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Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis,...
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Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Machine Learning and Artificial Intelligence in Diagnostics".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 51804

Special Issue Editor

Dr. Tim Duong

E-Mail Website
Guest Editor
Department of Radiology, Albert Einstein College of Medicine and Montefiore Health System, Bronx, NY 10461, USA
Interests: imaging methods; machine learning and image/data analysis; neuroscience; neurology; physiology; animal models and other disease domain expertise
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear COVID-19 researchers,

Since the first report of severe respiratory illness caused by coronavirus disease 2019 (COVID-19) in mid-December 2019, over 128 million individuals have been infected, resulting in over 2.8 million deaths worldwide as of 31 March 2021. Many COVID-19 patients have mild or asymptomatic infections, while others deteriorate rapidly with multi-organ failure. There are already multiple resurgences. A large array of clinical and demographic variables associated with COVID-19 have been identified. Remarkable progress has been made in our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenicity and disease manifestation. Public health measures are effective in curbing the spread of SARS-CoV-2, and new and effective treatments and vaccines are becoming available.

Machine learning methods are increasingly being used in medicine, including in the study of COVID-19. Machine learning employs computer algorithms to learn relationships amongst different data elements and inform outcomes. In contrast to conventional analysis methods (such as linear or logistic regression), the exact relationship amongst different data elements with respect to outcome variables does not need to be explicitly specified. In addition to approximating physician skills, machine learning algorithms can also find novel relationships not readily apparent to humans. Many studies have shown that machine learning outperforms logistic regression and classification tree models, as well as humans, in many tasks in medicine. Machine learning is particularly useful in dealing with large and complex datasets. With increasing computing power and the growing relevance of big data in medicine, machine learning is expected to play an important role in clinical practice.

I would like to invite you to participate in this very exciting Special Issue on “Machine Learning Applications in COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis”, with a focus on the use of machine learning algorithms to investigate how symptoms, clinical, demographic, laboratory, radiological imaging variables contribute to the diagnosis and prognosis of COVID-19. Examples of possible machine learning applications include, but are not limited to: i) diagnosis and prognosis of COVID-19 clinical outcomes (such as mortality and escalated care), ii) in-hospital acquired diagnosis (such as AKI and ARDS), iii) treatments (such as mechanical ventilation, steroids, and anticoagulants), and vi) diagnosis and prognosis post-acute COVID-19 sequelae. Studies on other related topics are also welcomed.

Dr. Tim Duong
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Machine learning
  • COVID-19 and its Complications
  • Screening
  • Diagnosis
  • Treatment
  • Prognosis
  • Imaging
  • Sequelae

Published Papers (16 papers)

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12 pages, 2263 KiB  
Article
Multi-Stage Temporal Convolution Network for COVID-19 Variant Classification
by Waseem Ullah, Amin Ullah, Khalid Mahmood Malik, Abdul Khader Jilani Saudagar, Muhammad Badruddin Khan, Mozaherul Hoque Abul Hasanat, Abdullah AlTameem and Mohammed AlKhathami
Diagnostics 2022, 12(11), 2736; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12112736 - 09 Nov 2022
Cited by 3 | Viewed by 1588
Abstract
The outbreak of the novel coronavirus disease COVID-19 (SARS-CoV-2) has developed into a global epidemic. Due to the pathogenic virus’s high transmission rate, accurate identification and early prediction are required for subsequent therapy. Moreover, the virus’s polymorphic nature allows it to evolve and [...] Read more.
