahem Albalkhi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Neuroradiology, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond St, London WC1N 3JH, United Kingdom.
| | - Ibrahim Serag
- Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Khalid Sarhan
- Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Ahmad A Abujaber
- Department of Nursing, Hazm Mebaireek General Hospital, Hamad Medical Corporation, Doha, Qatar.
| | - Alaa Abd-Alrazaq
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar.
| | - Mohamed A Yassin
- Hematology and Oncology, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar.
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Mumtaz H, Saqib M, Jabeen S, Muneeb M, Mughal W, Sohail H, Safdar M, Mehmood Q, Khan MA, Ismail SM. Exploring alternative approaches to precision medicine through genomics and artificial intelligence - a systematic review. Front Med (Lausanne) 2023; 10:1227168. [PMID: 37849490 PMCID: PMC10577305 DOI: 10.3389/fmed.2023.1227168] [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: 05/22/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
The core idea behind precision medicine is to pinpoint the subpopulations that differ from one another in terms of disease risk, drug responsiveness, and treatment outcomes due to differences in biology and other traits. Biomarkers are found through genomic sequencing. Multi-dimensional clinical and biological data are created using these biomarkers. Better analytic methods are needed for these multidimensional data, which can be accomplished by using artificial intelligence (AI). An updated review of 80 latest original publications is presented on four main fronts-preventive medicine, medication development, treatment outcomes, and diagnostic medicine-All these studies effectively illustrated the significance of AI in precision medicine. Artificial intelligence (AI) has revolutionized precision medicine by swiftly analyzing vast amounts of data to provide tailored treatments and predictive diagnostics. Through machine learning algorithms and high-resolution imaging, AI assists in precise diagnoses and early disease detection. AI's ability to decode complex biological factors aids in identifying novel therapeutic targets, allowing personalized interventions and optimizing treatment outcomes. Furthermore, AI accelerates drug discovery by navigating chemical structures and predicting drug-target interactions, expediting the development of life-saving medications. With its unrivaled capacity to comprehend and interpret data, AI stands as an invaluable tool in the pursuit of enhanced patient care and improved health outcomes. It's evident that AI can open a new horizon for precision medicine by translating complex data into actionable information. To get better results in this regard and to fully exploit the great potential of AI, further research is required on this pressing subject.
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Affiliation(s)
| | | | | | - Muhammad Muneeb
- Department of Medicine, Dow University of Health Sciences, Karachi, Pakistan
| | - Wajiha Mughal
- Department of Medicine, Dow University of Health Sciences, Karachi, Pakistan
| | - Hassan Sohail
- Department of Medicine, Dow University of Health Sciences, Karachi, Pakistan
| | - Myra Safdar
- Armed Forces Institute of Cardiology and National Institute of Heart Diseases (AFIC-NIHD), Rawalpindi, Pakistan
| | - Qasim Mehmood
- Department of Medicine, King Edward Medical University, Lahore, Pakistan
| | - Muhammad Ahsan Khan
- Department of Medicine, Dow University of Health Sciences, Karachi, Pakistan
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Vázquez-Marrufo M, Sarrias-Arrabal E, García-Torres M, Martín-Clemente R, Izquierdo G. A systematic review of the application of machine-learning algorithms in multiple sclerosis. Neurologia 2023; 38:577-590. [PMID: 35843587 DOI: 10.1016/j.nrleng.2020.10.013] [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: 06/05/2020] [Accepted: 10/11/2020] [Indexed: 10/17/2022] Open
Abstract
INTRODUCTION The applications of artificial intelligence, and in particular automatic learning or "machine learning" (ML), constitute both a challenge and a great opportunity in numerous scientific, technical, and clinical disciplines. Specific applications in the study of multiple sclerosis (MS) have been no exception, and constitute an area of increasing interest in recent years. OBJECTIVE We present a systematic review of the application of ML algorithms in MS. MATERIALS AND METHODS We used the PubMed search engine, which allows free access to the MEDLINE medical database, to identify studies including the keywords "machine learning" and "multiple sclerosis." We excluded review articles, studies written in languages other than English or Spanish, and studies that were mainly technical and did not specifically apply to MS. The final selection included 76 articles, and 38 were rejected. CONCLUSIONS After the review process, we established 4 main applications of ML in MS: 1) classifying MS subtypes; 2) distinguishing patients with MS from healthy controls and individuals with other diseases; 3) predicting progression and response to therapeutic interventions; and 4) other applications. Results found to date have shown that ML algorithms may offer great support for health professionals both in clinical settings and in research into MS.
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Affiliation(s)
- M Vázquez-Marrufo
- Departamento de Psicología Experimental, Facultad de Psicología, Universidad de Sevilla, Sevilla, Spain.
| | - E Sarrias-Arrabal
- Departamento de Psicología Experimental, Facultad de Psicología, Universidad de Sevilla, Sevilla, Spain
| | - M García-Torres
- Escuela Politécnica Superior, Universidad Pablo de Olavide, Sevilla, Spain
| | - R Martín-Clemente
- Departamento de Teoría de la Señal y Comunicaciones, Escuela Técnica Superior de Ingeniería, Universidad de Sevilla, Sevilla, Spain
| | - G Izquierdo
- Unidad de Esclerosis Múltiple, Hospital VITHAS, Sevilla, Spain
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Reeve K, On BI, Havla J, Burns J, Gosteli-Peter MA, Alabsawi A, Alayash Z, Götschi A, Seibold H, Mansmann U, Held U. Prognostic models for predicting clinical disease progression, worsening and activity in people with multiple sclerosis. Cochrane Database Syst Rev 2023; 9:CD013606. [PMID: 37681561 PMCID: PMC10486189 DOI: 10.1002/14651858.cd013606.pub2] [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] [Indexed: 09/09/2023]
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system that affects millions of people worldwide. The disease course varies greatly across individuals and many disease-modifying treatments with different safety and efficacy profiles have been developed recently. Prognostic models evaluated and shown to be valid in different settings have the potential to support people with MS and their physicians during the decision-making process for treatment or disease/life management, allow stratified and more precise interpretation of interventional trials, and provide insights into disease mechanisms. Many researchers have turned to prognostic models to help predict clinical outcomes in people with MS; however, to our knowledge, no widely accepted prognostic model for MS is being used in clinical practice yet. OBJECTIVES To identify and summarise multivariable prognostic models, and their validation studies for quantifying the risk of clinical disease progression, worsening, and activity in adults with MS. SEARCH METHODS We searched MEDLINE, Embase, and the Cochrane Database of Systematic Reviews from January 1996 until July 2021. We also screened the reference lists of included studies and relevant reviews, and references citing the included studies. SELECTION CRITERIA We included all statistically developed multivariable prognostic models aiming to predict clinical disease progression, worsening, and activity, as measured by disability, relapse, conversion to definite MS, conversion to progressive MS, or a composite of these in adult individuals with MS. We also included any studies evaluating the performance of (i.e. validating) these models. There were no restrictions based on language, data source, timing of prognostication, or timing of outcome. DATA COLLECTION AND ANALYSIS Pairs of review authors independently screened titles/abstracts and full texts, extracted data using a piloted form based on the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies (CHARMS), assessed risk of bias using the Prediction Model Risk Of Bias Assessment Tool (PROBAST), and assessed reporting deficiencies based on the checklist items in Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis (TRIPOD). The characteristics of the included models and their validations are described narratively. We planned to meta-analyse the discrimination and calibration of models with at least three external validations outside the model development study but no model met this criterion. We summarised between-study heterogeneity narratively but again could not perform the planned meta-regression. MAIN RESULTS We included 57 studies, from which we identified 75 model developments, 15 external validations corresponding to only 12 (16%) of the models, and six author-reported validations. Only two models were externally validated multiple times. None of the identified external validations were performed by researchers independent of those that developed the model. The outcome was related to disease progression in 39 (41%), relapses in 8 (8%), conversion to definite MS in 17 (18%), and conversion to progressive MS in 27 (28%) of the 96 models or validations. The disease and treatment-related characteristics of included participants, and definitions of considered predictors and outcome, were highly heterogeneous amongst the studies. Based on the publication year, we observed an increase in the percent of participants on treatment, diversification of the diagnostic criteria used, an increase in consideration of biomarkers or treatment as predictors, and increased use of machine learning methods over time. Usability and reproducibility All identified models contained at least one predictor requiring the skills of a medical specialist for measurement or assessment. Most of the models (44; 59%) contained predictors that require specialist equipment likely to be absent from primary care or standard hospital settings. Over half (52%) of the developed models were not accompanied by model coefficients, tools, or instructions, which hinders their application, independent validation or reproduction. The data used in model developments were made publicly available or reported to be available on request only in a few studies (two and six, respectively). Risk of bias We rated all but one of the model developments or validations as having high overall risk of bias. The main reason for this was the statistical methods used for the development or evaluation of prognostic models; we rated all but two of the included model developments or validations as having high risk of bias in the analysis domain. None of the model developments that were externally validated or these models' external validations had low risk of bias. There were concerns related to applicability of the models to our research question in over one-third (38%) of the models or their validations. Reporting deficiencies Reporting was poor overall and there was no observable increase in the quality of reporting over time. The items that were unclearly reported or not reported at all for most of the included models or validations were related to sample size justification, blinding of outcome assessors, details of the full model or how to obtain predictions from it, amount of missing data, and treatments received by the participants. Reporting of preferred model performance measures of discrimination and calibration was suboptimal. AUTHORS' CONCLUSIONS The current evidence is not sufficient for recommending the use of any of the published prognostic prediction models for people with MS in clinical routine today due to lack of independent external validations. The MS prognostic research community should adhere to the current reporting and methodological guidelines and conduct many more state-of-the-art external validation studies for the existing or newly developed models.
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Affiliation(s)
- Kelly Reeve
- Epidemiology, Biostatistics and Prevention Institute, University of Zürich, Zurich, Switzerland
| | - Begum Irmak On
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joachim Havla
- lnstitute of Clinical Neuroimmunology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacob Burns
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | | | - Albraa Alabsawi
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Zoheir Alayash
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Institute of Health Services Research in Dentistry, University of Münster, Muenster, Germany
| | - Andrea Götschi
- Epidemiology, Biostatistics and Prevention Institute, University of Zürich, Zurich, Switzerland
| | | | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Ulrike Held
- Epidemiology, Biostatistics and Prevention Institute, University of Zürich, Zurich, Switzerland
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Eskofier BM, Klucken J. Predictive Models for Health Deterioration: Understanding Disease Pathways for Personalized Medicine. Annu Rev Biomed Eng 2023; 25:131-156. [PMID: 36854259 DOI: 10.1146/annurev-bioeng-110220-030247] [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] [Indexed: 03/02/2023]
Abstract
Artificial intelligence (AI) and machine learning (ML) methods are currently widely employed in medicine and healthcare. A PubMed search returns more than 100,000 articles on these topics published between 2018 and 2022 alone. Notwithstanding several recent reviews in various subfields of AI and ML in medicine, we have yet to see a comprehensive review around the methods' use in longitudinal analysis and prediction of an individual patient's health status within a personalized disease pathway. This review seeks to fill that gap. After an overview of the AI and ML methods employed in this field and of specific medical applications of models of this type, the review discusses the strengths and limitations of current studies and looks ahead to future strands of research in this field. We aim to enable interested readers to gain a detailed impression of the research currently available and accordingly plan future work around predictive models for deterioration in health status.
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Affiliation(s)
- Bjoern M Eskofier
- Machine Learning and Data Analytics Lab, Department of Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany;
| | - Jochen Klucken
- Digital Medicine Group, Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Belvaux, Luxembourg
- Digital Medicine Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
- Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
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13
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Tayyab M, Metz LM, Li DKB, Kolind S, Carruthers R, Traboulsee A, Tam RC. Accounting for uncertainty in training data to improve machine learning performance in predicting new disease activity in early multiple sclerosis. Front Neurol 2023; 14:1165267. [PMID: 37305756 PMCID: PMC10251494 DOI: 10.3389/fneur.2023.1165267] [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: 02/13/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Machine learning (ML) has great potential for using health data to predict clinical outcomes in individual patients. Missing data are a common challenge in training ML algorithms, such as when subjects withdraw from a clinical study, leaving some samples with missing outcome labels. In this study, we have compared three ML models to determine whether accounting for label uncertainty can improve a model's predictions. Methods We used a dataset from a completed phase-III clinical trial that evaluated the efficacy of minocycline for delaying the conversion from clinically isolated syndrome to multiple sclerosis (MS), using the McDonald 2005 diagnostic criteria. There were a total of 142 participants, and at the 2-year follow-up 81 had converted to MS, 29 remained stable, and 32 had uncertain outcomes. In a stratified 7-fold cross-validation, we trained three random forest (RF) ML models using MRI volumetric features and clinical variables to predict the conversion outcome, which represented new disease activity within 2 years of a first clinical demyelinating event. One RF was trained using subjects with the uncertain labels excluded (RFexclude), another RF was trained using the entire dataset but with assumed labels for the uncertain group (RFnaive), and a third, a probabilistic RF (PRF, a type of RF that can model label uncertainty) was trained on the entire dataset, with probabilistic labels assigned to the uncertain group. Results Probabilistic random forest outperformed both the RF models with the highest AUC (0.76, compared to 0.69 for RFexclude and 0.71 for RFnaive) and F1-score (86.6% compared to 82.6% for RFexclude and 76.8% for RFnaive). Conclusion Machine learning algorithms capable of modeling label uncertainty can improve predictive performance in datasets in which a substantial number of subjects have unknown outcomes.
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Affiliation(s)
- Maryam Tayyab
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Luanne M Metz
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - David K B Li
- Department of Radiology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Shannon Kolind
- Department of Radiology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Robert Carruthers
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Traboulsee
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Roger C Tam
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- Department of Radiology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Hindsholm AM, Andersen FL, Cramer SP, Simonsen HJ, Askløf MG, Magyari M, Madsen PN, Hansen AE, Sellebjerg F, Larsson HBW, Langkilde AR, Frederiksen JL, Højgaard L, Ladefoged CN, Lindberg U. Scanner agnostic large-scale evaluation of MS lesion delineation tool for clinical MRI. Front Neurosci 2023; 17:1177540. [PMID: 37274207 PMCID: PMC10235534 DOI: 10.3389/fnins.2023.1177540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Patients with MS are MRI scanned continuously throughout their disease course resulting in a large manual workload for radiologists which includes lesion detection and size estimation. Though many models for automatic lesion segmentation have been published, few are used broadly in clinic today, as there is a lack of testing on clinical datasets. By collecting a large, heterogeneous training dataset directly from our MS clinic we aim to present a model which is robust to different scanner protocols and artefacts and which only uses MRI modalities present in routine clinical examinations. Methods We retrospectively included 746 patients from routine examinations at our MS clinic. The inclusion criteria included acquisition at one of seven different scanners and an MRI protocol including 2D or 3D T2-w FLAIR, T2-w and T1-w images. Reference lesion masks on the training (n = 571) and validation (n = 70) datasets were generated using a preliminary segmentation model and subsequent manual correction. The test dataset (n = 100) was manually delineated. Our segmentation model https://github.com/CAAI/AIMS/ was based on the popular nnU-Net, which has won several biomedical segmentation challenges. We tested our model against the published segmentation models HD-MS-Lesions, which is also based on nnU-Net, trained with a more homogenous patient cohort. We furthermore tested model robustness to data from unseen scanners by performing a leave-one-scanner-out experiment. Results We found that our model was able to segment MS white matter lesions with a performance comparable to literature: DSC = 0.68, precision = 0.90, recall = 0.70, f1 = 0.78. Furthermore, the model outperformed HD-MS-Lesions in all metrics except precision = 0.96. In the leave-one-scanner-out experiment there was no significant change in performance (p < 0.05) between any of the models which were only trained on part of the dataset and the full segmentation model. Conclusion In conclusion we have seen, that by including a large, heterogeneous dataset emulating clinical reality, we have trained a segmentation model which maintains a high segmentation performance while being robust to data from unseen scanners. This broadens the applicability of the model in clinic and paves the way for clinical implementation.
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Affiliation(s)
- Amalie Monberg Hindsholm
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Flemming Littrup Andersen
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Stig Præstekjær Cramer
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Helle Juhl Simonsen
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Mathias Gæde Askløf
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Melinda Magyari
- Department of Neurology, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Poul Nørgaard Madsen
- Center for IT and Medical Technology, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Adam Espe Hansen
- Department of Radiology, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Finn Sellebjerg
- Department of Neurology, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Bo Wiberg Larsson
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Jette Lautrup Frederiksen
- Department of Neurology, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Liselotte Højgaard
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Claes Nøhr Ladefoged
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
| | - Ulrich Lindberg
- Department of Clinical Physiology and Nuclear Medicine, Copenhagen University Hospital–Rigshospitalet, Copenhagen, Denmark
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Diakou I, Papakonstantinou E, Papageorgiou L, Pierouli K, Dragoumani K, Spandidos DA, Bacopoulou F, Chrousos GP, Goulielmos GΝ, Eliopoulos E, Vlachakis D. Multiple sclerosis and computational biology (Review). Biomed Rep 2022; 17:96. [PMID: 36382258 PMCID: PMC9634047 DOI: 10.3892/br.2022.1579] [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: 08/14/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune neurodegenerative disease whose prevalence has increased worldwide. The resultant symptoms may be debilitating and can substantially reduce the of patients. Computational biology, which involves the use of computational tools to answer biomedical questions, may provide the basis for novel healthcare approaches in the context of MS. The rapid accumulation of health data, and the ever-increasing computational power and evolving technology have helped to modernize and refine MS research. From the discovery of novel biomarkers to the optimization of treatment and a number of quality-of-life enhancements for patients, computational biology methods and tools are shaping the field of MS diagnosis, management and treatment. The final goal in such a complex disease would be personalized medicine, i.e., providing healthcare services that are tailored to the individual patient, in accordance to the particular biology of their disease and the environmental factors to which they are subjected. The present review article summarizes the current knowledge on MS, modern computational biology and the impact of modern computational approaches of MS.
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Affiliation(s)
- Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - Georges Ν. Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of The Academy of Athens, 11527 Athens, Greece
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Aslam N, Khan IU, Bashamakh A, Alghool FA, Aboulnour M, Alsuwayan NM, Alturaif RK, Brahimi S, Aljameel SS, Al Ghamdi K. Multiple Sclerosis Diagnosis Using Machine Learning and Deep Learning: Challenges and Opportunities. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22207856. [PMID: 36298206 PMCID: PMC9609137 DOI: 10.3390/s22207856] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/29/2022] [Accepted: 10/11/2022] [Indexed: 05/17/2023]
Abstract
Multiple Sclerosis (MS) is a disease that impacts the central nervous system (CNS), which can lead to brain, spinal cord, and optic nerve problems. A total of 2.8 million are estimated to suffer from MS. Globally, a new case of MS is reported every five minutes. In this review, we discuss the proposed approaches to diagnosing MS using machine learning (ML) published between 2011 and 2022. Numerous models have been developed using different types of data, including magnetic resonance imaging (MRI) and clinical data. We identified the methods that achieved the best results in diagnosing MS. The most implemented approaches are SVM, RF, and CNN. Moreover, we discussed the challenges and opportunities in MS diagnosis to improve AI systems to enable researchers and practitioners to enhance their approaches and improve the automated diagnosis of MS. The challenges faced by automated MS diagnosis include difficulty distinguishing the disease from other diseases showing similar symptoms, protecting the confidentiality of the patients' data, achieving reliable ML models that are also easily understood by non-experts, and the difficulty of collecting a large reliable dataset. Moreover, we discussed several opportunities in the field such as the implementation of secure platforms, employing better AI solutions, developing better disease prognosis systems, combining more than one data type for better MS prediction and using OCT data for diagnosis, utilizing larger, multi-center datasets to improve the reliability of the developed models, and commercialization.
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Affiliation(s)
- Nida Aslam
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
- Correspondence:
| | - Irfan Ullah Khan
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Asma Bashamakh
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Fatima A. Alghool
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Menna Aboulnour
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Noorah M. Alsuwayan
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Rawa’a K. Alturaif
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Samiha Brahimi
- Department of Computer Information Systems, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Sumayh S. Aljameel
- Department of Computer Science, College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Kholoud Al Ghamdi
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
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Jorge AM, Smith D, Wu Z, Chowdhury T, Costenbader K, Zhang Y, Choi HK, Feldman CH, Zhao Y. Exploration of machine learning methods to predict systemic lupus erythematosus hospitalizations. Lupus 2022; 31:1296-1305. [PMID: 35835534 PMCID: PMC9547899 DOI: 10.1177/09612033221114805] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a heterogeneous disease characterized by disease flares which can require hospitalization. Our objective was to apply machine learning methods to predict hospitalizations for SLE from electronic health record (EHR) data. METHODS We identified patients with SLE in a longitudinal EHR-based cohort with ≥2 outpatient rheumatology visits between 2012 and 2019. We applied multiple machine learning methods to predict hospitalizations with a primary diagnosis code for SLE, including decision tree, random forest, naive Bayes, logistic regression, and an ensemble method. Candidate predictors were derived from structured EHR features, including demographics, laboratory tests, medications, ICD-9/10 codes for SLE manifestations, and healthcare utilization. We used two approaches to assess these variables over longitudinal follow-up, including the incorporation of lagged features to capture changes over time of clinical data. The performance of each model was evaluated by overall accuracy, the F statistic, and the area under the receiver operator curve (AUC). RESULTS We identified 1996 patients with SLE. 4.6% were hospitalized for SLE in their most recent year of follow-up. Random forest models had highest performance in predicting SLE hospitalizations, with AUC 0.751 and AUC 0.772 for two approaches (averaging and progressive), respectively. The leading predictors of SLE hospitalizations included dsDNA positivity, C3 level, blood cell counts, and inflammatory markers as well as age and albumin. CONCLUSION We have demonstrated that machine learning methods can predict SLE hospitalizations. We identified key predictors of these events including known markers of SLE disease activity; further validation in external cohorts is warranted.