The outbreak of the novel coronavirus disease COVID-19 (SARS-CoV-2) has developed into a global epidemic. Due to the pathogenic virus’s high transmission rate, accurate identification and early prediction are required for subsequent therapy. Moreover, the virus’s polymorphic nature allows it to evolve and adapt to various environments, making prediction difficult. However, other diseases, such as dengue, MERS-CoV, Ebola, SARS-CoV-1, and influenza, necessitate the employment of a predictor based on their genomic information. To alleviate the situation, we propose a deep learning-based mechanism for the classification of various SARS-CoV-2 virus variants, including the most recent, Omicron. Our model uses a neural network with a temporal convolution neural network to accurately identify different variants of COVID-19. The proposed model first encodes the sequences in the numerical descriptor, and then the convolution operation is applied for discriminative feature extraction from the encoded sequences. The sequential relations between the features are collected using a temporal convolution network to classify COVID-19 variants accurately. We collected recent data from the NCBI, on which the proposed method outperforms various baselines with a high margin. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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16 pages, 848 KiB  
Article
Prognostic Model of COVID-19 Severity and Survival among Hospitalized Patients Using Machine Learning Techniques
by Ivano Lodato, Aditya Varna Iyer, Isaac Zachary To, Zhong-Yuan Lai, Helen Shuk-Ying Chan, Winnie Suk-Wai Leung, Tommy Hing-Cheung Tang, Victor Kai-Lam Cheung, Tak-Chiu Wu and George Wing-Yiu Ng
Diagnostics 2022, 12(11), 2728; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12112728 - 08 Nov 2022
Cited by 4 | Viewed by 2231
Abstract
We conducted a statistical study and developed a machine learning model to triage COVID-19 patients affected during the height of the COVID-19 pandemic in Hong Kong based on their medical records and test results (features) collected during their hospitalization. The correlation between the [...] Read more.
We conducted a statistical study and developed a machine learning model to triage COVID-19 patients affected during the height of the COVID-19 pandemic in Hong Kong based on their medical records and test results (features) collected during their hospitalization. The correlation between the values of these features is studied against discharge status and disease severity as a preliminary step to identify those features with a more pronounced effect on the patient outcome. Once identified, they constitute the inputs of four machine learning models, Decision Tree, Random Forest, Gradient and RUSBoosting, which predict both the Mortality and Severity associated with the disease. We test the accuracy of the models when the number of input features is varied, demonstrating their stability; i.e., the models are already highly predictive when run over a core set of (6) features. We show that Random Forest and Gradient Boosting classifiers are highly accurate in predicting patients’ Mortality (average accuracy ∼99%) as well as categorize patients (average accuracy ∼91%) into four distinct risk classes (Severity of COVID-19 infection). Our methodical and broad approach combines statistical insights with various machine learning models, which paves the way forward in the AI-assisted triage and prognosis of COVID-19 cases, which is potentially generalizable to other seasonal flus. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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19 pages, 1873 KiB  
Article
An Improved Machine-Learning Approach for COVID-19 Prediction Using Harris Hawks Optimization and Feature Analysis Using SHAP
by Kumar Debjit, Md Saiful Islam, Md. Abadur Rahman, Farhana Tazmim Pinki, Rajan Dev Nath, Saad Al-Ahmadi, Md. Shahadat Hossain, Khondoker Mirazul Mumenin and Md. Abdul Awal
Diagnostics 2022, 12(5), 1023; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12051023 - 19 Apr 2022
Cited by 19 | Viewed by 3563
Abstract
A healthcare monitoring system needs the support of recent technologies such as artificial intelligence (AI), machine learning (ML), and big data, especially during the COVID-19 pandemic. This global pandemic has already taken millions of lives. Both infected and uninfected people have generated big [...] Read more.
A healthcare monitoring system needs the support of recent technologies such as artificial intelligence (AI), machine learning (ML), and big data, especially during the COVID-19 pandemic. This global pandemic has already taken millions of lives. Both infected and uninfected people have generated big data where AI and ML can use to combat and detect COVID-19 at an early stage. Motivated by this, an improved ML framework for the early detection of this disease is proposed in this paper. The state-of-the-art Harris hawks optimization (HHO) algorithm with an improved objective function is proposed and applied to optimize the hyperparameters of the ML algorithms, namely HHO-based eXtreme gradient boosting (HHOXGB), light gradient boosting (HHOLGB), categorical boosting (HHOCAT), random forest (HHORF) and support vector classifier (HHOSVC). An ensemble technique was applied to these optimized ML models to improve the prediction performance. Our proposed method was applied to publicly available big COVID-19 data and yielded a prediction accuracy of 92.38% using the ensemble model. In contrast, HHOXGB provided the highest accuracy of 92.23% as a single optimized model. The performance of the proposed method was compared with the traditional algorithms and other ML-based methods. In both cases, our proposed method performed better. Furthermore, not only the classification improvement, but also the features are analyzed in terms of feature importance calculated by SHapely adaptive exPlanations (SHAP) values. A graphical user interface is also discussed as a potential tool for nonspecialist users such as clinical staff and nurses. The processed data, trained model, and codes related to this study are available at GitHub. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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23 pages, 19180 KiB  
Article
WMR-DepthwiseNet: A Wavelet Multi-Resolution Depthwise Separable Convolutional Neural Network for COVID-19 Diagnosis
by Happy Nkanta Monday, Jianping Li, Grace Ugochi Nneji, Md Altab Hossin, Saifun Nahar, Jehoiada Jackson and Ijeoma Amuche Chikwendu
Diagnostics 2022, 12(3), 765; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12030765 - 21 Mar 2022
Cited by 2 | Viewed by 2666
Abstract
Timely discovery of COVID-19 could aid in formulating a suitable treatment plan for disease mitigation and containment decisions. The widely used COVID-19 test necessitates a regular method and has a low sensitivity value. Computed tomography and chest X-ray are also other methods utilized [...] Read more.