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Affiliation(s)
- April M Jorge
- Division of Rheumatology, Allergy, and Immunology, Harvard Medical School, 2348Massachusetts General Hospital, Boston, MA, USA
| | - Dylan Smith
- Department of Computer and Information Sciences, 5923Fordham University, New York, NY, USA
| | - Zhiyao Wu
- Department of Computer and Information Sciences, 5923Fordham University, New York, NY, USA
| | - Tashrif Chowdhury
- Department of Computer and Information Sciences, 5923Fordham University, New York, NY, USA
| | - Karen Costenbader
- Division of Rheumatology, Inflammation, and Immunity, Harvard Medical School, 1861Brigham and Women's Hospital, Boston, MA, USA
| | - Yuqing Zhang
- Division of Rheumatology, Allergy, and Immunology, Harvard Medical School, 2348Massachusetts General Hospital, Boston, MA, USA
| | - Hyon K Choi
- Division of Rheumatology, Allergy, and Immunology, Harvard Medical School, 2348Massachusetts General Hospital, Boston, MA, USA
| | - Candace H Feldman
- Division of Rheumatology, Inflammation, and Immunity, Harvard Medical School, 1861Brigham and Women's Hospital, Boston, MA, USA
| | - Yijun Zhao
- Department of Computer and Information Sciences, 5923Fordham University, New York, NY, USA
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Comparing two machine learning approaches in predicting lupus hospitalization using longitudinal data. Sci Rep 2022; 12:16424. [PMID: 36180726 PMCID: PMC9525268 DOI: 10.1038/s41598-022-20845-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease characterized by flares ranging from mild to life-threatening. Severe flares and complications can require hospitalizations, which account for most of the direct costs of SLE care. This study investigates two machine learning approaches in predicting SLE hospitalizations using longitudinal data from 925 patients enrolled in a multicenter electronic health record (EHR)-based lupus cohort. Our first Differential approach accounts for the time dependencies in sequential data by introducing additional lagged variables between consecutive time steps. We next evaluate the performance of LSTM, a state-of-the-art deep learning model designed for time series. Our experimental results demonstrate that both methods can effectively predict lupus hospitalizations, but each has its strengths and limitations. Specifically, the Differential approach can be integrated into any non-temporal machine learning algorithms and is preferred for tasks with short observation periods. On the contrary, the LSTM model is desirable for studies utilizing long observation intervals attributing to its capability in capturing long-term dependencies embedded in the longitudinal data. Furthermore, the Differential approach has more options in handling class imbalance in the underlying data and delivers stable performance across different prognostic horizons. LSTM, on the other hand, demands more class-balanced training data and outperforms the Differential approach when there are sufficient positive samples facilitating model training. Capitalizing on our experimental results, we further study the optimal length of patient monitoring periods for different prediction horizons.
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Taloni A, Farrelly FA, Pontillo G, Petsas N, Giannì C, Ruggieri S, Petracca M, Brunetti A, Pozzilli C, Pantano P, Tommasin S. Evaluation of Disability Progression in Multiple Sclerosis via Magnetic-Resonance-Based Deep Learning Techniques. Int J Mol Sci 2022; 23:ijms231810651. [PMID: 36142563 PMCID: PMC9505100 DOI: 10.3390/ijms231810651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Short-term disability progression was predicted from a baseline evaluation in patients with multiple sclerosis (MS) using their three-dimensional T1-weighted (3DT1) magnetic resonance images (MRI). One-hundred-and-eighty-one subjects diagnosed with MS underwent 3T-MRI and were followed up for two to six years at two sites, with disability progression defined according to the expanded-disability-status-scale (EDSS) increment at the follow-up. The patients’ 3DT1 images were bias-corrected, brain-extracted, registered onto MNI space, and divided into slices along coronal, sagittal, and axial projections. Deep learning image classification models were applied on slices and devised as ResNet50 fine-tuned adaptations at first on a large independent dataset and secondly on the study sample. The final classifiers’ performance was evaluated via the area under the curve (AUC) of the false versus true positive diagram. Each model was also tested against its null model, obtained by reshuffling patients’ labels in the training set. Informative areas were found by intersecting slices corresponding to models fulfilling the disability progression prediction criteria. At follow-up, 34% of patients had disability progression. Five coronal and five sagittal slices had one classifier surviving the AUC evaluation and null test and predicted disability progression (AUC > 0.72 and AUC > 0.81, respectively). Likewise, fifteen combinations of classifiers and axial slices predicted disability progression in patients (AUC > 0.69). Informative areas were the frontal areas, mainly within the grey matter. Briefly, 3DT1 images may give hints on disability progression in MS patients, exploiting the information hidden in the MRI of specific areas of the brain.
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Affiliation(s)
- Alessandro Taloni
- Institute for Complex Systems, National Research Council (ISC-CNR), 00185 Rome, Italy
| | | | - Giuseppe Pontillo
- Department of Advanced Biomedical Sciences, Federico II University of Naples, 80131 Naples, Italy
- Department of Electrical Engineering and Information Technology, Federico II University of Naples, 80125 Naples, Italy
| | - Nikolaos Petsas
- Department of Radiology, IRCCS NEUROMED, 86077 Pozzilli, Italy
| | - Costanza Giannì
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Serena Ruggieri
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Neuroimmunology Unit, IRCSS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Maria Petracca
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Department of Neuroscience, Reproductive Sciences and Odontostomatology, Federico II University of Naples, 80131 Naples, Italy
| | - Arturo Brunetti
- Department of Advanced Biomedical Sciences, Federico II University of Naples, 80131 Naples, Italy
| | - Carlo Pozzilli
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Patrizia Pantano
- Department of Radiology, IRCCS NEUROMED, 86077 Pozzilli, Italy
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Tommasin
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
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Majumder R, Adak S, Jana S, Patra S, Kar TK. Change in Normal Health Condition Due to COVID-19 Infection: Analysis by ANFIS Technique. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022; 46:1327-1338. [PMID: 36105072 PMCID: PMC9463057 DOI: 10.1007/s40995-022-01344-z] [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: 06/22/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The COVID-19 pandemic has crippled the world population. Our present work aims to formulate a model to analyze the change in normal health conditions due to COVID-19 infection. For this purpose, we have collected data of seven parameters, namely, age, systolic pressure (SP), diastolic paper (DP), respiratory distress (RD), fasting blood sugar (FBS), cholesterol (CHL), and insomnia (INS) of 156 persons of Birnagar municipality, Nadia, India; before and after COVID-19 infection. Ultimately, using an adaptive neuro-fuzzy inference system (ANFIS), we have formulated our desired model, a Takagi–Sugeno fuzzy inference system. Further, with the help of this model, we have established one’s change in health condition with age due to COVID-19 infection. Finally, we have derived that older people are more affected by COVID-19 infection than younger people.
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Affiliation(s)
- Rabindranath Majumder
- Department of Physiology, Tamralipta Mahavidyalaya, Tamluk, Purba Medinipur, West Bengal 721636 India
- Birnagar Municipality Hospital, Birnagar, Nadia, West Bengal 741127 India
| | - Sayani Adak
- Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Soovoojeet Jana
- Department of Mathematics, Ramsaday College, Amta, Howrah, 711401 India
| | - Sova Patra
- Department of B.Ed., Bijoy Krishna Girls’ College, Kadamtala, Howrah, 711101 India
| | - T. K. Kar
- Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
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21
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Torkey H, Belal NA. An Enhanced Multiple Sclerosis Disease Diagnosis via an Ensemble Approach. Diagnostics (Basel) 2022; 12:1771. [PMID: 35885672 PMCID: PMC9316893 DOI: 10.3390/diagnostics12071771] [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: 04/27/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Multiple Sclerosis (MS) is a disease attacking the central nervous system. According to MS Atlas's most recent statistics, there are more than 2.8 million people worldwide diagnosed with MS. Recently, studies started to explore machine learning techniques to predict MS using various data. The objective of this paper is to develop an ensemble approach for diagnosis of MS using gene expression profiles, while handling the class imbalance problem associated with the data. A hierarchical ensemble approach employing voting and boosting techniques is proposed. This approach adopts a heterogeneous voting approach using two base learners, random forest and support vector machine. Experiments show that our approach outperforms state-of-the-art methods, with the highest recorded accuracy being 92.81% and 93.5% with BoostFS and DEGs for feature selection, respectively. Conclusively, the proposed approach is able to efficiently diagnose MS using the gene expression profiles that are more relevant to the disease. The approach is not merely an ensemble classifier outperforming previous work; it also identifies differentially expressed genes between normal samples and patients with multiple sclerosis using a genome-wide expression microarray. The results obtained show that the proposed approach is an efficient diagnostic tool for MS.
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Affiliation(s)
- Hanaa Torkey
- Computer Science and Engineering Department, Faculty of Electronic Engineering, Menoufia University, Menouf 32952, Egypt;
| | - Nahla A. Belal
- College of Computing and Information Technology, Arab Academy for Science, Technology, and Maritime Transport, Smart Village 12577, Egypt
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22
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Vohra R, Hussain A, Dudyala AK, Pahareeya J, Khan W. Multi-class classification algorithms for the diagnosis of anemia in an outpatient clinical setting. PLoS One 2022; 17:e0269685. [PMID: 35793343 PMCID: PMC9258850 DOI: 10.1371/journal.pone.0269685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
Anemia is one of the most pressing public health issues in the world with iron deficiency a major public health issue worldwide. The highest prevalence of anemia is in developing countries. The complete blood count is a blood test used to diagnose the prevalence of anemia. While earlier studies have framed the problem of diagnosis as a binary classification problem, this paper frames it as a multi class (three classes) classification problem with mild, moderate and severe classes. The three classes for the anemia classification (mild, moderate, severe) are so chosen as the world health organization (WHO) guidelines formalize this categorization based on the Haemoglobin (HGB) values of the chosen sample of patients in the Complete Blood Count (CBC) patient data set. Complete blood count test data was collected in an outpatient clinical setting in India. We used Feature selection with Majority voting to identify the key attributes in the input patient data set. In addition, since the original data set was imbalanced we used Synthetic Minority Oversampling Technique (SMOTE) to balance the data set. Four data sets including the original data set were used to perform the data experiments. Six standard machine learning algorithms were utilised to test our four data sets, performing multi class classification. Benchmarking these algorithms was performed and tabulated using both10 fold cross validation and hold out methods. The experimental results indicated that multilayer perceptron network was predominantly giving good recall values across mild and moderate class which are early and middle stages of the disease. With a good prediction model at early stages, medical intervention can provide preventive measure from further deterioration into severe stage or recommend the use of supplements to overcome this problem.
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Affiliation(s)
- Rajan Vohra
- School of Creative Technologies, University of Bolton, Bolton, United Kingdom
- * E-mail:
| | - Abir Hussain
- Department of Electrical Engineering, University of Sharjah, Sharjah, UAE
- Department of Computer Science, Liverpool John Moore’s University, Liverpool, United Kingdom
| | - Anil Kumar Dudyala
- Department of Computer Science, National Institute of Technology Patna (NIT Patna), Patna, India
| | - Jankisharan Pahareeya
- Department of Information Technology, Rustamji Institute of Technology, BSF Academy, Tekanpur, Gwalior, India
| | - Wasiq Khan
- Department of Computer Science, Liverpool John Moore’s University, Liverpool, United Kingdom
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Plati D, Tripoliti E, Zelilidou S, Vlachos K, Konitsiotis S, Fotiadis DI. Multiple Sclerosis Severity Estimation and Progression Prediction Based on Machine Learning Techniques. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:1109-1112. [PMID: 36085783 DOI: 10.1109/embc48229.2022.9871213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The aim of the study is to address the Multiple Sclerosis (MS) severity estimation problem based on EDSS score and the prediction of the disease's progression with the application of Machine Learning (ML) approaches. Several ML techniques are implemented. The data are provided by the Neurology Clinic of the University Hospital of Ioannina and were collected in the framework of the ProMiSi project. The features recorded are grouped into: general demographic information, MS clinical related data, results of special tests, treatment, and comorbidities. The records from 30 patients are utilized and are recorded in three time points. The ML methods provided quite high results with 94.87% accuracy for the MS severity estimation and 83.33% for the disease's progression prediction.
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Efficacy of Transcranial Direct Current Stimulation (tDCS) on Balance and Gait in Multiple Sclerosis Patients: A Machine Learning Approach. J Clin Med 2022; 11:jcm11123505. [PMID: 35743575 PMCID: PMC9224780 DOI: 10.3390/jcm11123505] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/05/2022] [Accepted: 06/15/2022] [Indexed: 02/06/2023] Open
Abstract
Transcranial direct current stimulation (tDCS) has emerged as an appealing rehabilitative approach to improve brain function, with promising data on gait and balance in people with multiple sclerosis (MS). However, single variable weights have not yet been adequately assessed. Hence, the aim of this pilot randomized controlled trial was to evaluate the tDCS effects on balance and gait in patients with MS through a machine learning approach. In this pilot randomized controlled trial (RCT), we included people with relapsing−remitting MS and an Expanded Disability Status Scale >1 and <5 that were randomly allocated to two groups—a study group, undergoing a 10-session anodal motor cortex tDCS, and a control group, undergoing a sham treatment. Both groups underwent a specific balance and gait rehabilitative program. We assessed as outcome measures the Berg Balance Scale (BBS), Fall Risk Index and timed up-and-go and 6-min-walking tests at baseline (T0), the end of intervention (T1) and 4 (T2) and 6 weeks after the intervention (T3) with an inertial motion unit. At each time point, we performed a multiple factor analysis through a machine learning approach to allow the analysis of the influence of the balance and gait variables, grouping the participants based on the results. Seventeen MS patients (aged 40.6 ± 14.4 years), 9 in the study group and 8 in the sham group, were included. We reported a significant repeated measures difference between groups for distances covered (6MWT (meters), p < 0.03). At T1, we showed a significant increase in distance (m) with a mean difference (MD) of 37.0 [−59.0, 17.0] (p = 0.003), and in BBS with a MD of 2.0 [−4.0, 3.0] (p = 0.03). At T2, these improvements did not seem to be significantly maintained; however, considering the machine learning analysis, the Silhouette Index of 0.34, with a low cluster overlap trend, confirmed the possible short-term effects (T2), even at 6 weeks. Therefore, this pilot RCT showed that tDCS may provide non-sustained improvements in gait and balance in MS patients. In this scenario, machine learning could suggest evidence of prolonged beneficial effects.
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Hossain MI, Habib MJ, Saleheen AAS, Kamruzzaman M, Rahman A, Roy S, Amit Hasan M, Haq I, Methun MIH, Nayan MIH, Rukonozzaman Rukon M. Performance Evaluation of Machine Learning Algorithm for Classification of Unintended Pregnancy among Married Women in Bangladesh. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:1460908. [PMID: 35669979 PMCID: PMC9167128 DOI: 10.1155/2022/1460908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Abstract
Intended pregnancy is one of the significant indicators of women's well-being. Globally, 74 million women become pregnant every year without planning. Unintended pregnancies account for 28% of all pregnancies among married women in Bangladesh. This study aimed to investigate the performance of six different machine learning (ML) algorithms applied to predict unintended pregnancies among married women in Bangladesh. From BDHS 2017-18, only 1129 pregnant women aged 15-49 were eligible for this study. An independent χ 2 test had performed before we considered six popular ML algorithms, such as logistic regression (LR), random forest (RF), support vector machine (SVM), k-nearest neighbor (KNN), naïve Bayes (NB), and elastic net regression (ENR) to predict the unintended pregnancy. Accuracy, sensitivity, specificity, Cohen's Kappa statistic, and area under curve (AUC) value were used as model evaluation. The bivariate analysis result showed that women aged 30-49 years, poor, not educated, and living in male-headed households had a higher percentage of unintended pregnancy. We found various performance parameters for the classification of unintended pregnancy: LR accuracy = 79.29%, LR AUC = 72.12%; RF accuracy = 77.81%, RF AUC = 72.17%; SVM accuracy = 76.92%, SVM AUC = 70.90%; KNN accuracy = 77.22%, KNN AUC = 70.27%; NB accuracy = 78%, NB AUC = 73.06%; and ENR accuracy = 77.51%, ENR AUC = 74.67%. Based on the AUC value, we can conclude that of all the ML algorithms we investigated, the ENR algorithm provides the most accurate classification for predicting unwanted pregnancy among Bangladeshi women. Our findings contribute to a better understanding of how to categorize pregnancy intentions among Bangladeshi women. As a result, the government can initiate an effective campaign to raise contraception awareness.
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Affiliation(s)
| | - Md. Jakaria Habib
- Department of Statistics, Jagannath University, Dhaka 1100, Bangladesh
| | | | - Md. Kamruzzaman
- Department of Statistics, Jagannath University, Dhaka 1100, Bangladesh
| | - Azizur Rahman
- Department of Statistics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sutopa Roy
- Department of Statistics, Jagannath University, Dhaka 1100, Bangladesh
| | - Md. Amit Hasan
- Department of Statistics, Jagannath University, Dhaka 1100, Bangladesh
| | - Iqramul Haq
- Department of Agricultural Statistics, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
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A machine learning-based model to evaluate multiple sclerosis predictor factors with emphasis on neurophysiological indices of physical activity. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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27
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Comparison of Machine Learning Methods Using Spectralis OCT for Diagnosis and Disability Progression Prognosis in Multiple Sclerosis. Ann Biomed Eng 2022; 50:507-528. [PMID: 35220529 PMCID: PMC9001622 DOI: 10.1007/s10439-022-02930-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/10/2022] [Indexed: 12/28/2022]
Abstract
Machine learning approaches in diagnosis and prognosis of multiple sclerosis (MS) were analysed using retinal nerve fiber layer (RNFL) thickness, measured by optical coherence tomography (OCT). A cross-sectional study (72 MS patients and 30 healthy controls) was used for diagnosis. These 72 MS patients were involved in a 10-year longitudinal follow-up study for prognostic purposes. Structural measurements of RNFL thickness were performed using different Spectralis OCT protocols: fast macular thickness protocol to measure macular RNFL, and fast RNFL thickness protocol and fast RNFL-N thickness protocol to measure peripapillary RNFL. Binary classifiers such as multiple linear regression (MLR), support vector machines (SVM), decision tree (DT), k-nearest neighbours (k-NN), Naïve Bayes (NB), ensemble classifier (EC) and long short-term memory (LSTM) recurrent neural network were tested. For MS diagnosis, the best acquisition protocol was fast macular thickness protocol using k-NN (accuracy: 95.8%; sensitivity: 94.4%; specificity: 97.2%; precision: 97.1%; AUC: 0.958). For MS prognosis, our model with a 3-year follow up to predict disability progression 8 years later was the best predictive model. DT performed best for fast macular thickness protocol (accuracy: 91.3%; sensitivity: 90.0%; specificity: 92.5%; precision: 92.3%; AUC: 0.913) and SVM for fast RNFL-N thickness protocol (accuracy: 91.3%; sensitivity: 87.5%; specificity: 95.0%; precision: 94.6%; AUC: 0.913). This work concludes that measurements of RNFL thickness obtained with Spectralis OCT have a good ability to diagnose MS and to predict disability progression in MS patients. This machine learning approach would help clinicians to have valuable information.
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Vedmurthy P, Pinto ALR, Lin DDM, Comi AM, Ou Y. Study protocol: retrospectively mining multisite clinical data to presymptomatically predict seizure onset for individual patients with Sturge-Weber. BMJ Open 2022; 12:e053103. [PMID: 35121603 PMCID: PMC8819809 DOI: 10.1136/bmjopen-2021-053103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/13/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Secondary analysis of hospital-hosted clinical data can save time and cost compared with prospective clinical trials for neuroimaging biomarker development. We present such a study for Sturge-Weber syndrome (SWS), a rare neurovascular disorder that affects 1 in 20 000-50 000 newborns. Children with SWS are at risk for developing neurocognitive deficit by school age. A critical period for early intervention is before 2 years of age, but early diagnostic and prognostic biomarkers are lacking. We aim to retrospectively mine clinical data for SWS at two national centres to develop presymptomatic biomarkers. METHODS AND ANALYSIS We will retrospectively collect clinical, MRI and neurocognitive outcome data for patients with SWS who underwent brain MRI before 2 years of age at two national SWS care centres. Expert review of clinical records and MRI quality control will be used to refine the cohort. The merged multisite data will be used to develop algorithms for abnormality detection, lesion-symptom mapping to identify neural substrate and machine learning to predict individual outcomes (presence or absence of seizures) by 2 years of age. Presymptomatic treatment in 0-2 years and before seizure onset may delay or prevent the onset of seizures by 2 years of age, and thereby improve neurocognitive outcomes. The proposed work, if successful, will be one of the largest and most comprehensive multisite databases for the presymptomatic phase of this rare disease. ETHICS AND DISSEMINATION This study involves human participants and was approved by Boston Children's Hospital Institutional Review Board: IRB-P00014482 and IRB-P00025916 Johns Hopkins School of Medicine Institutional Review Board: NA_00043846. Participants gave informed consent to participate in the study before taking part. The Institutional Review Boards at Kennedy Krieger Institute and Boston Children's Hospital approval have been obtained at each site to retrospectively study this data. Results will be disseminated by presentations, publication and sharing of algorithms generated.