Timely discovery of COVID-19 could aid in formulating a suitable treatment plan for disease mitigation and containment decisions. The widely used COVID-19 test necessitates a regular method and has a low sensitivity value. Computed tomography and chest X-ray are also other methods utilized by numerous studies for detecting COVID-19. In this article, we propose a CNN called depthwise separable convolution network with wavelet multiresolution analysis module (WMR-DepthwiseNet) that is robust to automatically learn details from both spatialwise and channelwise for COVID-19 identification with a limited radiograph dataset, which is critical due to the rapid growth of COVID-19. This model utilizes an effective strategy to prevent loss of spatial details, which is a prevalent issue in traditional convolutional neural network, and second, the depthwise separable connectivity framework ensures reusability of feature maps by directly connecting previous layer to all subsequent layers for extracting feature representations from few datasets. We evaluate the proposed model by utilizing a public domain dataset of COVID-19 confirmed case and other pneumonia illness. The proposed method achieves 98.63% accuracy, 98.46% sensitivity, 97.99% specificity, and 98.69% precision on chest X-ray dataset, whereas using the computed tomography dataset, the model achieves 96.83% accuracy, 97.78% sensitivity, 96.22% specificity, and 97.02% precision. According to the results of our experiments, our model achieves up-to-date accuracy with only a few training cases available, which is useful for COVID-19 screening. This latest paradigm is expected to contribute significantly in the battle against COVID-19 and other life-threatening diseases. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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10 pages, 3060 KiB  
Article
COVID-Net CXR-S: Deep Convolutional Neural Network for Severity Assessment of COVID-19 Cases from Chest X-ray Images
by Hossein Aboutalebi, Maya Pavlova, Mohammad Javad Shafiee, Ali Sabri, Amer Alaref and Alexander Wong
Diagnostics 2022, 12(1), 25; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12010025 - 23 Dec 2021
Cited by 22 | Viewed by 4033
Abstract
The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to [...] Read more.
The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to a significantly increased strain on healthcare resources. As such, an important part of managing and handling patients with SARS-CoV-2 infections within the clinical workflow is severity assessment, which is often conducted with the use of chest X-ray (CXR) images. In this work, we introduce COVID-Net CXR-S, a convolutional neural network for predicting the airspace severity of a SARS-CoV-2 positive patient based on a CXR image of the patient’s chest. More specifically, we leveraged transfer learning to transfer representational knowledge gained from over 16,000 CXR images from a multinational cohort of over 15,000 SARS-CoV-2 positive and negative patient cases into a custom network architecture for severity assessment. Experimental results using the RSNA RICORD dataset showed that the proposed COVID-Net CXR-S has potential to be a powerful tool for computer-aided severity assessment of CXR images of COVID-19 positive patients. Furthermore, radiologist validation on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, showed consistency between radiologist interpretation and critical factors leveraged by COVID-Net CXR-S for severity assessment. While not a production-ready solution, the ultimate goal for the open source release of COVID-Net CXR-S is to act as a catalyst for clinical scientists, machine learning researchers, as well as citizen scientists to develop innovative new clinical decision support solutions for helping clinicians around the world manage the continuing pandemic. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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30 pages, 6769 KiB  
Article
Kynurenine and Hemoglobin as Sex-Specific Variables in COVID-19 Patients: A Machine Learning and Genetic Algorithms Approach
by Jose M. Celaya-Padilla, Karen E. Villagrana-Bañuelos, Juan José Oropeza-Valdez, Joel Monárrez-Espino, Julio E. Castañeda-Delgado, Ana Sofía Herrera-Van Oostdam, Julio César Fernández-Ruiz, Fátima Ochoa-González, Juan Carlos Borrego, Jose Antonio Enciso-Moreno, Jesús Adrián López, Yamilé López-Hernández and Carlos E. Galván-Tejada
Diagnostics 2021, 11(12), 2197; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11122197 - 25 Nov 2021
Cited by 5 | Viewed by 3091
Abstract
Differences in clinical manifestations, immune response, metabolic alterations, and outcomes (including disease severity and mortality) between men and women with COVID-19 have been reported since the pandemic outbreak, making it necessary to implement sex-specific biomarkers for disease diagnosis and treatment. This study aimed [...] Read more.