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Affiliation(s)
- Pooja Vedmurthy
- Department of Neurology and Developmental Medicine, Hugo Moser Research Institute, Baltimore, Maryland, USA
- Department of Neurology and Pediatrics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Anna L R Pinto
- Department of Neurology, Division of Epilepsy, Harvard Medical School, Boston, Massachusetts, USA
| | - Doris D M Lin
- Neuroradiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Anne M Comi
- Department of Neurology and Developmental Medicine, Hugo Moser Research Institute, Baltimore, Maryland, USA
- Department of Neurology and Pediatrics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Yangming Ou
- Fetal-Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Boston, Massachusetts, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Radiology, Boston Children's Hospital; Harvard Medical School, Boston, MA, USA
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A Deep Learning Approach to Predicting Disease Progression in Multiple Sclerosis Using Magnetic Resonance Imaging. Invest Radiol 2022; 57:423-432. [DOI: 10.1097/rli.0000000000000854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Adak S, Majumder R, Majee S, Jana S, Kar TK. An ANFIS model-based approach to investigate the effect of lockdown due to COVID-19 on public health. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2022; 231:3317-3327. [PMID: 35818512 PMCID: PMC9258467 DOI: 10.1140/epjs/s11734-022-00621-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 05/25/2022] [Indexed: 05/08/2023]
Abstract
During the first and second quarters of the year 2020, most of the countries had implemented complete or partial lockdown policies to slow down the transmission of the COVID-19. To cultivate the effect of lockdown due to COVID-19 on public health, we have collected the data of six primary parameters, namely systolic blood pressure, diastolic blood pressure, fasting blood sugar, insomnia, cholesterol, and respiratory distress of 200 randomly chosen people from a municipality region of West Bengal, India before and after lockdown. With the help of these data and Adaptive Neuro-Fuzzy Inference System (ANFIS), we have formulated a model that has established that lockdown due to COVID-19 has negligible impacts on the individuals with better health condition but has significant effects on the health conditions to those populations who have poor health.
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Affiliation(s)
- Sayani Adak
- Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Rabindranath Majumder
- Department of Physiology, Tamralipta Mahavidyalaya, Tamluk, Purba Medinipur, West Bengal 721636 India
- Birnagar Municipality Hospital, Birnagar, Nadia, West Bengal 741127 India
| | - Suvankar Majee
- Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
| | - Soovoojeet Jana
- Department of Mathematics, Ramsaday College, Amta, Howrah, 711401 India
| | - T. K. Kar
- Department of Mathematics, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, 711103 India
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Tozlu C, Jamison K, Gauthier SA, Kuceyeski A. Dynamic Functional Connectivity Better Predicts Disability Than Structural and Static Functional Connectivity in People With Multiple Sclerosis. Front Neurosci 2021; 15:763966. [PMID: 34966255 PMCID: PMC8710545 DOI: 10.3389/fnins.2021.763966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/17/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Advanced imaging techniques such as diffusion and functional MRI can be used to identify pathology-related changes to the brain's structural and functional connectivity (SC and FC) networks and mapping of these changes to disability and compensatory mechanisms in people with multiple sclerosis (pwMS). No study to date performed a comparison study to investigate which connectivity type (SC, static or dynamic FC) better distinguishes healthy controls (HC) from pwMS and/or classifies pwMS by disability status. Aims: We aim to compare the performance of SC, static FC, and dynamic FC (dFC) in classifying (a) HC vs. pwMS and (b) pwMS who have no disability vs. with disability. The secondary objective of the study is to identify which brain regions' connectome measures contribute most to the classification tasks. Materials and Methods: One hundred pwMS and 19 HC were included. Expanded Disability Status Scale (EDSS) was used to assess disability, where 67 pwMS who had EDSS<2 were considered as not having disability. Diffusion and resting-state functional MRI were used to compute the SC and FC matrices, respectively. Logistic regression with ridge regularization was performed, where the models included demographics/clinical information and either pairwise entries or regional summaries from one of the following matrices: SC, FC, and dFC. The performance of the models was assessed using the area under the receiver operating curve (AUC). Results: In classifying HC vs. pwMS, the regional SC model significantly outperformed others with a median AUC of 0.89 (p <0.05). In classifying pwMS by disability status, the regional dFC and dFC metrics models significantly outperformed others with a median AUC of 0.65 and 0.61 (p < 0.05). Regional SC in the dorsal attention, subcortical and cerebellar networks were the most important variables in the HC vs. pwMS classification task. Increased regional dFC in dorsal attention and visual networks and decreased regional dFC in frontoparietal and cerebellar networks in certain dFC states was associated with being in the group of pwMS with evidence of disability. Discussion: Damage to SCs is a hallmark of MS and, unsurprisingly, the most accurate connectomic measure in classifying patients and controls. On the other hand, dynamic FC metrics were most important for determining disability level in pwMS, and could represent functional compensation in response to white matter pathology in pwMS.
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Affiliation(s)
- Ceren Tozlu
- Department of Radiology, Weill Cornell Medicine, New York, NY, United States
| | - Keith Jamison
- Department of Radiology, Weill Cornell Medicine, New York, NY, United States
| | - Susan A. Gauthier
- Department of Radiology, Weill Cornell Medicine, New York, NY, United States
- Judith Jaffe Multiple Sclerosis Center, Weill Cornell Medicine, New York, NY, United States
- Department of Neurology, Weill Cornell Medical College, New York, NY, United States
| | - Amy Kuceyeski
- Department of Radiology, Weill Cornell Medicine, New York, NY, United States
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
- *Correspondence: Amy Kuceyeski
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Denissen S, Chén OY, De Mey J, De Vos M, Van Schependom J, Sima DM, Nagels G. Towards Multimodal Machine Learning Prediction of Individual Cognitive Evolution in Multiple Sclerosis. J Pers Med 2021; 11:1349. [PMID: 34945821 PMCID: PMC8707909 DOI: 10.3390/jpm11121349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022] Open
Abstract
Multiple sclerosis (MS) manifests heterogeneously among persons suffering from it, making its disease course highly challenging to predict. At present, prognosis mostly relies on biomarkers that are unable to predict disease course on an individual level. Machine learning is a promising technique, both in terms of its ability to combine multimodal data and through the capability of making personalized predictions. However, most investigations on machine learning for prognosis in MS were geared towards predicting physical deterioration, while cognitive deterioration, although prevalent and burdensome, remained largely overlooked. This review aims to boost the field of machine learning for cognitive prognosis in MS by means of an introduction to machine learning and its pitfalls, an overview of important elements for study design, and an overview of the current literature on cognitive prognosis in MS using machine learning. Furthermore, the review discusses new trends in the field of machine learning that might be adopted for future studies in the field.
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Affiliation(s)
- Stijn Denissen
- AIMS Laboratory, Center for Neurosciences, UZ Brussel, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (J.D.M.); (J.V.S.); (D.M.S.); (G.N.)
- icometrix, 3012 Leuven, Belgium
| | - Oliver Y. Chén
- Faculty of Social Sciences and Law, University of Bristol, Bristol BS8 1QU, UK;
- Department of Engineering, University of Oxford, Oxford OX1 3PJ, UK
| | - Johan De Mey
- AIMS Laboratory, Center for Neurosciences, UZ Brussel, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (J.D.M.); (J.V.S.); (D.M.S.); (G.N.)
- Department of Radiology, UZ Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Maarten De Vos
- Faculty of Engineering Science, KU Leuven, 3001 Leuven, Belgium;
- Faculty of Medicine, KU Leuven, 3001 Leuven, Belgium
| | - Jeroen Van Schependom
- AIMS Laboratory, Center for Neurosciences, UZ Brussel, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (J.D.M.); (J.V.S.); (D.M.S.); (G.N.)
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Diana Maria Sima
- AIMS Laboratory, Center for Neurosciences, UZ Brussel, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (J.D.M.); (J.V.S.); (D.M.S.); (G.N.)
- icometrix, 3012 Leuven, Belgium
| | - Guy Nagels
- AIMS Laboratory, Center for Neurosciences, UZ Brussel, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (J.D.M.); (J.V.S.); (D.M.S.); (G.N.)
- icometrix, 3012 Leuven, Belgium
- St Edmund Hall, Queen’s Ln, Oxford OX1 4AR, UK
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Dahlke F, Arnold DL, Aarden P, Ganjgahi H, Häring DA, Čuklina J, Nichols TE, Gardiner S, Bermel R, Wiendl H. Characterisation of MS phenotypes across the age span using a novel data set integrating 34 clinical trials (NO.MS cohort): Age is a key contributor to presentation. Mult Scler 2021; 27:2062-2076. [PMID: 33507835 PMCID: PMC8564259 DOI: 10.1177/1352458520988637] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 11/15/2022]
Abstract
BACKGROUND The Oxford Big Data Institute, multiple sclerosis (MS) physicians and Novartis aim to address unresolved questions in MS with a novel comprehensive clinical trial data set. OBJECTIVE The objective of this study is to describe the Novartis-Oxford MS (NO.MS) data set and to explore the relationships between age, disease activity and disease worsening across MS phenotypes. METHODS We report key characteristics of NO.MS. We modelled MS lesion formation, relapse frequency, brain volume change and disability worsening cross-sectionally, as a function of patients' baseline age, using phase III study data (≈8000 patients). RESULTS NO.MS contains data of ≈35,000 patients (>200,000 brain images from ≈10,000 patients), with >10 years follow-up. (1) Focal disease activity is highest in paediatric patients and decreases with age, (2) brain volume loss is similar across age and phenotypes and (3) the youngest patients have the lowest likelihood (<25%) of disability worsening over 2 years while risk is higher (25%-75%) in older, disabled or progressive MS patients. Young patients benefit most from treatment. CONCLUSION NO.MS will illuminate questions related to MS characterisation, progression and prognosis. Age modulates relapse frequency and, thus, the phenotypic presentation of MS. Disease worsening across all phenotypes is mediated by age and appears to some extent be independent from new focal inflammatory activity.
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Affiliation(s)
| | - Douglas L Arnold
- Brain Imaging Centre, Montreal Neurological
Institute and Hospital, McGill University, Montréal, QC, Canada
| | | | - Habib Ganjgahi
- Oxford Big Data Institute, Li Ka Shing Centre
for Health Information and Discovery, Nuffield Department of Population
Health, University of Oxford, Oxford, UK
| | | | | | - Thomas E Nichols
- Oxford Big Data Institute, Li Ka Shing Centre
for Health Information and Discovery, Nuffield Department of Population
Health, University of Oxford, Oxford, UK
| | | | - Robert Bermel
- Department of Neurology, Mellen MS Center,
Cleveland Clinic, Cleveland, OH, USA
| | - Heinz Wiendl
- Department of Neurology, University Hospital
Münster, Münster, Germany
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34
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Xin B, Huang J, Zhang L, Zheng C, Zhou Y, Lu J, Wang X. Dynamic topology analysis for spatial patterns of multifocal lesions on MRI. Med Image Anal 2021; 76:102267. [PMID: 34929461 DOI: 10.1016/j.media.2021.102267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/26/2021] [Accepted: 10/07/2021] [Indexed: 01/01/2023]
Abstract
Quantitatively analysing the spatial patterns of multifocal lesions on clinical MRI is an important step towards a better understanding of the disease and for precision medicine, which is yet to be properly explored by feature engineering and deep learning methods. Network science addresses this issue by explicitly modeling the inter-lesion topology. However, the construction of the informative graph with optimal edge sparsity and quantification of community graph structures are the current challenges in network science. In this paper, we address these challenges with a novel Dynamic Topology Analysis framework on the basis of persistent homology, aiming to investigate the predictive values of global geometry and local clusters of multifocal lesions. Firstly, Dynamic Hierarchical Network is proposed to construct informative global and community-level topology over multi-scale networks from sparse to dense. Multi-scale global topology is constructed with a nested sequence of Rips complexes, from which a new K-simplex Filtration is designed to generate a higher-level topological abstraction for community identification based on the connectivity of k-simplices in the Rips Complex. Secondly, to quantify multi-scale community structures, we design a new Decomposed Community Persistence algorithm to track the dynamic evolution of communities, and then summarise the evolutionary communities incorporated with a customisable descriptor. The quantified community features are encapsulated with global geometric invariants for topological pattern analysis. The proposed framework was evaluated on both diagnostic differentiation and prognostic prediction for multiple sclerosis that is a typical multifocal disease, and achieved ROC_AUC 0.875 and 0.767, respectively, outperforming seven state-of-the-art persistent homology methods and the reported performance of six feature engineering and deep learning methods.
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Affiliation(s)
- Bowen Xin
- School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Jing Huang
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lin Zhang
- School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Chaojie Zheng
- Central Research Institute, United Imaging Healthcare Group Co, Ltd, Shanghai, China
| | - Yun Zhou
- Central Research Institute, United Imaging Healthcare Group Co, Ltd, Shanghai, China
| | - Jie Lu
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Xiuying Wang
- School of Computer Science, The University of Sydney, Sydney, NSW, Australia.
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Abstract
OBJECTIVE Child undernutrition is a global public health problem with serious implications. In this study, we estimate predictive algorithms for the determinants of childhood stunting by using various machine learning (ML) algorithms. DESIGN This study draws on data from the Ethiopian Demographic and Health Survey of 2016. Five ML algorithms including eXtreme gradient boosting, k-nearest neighbours (k-NN), random forest, neural network and the generalised linear models were considered to predict the socio-demographic risk factors for undernutrition in Ethiopia. SETTING Households in Ethiopia. PARTICIPANTS A total of 9471 children below 5 years of age participated in this study. RESULTS The descriptive results show substantial regional variations in child stunting, wasting and underweight in Ethiopia. Also, among the five ML algorithms, xgbTree algorithm shows a better prediction ability than the generalised linear mixed algorithm. The best predicting algorithm (xgbTree) shows diverse important predictors of undernutrition across the three outcomes which include time to water source, anaemia history, child age greater than 30 months, small birth size and maternal underweight, among others. CONCLUSIONS The xgbTree algorithm was a reasonably superior ML algorithm for predicting childhood undernutrition in Ethiopia compared to other ML algorithms considered in this study. The findings support improvement in access to water supply, food security and fertility regulation, among others, in the quest to considerably improve childhood nutrition in Ethiopia.
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36
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Liu Y, Lin D, Li L, Chen Y, Wen J, Lin Y, He X. Using machine-learning algorithms to identify patients at high risk of upper gastrointestinal lesions for endoscopy. J Gastroenterol Hepatol 2021; 36:2735-2744. [PMID: 33929063 DOI: 10.1111/jgh.15530] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/13/2021] [Accepted: 04/25/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND AIM Endoscopic screening for early detection of upper gastrointestinal (UGI) lesions is important. However, population-based endoscopic screening is difficult to implement in populous countries. By identifying high-risk individuals from the general population, the screening targets can be narrowed to individuals who are in most need of an endoscopy. This study was designed to develop an artificial intelligence (AI)-based model to predict patient risk of UGI lesions to identify high-risk individuals for endoscopy. METHODS A total of 620 patients (from 5300 participants) were equally allocated into 10 parts for 10-fold cross validation experiments. The machine-learning predictive models for UGI lesion risk were constructed using random forest, logistic regression, decision tree, and support vector machine (SVM) algorithms. A total of 48 variables covering lifestyles, social-economic status, clinical symptoms, serological results, and pathological data were used in the model construction. RESULTS The accuracies of the four models were between 79.3% and 93.4% in the training set and between 77.2% and 91.2% in the testing dataset (logistics regression: 77.2%; decision tree: 87.3%; random forest: 88.2%; SVM: 91.2%;). The AUCs of four models showed impressive predictive ability. Comparing the four models with the different algorithms, the SVM model featured the best sensitivity and specificity in all datasets tested. CONCLUSIONS Machine-learning algorithms can accurately and reliably predict the risk of UGI lesions based on readily available parameters. The predictive models have the potential to be used clinically for identifying patients with high risk of UGI lesions and stratifying patients for necessary endoscopic screening.
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Affiliation(s)
- Yongjia Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Da Lin
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Lan Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiayao Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiguang Lin
- School of Life Sciences, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Xingxiang He
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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37
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Rose DR, Amin M, Ontaneda D. Prediction in treatment outcomes in multiple sclerosis: challenges and recent advances. Expert Rev Clin Immunol 2021; 17:1187-1198. [PMID: 34570656 DOI: 10.1080/1744666x.2021.1986005] [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: 10/20/2022]
Abstract
INTRODUCTION Multiple Sclerosis (MS) is a chronic autoimmune and neurodegenerative disease of the central nervous system with a course dependent on early treatment response. Increasing evidence also suggests that despite eliminating disease activity (relapses and lesions), many patients continue to accrue disability, highlighting the need for a more comprehensive definition of treatment success. Optimizing disability outcome measures, as well as continuously improving our understanding of neuroinflammatory and neurodegenerative biomarkers is required. AREAS COVERED This review describes the challenges inherent in classifying and monitoring disease phenotype in MS. The review also provides an assessment of clinical, radiological, and blood biomarker tools for current and future practice. EXPERT OPINION Emerging MRI techniques and standardized patient outcome assessments will increase the accuracy of initial diagnosis and understanding of disease progression.
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Affiliation(s)
- Deja R Rose
- Cleveland Clinic, Mellen Center for Multiple Sclerosis, Cleveland Ohio, United States
| | - Moein Amin
- Cleveland Clinic, Mellen Center for Multiple Sclerosis, Cleveland Ohio, United States.,Department of Neurology, Cleveland Clinic, Cleveland Ohio, United States
| | - Daniel Ontaneda
- Cleveland Clinic, Mellen Center for Multiple Sclerosis, Cleveland Ohio, United States.,Department of Neurology, Cleveland Clinic, Cleveland Ohio, United States
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38
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De Brouwer E, Becker T, Moreau Y, Havrdova EK, Trojano M, Eichau S, Ozakbas S, Onofrj M, Grammond P, Kuhle J, Kappos L, Sola P, Cartechini E, Lechner-Scott J, Alroughani R, Gerlach O, Kalincik T, Granella F, Grand'Maison F, Bergamaschi R, José Sá M, Van Wijmeersch B, Soysal A, Sanchez-Menoyo JL, Solaro C, Boz C, Iuliano G, Buzzard K, Aguera-Morales E, Terzi M, Trivio TC, Spitaleri D, Van Pesch V, Shaygannejad V, Moore F, Oreja-Guevara C, Maimone D, Gouider R, Csepany T, Ramo-Tello C, Peeters L. Longitudinal machine learning modeling of MS patient trajectories improves predictions of disability progression. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 208:106180. [PMID: 34146771 DOI: 10.1016/j.cmpb.2021.106180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/08/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND OBJECTIVES Research in Multiple Sclerosis (MS) has recently focused on extracting knowledge from real-world clinical data sources. This type of data is more abundant than data produced during clinical trials and potentially more informative about real-world clinical practice. However, this comes at the cost of less curated and controlled data sets. In this work we aim to predict disability progression by optimally extracting information from longitudinal patient data in the real-world setting, with a special focus on the sporadic sampling problem. METHODS We use machine learning methods suited for patient trajectories modeling, such as recurrent neural networks and tensor factorization. A subset of 6682 patients from the MSBase registry is used. RESULTS We can predict disability progression of patients in a two-year horizon with an ROC-AUC of 0.85, which represents a 32% decrease in the ranking pair error (1-AUC) compared to reference methods using static clinical features. CONCLUSIONS Compared to the models available in the literature, this work uses the most complete patient history for MS disease progression prediction and represents a step forward towards AI-assisted precision medicine in MS.
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Affiliation(s)
| | - Thijs Becker
- I-Biostat, Data Science Institute, Hasselt University, Diepenbeek, Belgium.
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, Leuven 3001, Belgium.
| | | | - Maria Trojano
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari, Bari, Italy
| | - Sara Eichau
- Hospital Universitario Virgen Macarena, Sevilla, Spain
| | | | | | | | - Jens Kuhle
- Neurologic Clinic and Policlinic, MS Center and Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ludwig Kappos
- Neurologic Clinic and Policlinic, MS Center and Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | | | | | | | | | | | - Tomas Kalincik
- Melbourne MS Centre, Department of Neurology, Royal Melbourne Hospital, Melbourne, Australia; CORe, Department of Medicine, University of Melbourne, Melbourne, Australia
| | | | | | | | - Maria José Sá
- Department of Neurology, Centro Hospitalar Universitario de So Joo and University Fernando Pessoa, Porto, Portugal
| | | | - Aysun Soysal
- Bakirkoy Education and Research Hospital for Psychiatric and Neurological Diseases, Istanbul, Turkey
| | | | - Claudio Solaro
- Dept of Rehabilitation mons L Novarese Hospital, Moncrivello, Italy
| | - Cavit Boz
- KTU Medical Faculty Farabi Hospital, Trabzon, Turkey
| | | | | | | | | | | | - Daniele Spitaleri
- Azienda Ospedaliera di Rilievo Nazionale San Giuseppe Moscati Avellino, Avellino, Italy
| | | | - Vahid Shaygannejad
- Isfahan Neurosciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | | | | | | | | | | | - Liesbet Peeters
- I-Biostat, Data Science Institute, Hasselt University, Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, Diepenbeek 3590, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, Diepenbeek 3590, Belgium; I-Biostat, Data Science Institute, Hasselt University, Diepenbeek, Belgium.
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39
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Ashrafuzzaman M. Artificial Intelligence, Machine Learning and Deep Learning in Ion Channel Bioinformatics. MEMBRANES 2021; 11:membranes11090672. [PMID: 34564489 PMCID: PMC8467682 DOI: 10.3390/membranes11090672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Ion channels are linked to important cellular processes. For more than half a century, we have been learning various structural and functional aspects of ion channels using biological, physiological, biochemical, and biophysical principles and techniques. In recent days, bioinformaticians and biophysicists having the necessary expertise and interests in computer science techniques including versatile algorithms have started covering a multitude of physiological aspects including especially evolution, mutations, and genomics of functional channels and channel subunits. In these focused research areas, the use of artificial intelligence (AI), machine learning (ML), and deep learning (DL) algorithms and associated models have been found very popular. With the help of available articles and information, this review provide an introduction to this novel research trend. Ion channel understanding is usually made considering the structural and functional perspectives, gating mechanisms, transport properties, channel protein mutations, etc. Focused research on ion channels and related findings over many decades accumulated huge data which may be utilized in a specialized scientific manner to fast conclude pinpointed aspects of channels. AI, ML, and DL techniques and models may appear as helping tools. This review aims at explaining the ways we may use the bioinformatics techniques and thus draw a few lines across the avenue to let the ion channel features appear clearer.