Differences in clinical manifestations, immune response, metabolic alterations, and outcomes (including disease severity and mortality) between men and women with COVID-19 have been reported since the pandemic outbreak, making it necessary to implement sex-specific biomarkers for disease diagnosis and treatment. This study aimed to identify sex-associated differences in COVID-19 patients by means of a genetic algorithm (GALGO) and machine learning, employing support vector machine (SVM) and logistic regression (LR) for the data analysis. Both algorithms identified kynurenine and hemoglobin as the most important variables to distinguish between men and women with COVID-19. LR and SVM identified C10:1, cough, and lysoPC a 14:0 to discriminate between men with COVID-19 from men without, with LR being the best model. In the case of women with COVID-19 vs. women without, SVM had a higher performance, and both models identified a higher number of variables, including 10:2, lysoPC a C26:0, lysoPC a C28:0, alpha-ketoglutaric acid, lactic acid, cough, fever, anosmia, and dysgeusia. Our results demonstrate that differences in sexes have implications in the diagnosis and outcome of the disease. Further, genetic and machine learning algorithms are useful tools to predict sex-associated differences in COVID-19. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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18 pages, 2401 KiB  
Article
Ensemble Machine Learning Model to Predict SARS-CoV-2 T-Cell Epitopes as Potential Vaccine Targets
by Syed Nisar Hussain Bukhari, Amit Jain, Ehtishamul Haq, Abolfazl Mehbodniya and Julian Webber
Diagnostics 2021, 11(11), 1990; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11111990 - 26 Oct 2021
Cited by 25 | Viewed by 3123
Abstract
An ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by a single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide pandemic that continues to date. Vaccination has proven to be the most effective technique, by far, for [...] Read more.
An ongoing outbreak of coronavirus disease 2019 (COVID-19), caused by a single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide pandemic that continues to date. Vaccination has proven to be the most effective technique, by far, for the treatment of COVID-19 and to combat the outbreak. Among all vaccine types, epitope-based peptide vaccines have received less attention and hold a large untapped potential for boosting vaccine safety and immunogenicity. Peptides used in such vaccine technology are chemically synthesized based on the amino acid sequences of antigenic proteins (T-cell epitopes) of the target pathogen. Using wet-lab experiments to identify antigenic proteins is very difficult, expensive, and time-consuming. We hereby propose an ensemble machine learning (ML) model for the prediction of T-cell epitopes (also known as immune relevant determinants or antigenic determinants) against SARS-CoV-2, utilizing physicochemical properties of amino acids. To train the model, we retrieved the experimentally determined SARS-CoV-2 T-cell epitopes from Immune Epitope Database and Analysis Resource (IEDB) repository. The model so developed achieved accuracy, AUC (Area under the ROC curve), Gini, specificity, sensitivity, F-score, and precision of 98.20%, 0.991, 0.994, 0.971, 0.982, 0.990, and 0.981, respectively, using a test set consisting of SARS-CoV-2 peptides (T-cell epitopes and non-epitopes) obtained from IEDB. The average accuracy of 97.98% was recorded in repeated 5-fold cross validation. Its comparison with 05 robust machine learning classifiers and existing T-cell epitope prediction techniques, such as NetMHC and CTLpred, suggest the proposed work as a better model. The predicted epitopes from the current model could possess a high probability to act as potential peptide vaccine candidates subjected to in vitro and in vivo scientific assessments. The model developed would help scientific community working in vaccine development save time to screen the active T-cell epitope candidates of SARS-CoV-2 against the inactive ones. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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20 pages, 5413 KiB  
Article
Predicting Mechanical Ventilation and Mortality in COVID-19 Using Radiomics and Deep Learning on Chest Radiographs: A Multi-Institutional Study
by Joseph Bae, Saarthak Kapse, Gagandeep Singh, Rishabh Gattu, Syed Ali, Neal Shah, Colin Marshall, Jonathan Pierce, Tej Phatak, Amit Gupta, Jeremy Green, Nikhil Madan and Prateek Prasanna
Diagnostics 2021, 11(10), 1812; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101812 - 30 Sep 2021
Cited by 16 | Viewed by 2296
Abstract
In this study, we aimed to predict mechanical ventilation requirement and mortality using computational modeling of chest radiographs (CXRs) for coronavirus disease 2019 (COVID-19) patients. This two-center, retrospective study analyzed 530 deidentified CXRs from 515 COVID-19 patients treated at Stony Brook University Hospital [...] Read more.