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Affiliation(s)
- Md Ashrafuzzaman
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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40
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Shoeibi A, Khodatars M, Jafari M, Moridian P, Rezaei M, Alizadehsani R, Khozeimeh F, Gorriz JM, Heras J, Panahiazar M, Nahavandi S, Acharya UR. Applications of deep learning techniques for automated multiple sclerosis detection using magnetic resonance imaging: A review. Comput Biol Med 2021; 136:104697. [PMID: 34358994 DOI: 10.1016/j.compbiomed.2021.104697] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/18/2022]
Abstract
Multiple Sclerosis (MS) is a type of brain disease which causes visual, sensory, and motor problems for people with a detrimental effect on the functioning of the nervous system. In order to diagnose MS, multiple screening methods have been proposed so far; among them, magnetic resonance imaging (MRI) has received considerable attention among physicians. MRI modalities provide physicians with fundamental information about the structure and function of the brain, which is crucial for the rapid diagnosis of MS lesions. Diagnosing MS using MRI is time-consuming, tedious, and prone to manual errors. Research on the implementation of computer aided diagnosis system (CADS) based on artificial intelligence (AI) to diagnose MS involves conventional machine learning and deep learning (DL) methods. In conventional machine learning, feature extraction, feature selection, and classification steps are carried out by using trial and error; on the contrary, these steps in DL are based on deep layers whose values are automatically learn. In this paper, a complete review of automated MS diagnosis methods performed using DL techniques with MRI neuroimaging modalities is provided. Initially, the steps involved in various CADS proposed using MRI modalities and DL techniques for MS diagnosis are investigated. The important preprocessing techniques employed in various works are analyzed. Most of the published papers on MS diagnosis using MRI modalities and DL are presented. The most significant challenges facing and future direction of automated diagnosis of MS using MRI modalities and DL techniques are also provided.
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Affiliation(s)
- Afshin Shoeibi
- Faculty of Electrical Engineering, Biomedical Data Acquisition Lab (BDAL), K. N. Toosi University of Technology, Tehran, Iran.
| | - Marjane Khodatars
- Faculty of Engineering, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mahboobeh Jafari
- Electrical and Computer Engineering Faculty, Semnan University, Semnan, Iran
| | - Parisa Moridian
- Faculty of Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mitra Rezaei
- Electrical and Computer Engineering Dept., Tarbiat Modares University, Tehran, Iran
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Geelong, Australia
| | - Fahime Khozeimeh
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Geelong, Australia
| | - Juan Manuel Gorriz
- Department of Signal Theory, Networking and Communications, Universidad de Granada, Spain; Department of Psychiatry. University of Cambridge, UK
| | - Jónathan Heras
- Department of Mathematics and Computer Science, University of La Rioja, La Rioja, Spain
| | | | - Saeid Nahavandi
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Geelong, Australia
| | - U Rajendra Acharya
- Department of Biomedical Engineering, School of Science and Technology, Singapore University of Social Sciences, Singapore; Dept. of Electronics and Computer Engineering, Ngee Ann Polytechnic, 599489, Singapore; Department of Bioinformatics and Medical Engineering, Asia University, Taiwan
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Barile B, Marzullo A, Stamile C, Durand-Dubief F, Sappey-Marinier D. Ensemble Learning for Multiple Sclerosis Disability Estimation Using Brain Structural Connectivity. Brain Connect 2021; 12:476-488. [PMID: 34269618 DOI: 10.1089/brain.2020.1003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Multiple Sclerosis (MS) is an autoimmune inflammatory disease of the central nervous system characterized by demyelination and neurodegeneration processes. It leads to different clinical courses and degrees of disability that need to be anticipated by the neurologist for personalized therapy. Recently, machine learning (ML) techniques have reached a high level of performance in brain disease diagnosis and/or prognosis, but the decision process of a trained ML system is typically non-transparent. Using brain structural connectivity data, a fully automatic ensemble learning model, augmented with an interpretable model, is proposed for the estimation of MS patients' disability, measured by the Expanded Disability Status Scale (EDSS). METHOD An ensemble of four boosting-based models (GBM, XGBoost, CatBoost, LightBoost) organized following a stacking generalization scheme, was developed using DTI-based structural connectivity data. In addition, an interpretable model based on conditional logistic regression was developed to explain the best performances in terms of white matter (WM) links for three classes of EDSS (Low, Medium, High). RESULTS The ensemble model reached excellent level of performance (RMSE of 0.92 ± 0.28) compared to single-based models and provided a better EDSS estimation using DTI-based structural connectivity data compared to conventional MRI measures associated with patient data (age, gender and disease duration). Used for interpretation of the estimation process, the counterfactual method showed the importance of certain brain networks, corresponding mainly to left hemisphere WM links, connecting the left superior temporal with the left posterior cingulate and the right precuneus gray matter regions, and the inter-hemispheric WM links constituting the corpus callosum. Also, a better accuracy estimation was found for the high disability class. CONCLUSION The combination of advanced ML models and sensitive techniques such as DTI-based structural connectivity demonstrated to be useful for the estimation of MS patients' disability and to point out the most important brain WM networks involved in disability.
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Affiliation(s)
- Berardino Barile
- Université Claude Bernard Lyon 1, 27098, 1CREATIS (UMR5220 & INSERM U1206), 43 Boulevard du 11 Novembre 1918, Villeurbanne, Villeurbanne, France, 69100;
| | - Aldo Marzullo
- University of Calabria, 18950, Mathematics and Computer Science, Arcavacata di Rende, Calabria, Italy;
| | | | - Francoise Durand-Dubief
- Hospices Civils de Lyon, 26900, Lyon, Auvergne-Rhône-Alpes , France.,Université Claude Bernard Lyon 1, 27098, CREATIS (UMR5220 & INSERM U1206), Villeurbanne, Auvergne-Rhône-Alpes , France;
| | - Dominique Sappey-Marinier
- Université de Lyon, 133614, Lyon, Auvergne-Rhône-Alpes , France.,Université Claude Bernard Lyon 1, 27098, CREATIS (UMR5220 & INSERM U1206), Villeurbanne, Auvergne-Rhône-Alpes , France;
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42
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Tommasin S, Cocozza S, Taloni A, Giannì C, Petsas N, Pontillo G, Petracca M, Ruggieri S, De Giglio L, Pozzilli C, Brunetti A, Pantano P. Machine learning classifier to identify clinical and radiological features relevant to disability progression in multiple sclerosis. J Neurol 2021; 268:4834-4845. [PMID: 33970338 PMCID: PMC8563671 DOI: 10.1007/s00415-021-10605-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/05/2021] [Accepted: 05/05/2021] [Indexed: 01/22/2023]
Abstract
Objectives To evaluate the accuracy of a data-driven approach, such as machine learning classification, in predicting disability progression in MS. Methods We analyzed structural brain images of 163 subjects diagnosed with MS acquired at two different sites. Participants were followed up for 2–6 years, with disability progression defined according to the expanded disability status scale (EDSS) increment at follow-up. T2-weighted lesion load (T2LL), thalamic and cerebellar gray matter (GM) volumes, fractional anisotropy of the normal appearing white matter were calculated at baseline and included in supervised machine learning classifiers. Age, sex, phenotype, EDSS at baseline, therapy and time to follow-up period were also included. Classes were labeled as stable or progressed disability. Participants were randomly chosen from both sites to build a sample including 50% patients showing disability progression and 50% patients being stable. One-thousand machine learning classifiers were applied to the resulting sample, and after testing for overfitting, classifier confusion matrix, relative metrics and feature importance were evaluated. Results At follow-up, 36% of participants showed disability progression. The classifier with the highest resulting metrics had accuracy of 0.79, area under the true positive versus false positive rates curve of 0.81, sensitivity of 0.90 and specificity of 0.71. T2LL, thalamic volume, disability at baseline and administered therapy were identified as important features in predicting disability progression. Classifiers built on radiological features had higher accuracy than those built on clinical features. Conclusions Disability progression in MS may be predicted via machine learning classifiers, mostly evaluating neuroradiological features. Supplementary Information The online version contains supplementary material available at 10.1007/s00415-021-10605-7.
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Affiliation(s)
- Silvia Tommasin
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy.
| | - Sirio Cocozza
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Alessandro Taloni
- Institute for Complex Systems, Italian National Research Council, Rome, Italy
| | - Costanza Giannì
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy
| | | | - Giuseppe Pontillo
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, Naples, Italy.,Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Maria Petracca
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy.,Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Serena Ruggieri
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy.,Neuroimmunology Unit, IRCSS Fondazione Santa Lucia, Rome, Italy
| | - Laura De Giglio
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy.,Neurology Unit, Medicine Department, San Filippo Neri Hospital, Rome, Italy
| | - Carlo Pozzilli
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy
| | - Arturo Brunetti
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Patrizia Pantano
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy.,Department of Radiology, IRCCS NEUROMED, Pozzilli, Italy
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Voigt I, Inojosa H, Dillenseger A, Haase R, Akgün K, Ziemssen T. Digital Twins for Multiple Sclerosis. Front Immunol 2021; 12:669811. [PMID: 34012452 PMCID: PMC8128142 DOI: 10.3389/fimmu.2021.669811] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022] Open
Abstract
An individualized innovative disease management is of great importance for people with multiple sclerosis (pwMS) to cope with the complexity of this chronic, multidimensional disease. However, an individual state of the art strategy, with precise adjustment to the patient's characteristics, is still far from being part of the everyday care of pwMS. The development of digital twins could decisively advance the necessary implementation of an individualized innovative management of MS. Through artificial intelligence-based analysis of several disease parameters - including clinical and para-clinical outcomes, multi-omics, biomarkers, patient-related data, information about the patient's life circumstances and plans, and medical procedures - a digital twin paired to the patient's characteristic can be created, enabling healthcare professionals to handle large amounts of patient data. This can contribute to a more personalized and effective care by integrating data from multiple sources in a standardized manner, implementing individualized clinical pathways, supporting physician-patient communication and facilitating a shared decision-making. With a clear display of pre-analyzed patient data on a dashboard, patient participation and individualized clinical decisions as well as the prediction of disease progression and treatment simulation could become possible. In this review, we focus on the advantages, challenges and practical aspects of digital twins in the management of MS. We discuss the use of digital twins for MS as a revolutionary tool to improve diagnosis, monitoring and therapy refining patients' well-being, saving economic costs, and enabling prevention of disease progression. Digital twins will help make precision medicine and patient-centered care a reality in everyday life.