In this study, we aimed to predict mechanical ventilation requirement and mortality using computational modeling of chest radiographs (CXRs) for coronavirus disease 2019 (COVID-19) patients. This two-center, retrospective study analyzed 530 deidentified CXRs from 515 COVID-19 patients treated at Stony Brook University Hospital and Newark Beth Israel Medical Center between March and August 2020. Linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), and random forest (RF) machine learning classifiers to predict mechanical ventilation requirement and mortality were trained and evaluated using radiomic features extracted from patients’ CXRs. Deep learning (DL) approaches were also explored for the clinical outcome prediction task and a novel radiomic embedding framework was introduced. All results are compared against radiologist grading of CXRs (zone-wise expert severity scores). Radiomic classification models had mean area under the receiver operating characteristic curve (mAUCs) of 0.78 ± 0.05 (sensitivity = 0.72 ± 0.07, specificity = 0.72 ± 0.06) and 0.78 ± 0.06 (sensitivity = 0.70 ± 0.09, specificity = 0.73 ± 0.09), compared with expert scores mAUCs of 0.75 ± 0.02 (sensitivity = 0.67 ± 0.08, specificity = 0.69 ± 0.07) and 0.79 ± 0.05 (sensitivity = 0.69 ± 0.08, specificity = 0.76 ± 0.08) for mechanical ventilation requirement and mortality prediction, respectively. Classifiers using both expert severity scores and radiomic features for mechanical ventilation (mAUC = 0.79 ± 0.04, sensitivity = 0.71 ± 0.06, specificity = 0.71 ± 0.08) and mortality (mAUC = 0.83 ± 0.04, sensitivity = 0.79 ± 0.07, specificity = 0.74 ± 0.09) demonstrated improvement over either artificial intelligence or radiologist interpretation alone. Our results also suggest instances in which the inclusion of radiomic features in DL improves model predictions over DL alone. The models proposed in this study and the prognostic information they provide might aid physician decision making and efficient resource allocation during the COVID-19 pandemic. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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24 pages, 7441 KiB  
Article
CSGBBNet: An Explainable Deep Learning Framework for COVID-19 Detection
by Xu-Jing Yao, Zi-Quan Zhu, Shui-Hua Wang and Yu-Dong Zhang
Diagnostics 2021, 11(9), 1712; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11091712 - 18 Sep 2021
Cited by 8 | Viewed by 3346
Abstract
The COVID-19 virus has swept the world and brought great impact to various fields, gaining wide attention from all walks of life since the end of 2019. At present, although the global epidemic situation is leveling off and vaccine doses have been administered [...] Read more.