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Affiliation(s)
| | | | | | | | | | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Department of Neurology, University Hospital Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
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Dukhi N, Sewpaul R, Derrick Sekgala M, Olawale Awe O. Artificial Intelligence Approach for Analyzing Anaemia Prevalence in Children and Adolescents in BRICS Countries: A Review. CURRENT RESEARCH IN NUTRITION AND FOOD SCIENCE JOURNAL 2021. [DOI: 10.12944/crnfsj.9.1.01] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Anemia prevalence, especially among children and adolescents, is a serious public health burden in the BRICS countries. This article gives an overview of the current anaemia status in children and adolescents in three BRICS countries, as part of a study that utilizes an artificial intelligence approach for analyzing anaemia prevalence in children and adolescents in South Africa, India and Russia. It posits that the use of machine learning in this area of health research is still novel. The weightage assessment of the crosslink between anaemia risk indicators using a machine learning approach will assist policy makers in identifying the areas of priority to intervene in the BRICS participating countries. Health interventions utilizing artificial intelligence and more specifically, machine learning techniques, remains nascent in LMICs but could lead to improved health outcomes.
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Affiliation(s)
- Natisha Dukhi
- 1Human and Social Capabilities Division, Human Sciences Research Council, Merchant House, 116-118 Buitengracht Street, Cape Town, South Africa
| | - Ronel Sewpaul
- 1Human and Social Capabilities Division, Human Sciences Research Council, Merchant House, 116-118 Buitengracht Street, Cape Town, South Africa
| | - Machoene Derrick Sekgala
- 1Human and Social Capabilities Division, Human Sciences Research Council, Merchant House, 116-118 Buitengracht Street, Cape Town, South Africa
| | - Olushina Olawale Awe
- 2Department of Mathematical Sciences, Anchor University Lagos, Lagos, Nigeria. 3Institute of Mathematics and Statistics, Federal University of Bahia (UFBA), Salvador, Brazil
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DARVISHI SONIA, HAMIDI OMID, POOROLAJAL JALAL. Prediction of Multiple sclerosis disease using machine learning classifiers: a comparative study. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2021; 62:E192-E199. [PMID: 34322636 PMCID: PMC8283630 DOI: 10.15167/2421-4248/jpmh2021.62.1.1651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/16/2021] [Indexed: 11/24/2022]
Abstract
Introduction Hamedan Province is one of Iran’s high-risk regions for Multiple Sclerosis (MS). Early diagnosis of MS based on an accurate system can control the disease. The aim of this study was to compare the performance of four machine learning techniques with traditional methods for predicting MS patients. Methods The study used information regarding 200 patients through a case-control study conducted in Hamadan, Western Iran, from 2013 to 2015. The performance of six classifiers was used to compare their performance in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (LR+), negative likelihood ratio (LR-) and total accuracy. Results Random Forest (RF) model illustrated better performance among other models in both scenarios. It had greater specificity (0.67), PPV (0.68) and total accuracy (0.68). The most influential diagnostic factors for MS were age, birth season and gender. Conclusions Our findings showed that despite all the six methods performed almost similarly, the RF model performed slightly better in terms of different criteria in prediction accuracy. Accordingly, this approach is an effective classifier for predicting MS in the early stage and control the disease.
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Affiliation(s)
- SONIA DARVISHI
- Social Determinants of Health Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - OMID HAMIDI
- Department of Science, Hamedan University of Technology, Hamedan, Iran
- Correspondence: Omid Hamidi, Department of Science, Hamedan University of Technology, Hamedan, 65155 Iran - Tel.: +98 81 38411533 - E-mail:
| | - JALAL POOROLAJAL
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran - Modeling of Noncommunicable Disease Research Center, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
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Saad G, Jaber B, Al-hajri M, Househ M, Ahmed A, Abd-alrazaq A. Artificial Intelligence in Diagnosis and Prediction of the Multiple Sclerosis Progression: A Scoping Review (Preprint).. [DOI: 10.2196/preprints.29720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
BACKGROUND
Multiple Sclerosis (MS) is an autoimmune disease that results from the demyelination of the nerves in the Central Nervous System. The diagnosis depends on clinical history, neurological examination, and radiological images. Artificial Intelligence proved to be an effective tool in enhancing the diagnostic tools of MS.
OBJECTIVE
To explore how AI assisted in diagnosis and predicting the progression of MS.
METHODS
We used three bibliographic databases in our search: PubMed IEEE Xplore and Cochrane in our search. The study selection process included: removal of duplicated articles, screening titles and abstracts, and reading the full text. This process was performed by two reviewers. The data extracted from the included studies have been filled in an Excel sheet. This step had been done by each reviewer accordingly to the assigned articles. The extracted data sheet was checked by two reviewers to have accuracy ensured. The narrative approach is applied in data synthesis.
RESULTS
The search conducted resulted in 320 articles Removing duplicates and excluding the ineligible articles due to irrelevancy to the population, intervention, and outcomes resulted in excluding 299 articles. Thus, our review will include 21 articles for data extraction and data synthesis.
CONCLUSIONS
Artificial Intelligence is becoming a trend in the medical field. Its contribution in enhancing the diagnostic tools of many diseases, as in MS, is prominent and can be built on in further development plans. However, the implementation of Artificial Intelligence in Multiple Sclerosis is not widespread to confirm the benefits gained, and the datasets involved in the current practice are relatively small. It is recommended to have more studies that focus on the relationship between the employment of AI in diagnosis and monitoring progression and the accuracy gained by this employment.
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Hartmann M, Fenton N, Dobson R. Current review and next steps for artificial intelligence in multiple sclerosis risk research. Comput Biol Med 2021; 132:104337. [PMID: 33773193 DOI: 10.1016/j.compbiomed.2021.104337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022]
Abstract
In the last few decades, the prevalence of multiple sclerosis (MS), a chronic inflammatory disease of the nervous system, has increased, particularly in Northern European countries, the United States, and United Kingdom. The promise of artificial intelligence (AI) and machine learning (ML) as tools to address problems in MS research has attracted increasing interest in these methods. Bayesian networks offer a clear advantage since they can integrate data and causal knowledge allowing for visualizing interactions between dependent variables and potential confounding factors. A review of AI/ML research methods applied to MS found 216 papers using terms "Multiple Sclerosis", "machine learning", "artificial intelligence", "Bayes", and "Bayesian", of which 90 were relevant and recently published. More than half of these involve the detection and segmentation of MS lesions for quantitative analysis; however clinical and lifestyle risk factor assessment and prediction have largely been ignored. Of those that address risk factors, most provide only association studies for some factors and often fail to include the potential impact of confounding factors and bias (especially where these have causal explanations) that could affect data interpretation, such as reporting quality and medical care access in various countries. To address these gaps in the literature, we propose a causal Bayesian network approach to assessing risk factors for MS, which can address deficiencies in current epidemiological methods of producing risk measurements and makes better use of observational data.
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Affiliation(s)
- Morghan Hartmann
- Risk and Information Management Research Group, School of Electronic Engineering and Computer Science, Queen Mary University of London, London, E1 4NS, UK.
| | - Norman Fenton
- Risk and Information Management Research Group, School of Electronic Engineering and Computer Science, Queen Mary University of London, London, E1 4NS, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, E1 4NS, UK
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Healy BC. Machine and deep learning in MS research are just powerful statistics - No. Mult Scler 2021; 27:663-664. [PMID: 33625302 DOI: 10.1177/1352458520978648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Brian C Healy
- Partners Multiple Sclerosis Center, Brigham and Women's Hospital, Boston, MA, USA/Department of Neurology, Harvard Medical School, Boston, MA, USA/Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA
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Seccia R, Romano S, Salvetti M, Crisanti A, Palagi L, Grassi F. Machine Learning Use for Prognostic Purposes in Multiple Sclerosis. Life (Basel) 2021; 11:life11020122. [PMID: 33562572 PMCID: PMC7914671 DOI: 10.3390/life11020122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/28/2022] Open
Abstract
The course of multiple sclerosis begins with a relapsing-remitting phase, which evolves into a secondarily progressive form over an extremely variable period, depending on many factors, each with a subtle influence. To date, no prognostic factors or risk score have been validated to predict disease course in single individuals. This is increasingly frustrating, since several treatments can prevent relapses and slow progression, even for a long time, although the possible adverse effects are relevant, in particular for the more effective drugs. An early prediction of disease course would allow differentiation of the treatment based on the expected aggressiveness of the disease, reserving high-impact therapies for patients at greater risk. To increase prognostic capacity, approaches based on machine learning (ML) algorithms are being attempted, given the failure of other approaches. Here we review recent studies that have used clinical data, alone or with other types of data, to derive prognostic models. Several algorithms that have been used and compared are described. Although no study has proposed a clinically usable model, knowledge is building up and in the future strong tools are likely to emerge.
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Affiliation(s)
- Ruggiero Seccia
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, 00185 Rome, Italy; (R.S.); (L.P.)
| | - Silvia Romano
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (S.R.); (M.S.)
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy; (S.R.); (M.S.)
- Mediterranean Neurological Institute Neuromed, 86077 Pozzilli, Italy
| | - Andrea Crisanti
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy;
| | - Laura Palagi
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, 00185 Rome, Italy; (R.S.); (L.P.)
| | - Francesca Grassi
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
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Vázquez-Marrufo M, Sarrias-Arrabal E, García-Torres M, Martín-Clemente R, Izquierdo G. A systematic review of the application of machine-learning algorithms in multiple sclerosis. Neurologia 2021; 38:S0213-4853(20)30431-X. [PMID: 33549371 DOI: 10.1016/j.nrl.2020.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/20/2020] [Accepted: 10/11/2020] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The applications of artificial intelligence, and in particular automatic learning or "machine learning" (ML), constitute both a challenge and a great opportunity in numerous scientific, technical, and clinical disciplines. Specific applications in the study of multiple sclerosis (MS) have been no exception, and constitute an area of increasing interest in recent years. OBJECTIVE We present a systematic review of the application of ML algorithms in MS. MATERIALS AND METHODS We used the PubMed search engine, which allows free access to the MEDLINE medical database, to identify studies including the keywords "machine learning" and "multiple sclerosis." We excluded review articles, studies written in languages other than English or Spanish, and studies that were mainly technical and did not specifically apply to MS. The final selection included 76 articles, and 38 were rejected. CONCLUSIONS After the review process, we established 4 main applications of ML in MS: 1) classifying MS subtypes; 2) distinguishing patients with MS from healthy controls and individuals with other diseases; 3) predicting progression and response to therapeutic interventions; and 4) other applications. Results found to date have shown that ML algorithms may offer great support for health professionals both in clinical settings and in research into MS.
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Affiliation(s)
- M Vázquez-Marrufo
- Departamento de Psicología Experimental, Facultad de Psicología, Universidad de Sevilla, Sevilla, España.
| | - E Sarrias-Arrabal
- Departamento de Psicología Experimental, Facultad de Psicología, Universidad de Sevilla, Sevilla, España
| | - M García-Torres
- Escuela Politécnica Superior, Universidad Pablo de Olavide, Sevilla, España
| | - R Martín-Clemente
- Departamento de Teoría de la Señal y Comunicaciones, Escuela Técnica Superior de Ingeniería, Universidad de Sevilla, Sevilla, España
| | - G Izquierdo
- Unidad de Esclerosis Múltiple, Hospital VITHAS, Sevilla, España
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