The COVID-19 virus has swept the world and brought great impact to various fields, gaining wide attention from all walks of life since the end of 2019. At present, although the global epidemic situation is leveling off and vaccine doses have been administered in a large amount, confirmed cases are still emerging around the world. To make up for the missed diagnosis caused by the uncertainty of nucleic acid polymerase chain reaction (PCR) test, utilizing lung CT examination as a combined detection method to improve the diagnostic rate becomes a necessity. Our research considered the time-consuming and labor-intensive characteristics of the traditional CT analyzing process, and developed an efficient deep learning framework named CSGBBNet to solve the binary classification task of COVID-19 images based on a COVID-Seg model for image preprocessing and a GBBNet for classification. The five runs with random seed on the test set showed our novel framework can rapidly analyze CT scan images and give out effective results for assisting COVID-19 detection, with the mean accuracy of 98.49 ± 1.23%, the sensitivity of 99.00 ± 2.00%, the specificity of 97.95 ± 2.51%, the precision of 98.10 ± 2.61%, and the F1 score of 98.51 ± 1.22%. Moreover, our model CSGBBNet performs better when compared with seven previous state-of-the-art methods. In this research, the aim is to link together biomedical research and artificial intelligence and provide some insights into the field of COVID-19 detection. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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18 pages, 1334 KiB  
Article
Residual-Shuffle Network with Spatial Pyramid Pooling Module for COVID-19 Screening
by Mohd Asyraf Zulkifley, Siti Raihanah Abdani, Nuraisyah Hani Zulkifley and Mohamad Ibrani Shahrimin
Diagnostics 2021, 11(8), 1497; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11081497 - 19 Aug 2021
Cited by 3 | Viewed by 2208
Abstract
Since the start of the COVID-19 pandemic at the end of 2019, more than 170 million patients have been infected with the virus that has resulted in more than 3.8 million deaths all over the world. This disease is easily spreadable from one [...] Read more.
Since the start of the COVID-19 pandemic at the end of 2019, more than 170 million patients have been infected with the virus that has resulted in more than 3.8 million deaths all over the world. This disease is easily spreadable from one person to another even with minimal contact, even more for the latest mutations that are more deadly than its predecessor. Hence, COVID-19 needs to be diagnosed as early as possible to minimize the risk of spreading among the community. However, the laboratory results on the approved diagnosis method by the World Health Organization, the reverse transcription-polymerase chain reaction test, takes around a day to be processed, where a longer period is observed in the developing countries. Therefore, a fast screening method that is based on existing facilities should be developed to complement this diagnosis test, so that a suspected patient can be isolated in a quarantine center. In line with this motivation, deep learning techniques were explored to provide an automated COVID-19 screening system based on X-ray imaging. This imaging modality is chosen because of its low-cost procedures that are widely available even in many small clinics. A new convolutional neural network (CNN) model is proposed instead of utilizing pre-trained networks of the existing models. The proposed network, Residual-Shuffle-Net, comprises four stacks of the residual-shuffle unit followed by a spatial pyramid pooling (SPP) unit. The architecture of the residual-shuffle unit follows an hourglass design with reduced convolution filter size in the middle layer, where a shuffle operation is performed right after the split branches have been concatenated back. Shuffle operation forces the network to learn multiple sets of features relationship across various channels instead of a set of global features. The SPP unit, which is placed at the end of the network, allows the model to learn multi-scale features that are crucial to distinguish between the COVID-19 and other types of pneumonia cases. The proposed network is benchmarked with 12 other state-of-the-art CNN models that have been designed and tuned specially for COVID-19 detection. The experimental results show that the Residual-Shuffle-Net produced the best performance in terms of accuracy and specificity metrics with 0.97390 and 0.98695, respectively. The model is also considered as a lightweight model with slightly more than 2 million parameters, which makes it suitable for mobile-based applications. For future work, an attention mechanism can be integrated to target certain regions of interest in the X-ray images that are deemed to be more informative for COVID-19 diagnosis. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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30 pages, 6327 KiB  
Article
Transfer Learning for the Detection and Diagnosis of Types of Pneumonia including Pneumonia Induced by COVID-19 from Chest X-ray Images
by Yusuf Brima, Marcellin Atemkeng, Stive Tankio Djiokap, Jaures Ebiele and Franklin Tchakounté
Diagnostics 2021, 11(8), 1480; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11081480 - 16 Aug 2021
Cited by 15 | Viewed by 3970
Abstract
Accurate early diagnosis of COVID-19 viral pneumonia, primarily in asymptomatic people, is essential to reduce the spread of the disease, the burden on healthcare capacity, and the overall death rate. It is essential to design affordable and accessible solutions to distinguish pneumonia caused [...] Read more.
Accurate early diagnosis of COVID-19 viral pneumonia, primarily in asymptomatic people, is essential to reduce the spread of the disease, the burden on healthcare capacity, and the overall death rate. It is essential to design affordable and accessible solutions to distinguish pneumonia caused by COVID-19 from other types of pneumonia. In this work, we propose a reliable approach based on deep transfer learning that requires few computations and converges faster. Experimental results demonstrate that our proposed framework for transfer learning is a potential and effective approach to detect and diagnose types of pneumonia from chest X-ray images with a test accuracy of 94.0%. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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18 pages, 10593 KiB  
Article
Machine Learning Approaches to Identify Patient Comorbidities and Symptoms That Increased Risk of Mortality in COVID-19
by Sakifa Aktar, Ashis Talukder, Md. Martuza Ahamad, A. H. M. Kamal, Jahidur Rahman Khan, Md. Protikuzzaman, Nasif Hossain, A. K. M. Azad, Julian M. W. Quinn, Mathew A. Summers, Teng Liaw, Valsamma Eapen and Mohammad Ali Moni
Diagnostics 2021, 11(8), 1383; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11081383 - 31 Jul 2021
Cited by 24 | Viewed by 5273
Abstract
Providing appropriate care for people suffering from COVID-19, the disease caused by the pandemic SARS-CoV-2 virus, is a significant global challenge. Many individuals who become infected may have pre-existing conditions that may interact with COVID-19 to increase symptom severity and mortality risk. COVID-19 [...] Read more.
Providing appropriate care for people suffering from COVID-19, the disease caused by the pandemic SARS-CoV-2 virus, is a significant global challenge. Many individuals who become infected may have pre-existing conditions that may interact with COVID-19 to increase symptom severity and mortality risk. COVID-19 patient comorbidities are likely to be informative regarding the individual risk of severe illness and mortality. Determining the degree to which comorbidities are associated with severe symptoms and mortality would thus greatly assist in COVID-19 care planning and provision. To assess this we performed a meta-analysis of published global literature, and machine learning predictive analysis using an aggregated COVID-19 global dataset. Our meta-analysis suggested that chronic obstructive pulmonary disease (COPD), cerebrovascular disease (CEVD), cardiovascular disease (CVD), type 2 diabetes, malignancy, and hypertension as most significantly associated with COVID-19 severity in the current published literature. Machine learning classification using novel aggregated cohort data similarly found COPD, CVD, CKD, type 2 diabetes, malignancy, and hypertension, as well as asthma, as the most significant features for classifying those deceased versus those who survived COVID-19. While age and gender were the most significant predictors of mortality, in terms of symptom–comorbidity combinations, it was observed that Pneumonia–Hypertension, Pneumonia–Diabetes, and Acute Respiratory Distress Syndrome (ARDS)–Hypertension showed the most significant associations with COVID-19 mortality. These results highlight the patient cohorts most likely to be at risk of COVID-19-related severe morbidity and mortality, which have implications for prioritization of hospital resources. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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11 pages, 1971 KiB  
Article
A Meta-Analysis of Computerized Tomography-Based Radiomics for the Diagnosis of COVID-19 and Viral Pneumonia
by Yung-Shuo Kao and Kun-Te Lin
Diagnostics 2021, 11(6), 991; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11060991 - 29 May 2021
Cited by 10 | Viewed by 3615
Abstract
Introduction: Coronavirus disease 2019 (COVID-19) led to a global pandemic. Although reverse transcription polymerase chain reaction (RT-PCR) of viral nucleic acid is the gold standard for COVID-19 diagnosis, its sensitivity was found to not be high enough in many reports. As radiomics-based diagnosis [...] Read more.
Introduction: Coronavirus disease 2019 (COVID-19) led to a global pandemic. Although reverse transcription polymerase chain reaction (RT-PCR) of viral nucleic acid is the gold standard for COVID-19 diagnosis, its sensitivity was found to not be high enough in many reports. As radiomics-based diagnosis research has recently emerged, we aimed to use computerized tomography (CT)-based radiomics models to differentiate COVID-19 pneumonia from other viral pneumonia infections. Materials and methods: This study was performed according to the preferred reporting items for systematic review and meta-analysis diagnostic test accuracy studies (PRISMA-DTA) guidelines. The Pubmed, Cochrane, and Embase databases were searched. The pooled sensitivity and pooled specificity were calculated. A summary receiver operating characteristic (sROC) curve was constructed. The study quality was evaluated based on the radiomics quality score. Results: A total of 10,300 patients were involved in this meta-analysis. The radiomics quality score ranged from 13 to 16 (maximum score: 36). The pooled sensitivity was 0.885 (95% CI: 0.818–0.929), and the pooled specificity was 0.811 (95% CI: 0.667–0.902). The pooled AUC was 906. Conclusion: Our meta-analysis showed that CT-based radiomics feature models can successfully differentiate COVID-19 from other viral pneumonias. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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Review

Jump to: Research

14 pages, 1626 KiB  
Review
The Capacity of Artificial Intelligence in COVID-19 Response: A Review in Context of COVID-19 Screening and Diagnosis
by Dilber Uzun Ozsahin, Nuhu Abdulhaqq Isa and Berna Uzun
Diagnostics 2022, 12(12), 2943; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12122943 - 25 Nov 2022
Cited by 2 | Viewed by 1774
Abstract
Artificial intelligence (AI) has been shown to solve several issues affecting COVID-19 diagnosis. This systematic review research explores the impact of AI in early COVID-19 screening, detection, and diagnosis. A comprehensive survey of AI in the COVID-19 literature, mainly in the context of [...] Read more.
Artificial intelligence (AI) has been shown to solve several issues affecting COVID-19 diagnosis. This systematic review research explores the impact of AI in early COVID-19 screening, detection, and diagnosis. A comprehensive survey of AI in the COVID-19 literature, mainly in the context of screening and diagnosis, was observed by applying the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Data sources for the years 2020, 2021, and 2022 were retrieved from google scholar, web of science, Scopus, and PubMed, with target keywords relating to AI in COVID-19 screening and diagnosis. After a comprehensive review of these studies, the results found that AI contributed immensely to improving COVID-19 screening and diagnosis. Some proposed AI models were shown to have comparable (sometimes even better) clinical decision outcomes, compared to experienced radiologists in the screening/diagnosing of COVID-19. Additionally, AI has the capacity to reduce physician work burdens and fatigue and reduce the problems of several false positives, associated with the RT-PCR test (with lower sensitivity of 60–70%) and medical imaging analysis. Even though AI was found to be timesaving and cost-effective, with less clinical errors, it works optimally under the supervision of a physician or other specialists. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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24 pages, 1217 KiB  
Review
COVID-19 Diagnosis and Classification Using Radiological Imaging and Deep Learning Techniques: A Comparative Study
by Saloni Laddha, Sami Mnasri, Mansoor Alghamdi, Vijay Kumar, Manjit Kaur, Malek Alrashidi, Abdullah Almuhaimeed, Ali Alshehri, Majed Abdullah Alrowaily and Ibrahim Alkhazi
Diagnostics 2022, 12(8), 1880; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12081880 - 03 Aug 2022
Cited by 8 | Viewed by 2197
Abstract
In December 2019, the novel coronavirus disease 2019 (COVID-19) appeared. Being highly contagious and with no effective treatment available, the only solution was to detect and isolate infected patients to further break the chain of infection. The shortage of test kits and other [...] Read more.
In December 2019, the novel coronavirus disease 2019 (COVID-19) appeared. Being highly contagious and with no effective treatment available, the only solution was to detect and isolate infected patients to further break the chain of infection. The shortage of test kits and other drawbacks of lab tests motivated researchers to build an automated diagnosis system using chest X-rays and CT scanning. The reviewed works in this study use AI coupled with the radiological image processing of raw chest X-rays and CT images to train various CNN models. They use transfer learning and numerous types of binary and multi-class classifications. The models are trained and validated on several datasets, the attributes of which are also discussed. The obtained results of various algorithms are later compared using performance metrics such as accuracy, F1 score, and AUC. Major challenges faced in this research domain are the limited availability of COVID image data and the high accuracy of the prediction of the severity of patients using deep learning compared to well-known methods of COVID-19 detection such as PCR tests. These automated detection systems using CXR technology are reliable enough to help radiologists in the initial screening and in the immediate diagnosis of infected individuals. They are preferred because of their low cost, availability, and fast results. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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46 pages, 1663 KiB  
Review
A Comprehensive Review of Machine Learning Used to Combat COVID-19
by Rahul Gomes, Connor Kamrowski, Jordan Langlois, Papia Rozario, Ian Dircks, Keegan Grottodden, Matthew Martinez, Wei Zhong Tee, Kyle Sargeant, Corbin LaFleur and Mitchell Haley
Diagnostics 2022, 12(8), 1853; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12081853 - 31 Jul 2022
Cited by 17 | Viewed by 2691
Abstract
Coronavirus disease (COVID-19) has had a significant impact on global health since the start of the pandemic in 2019. As of June 2022, over 539 million cases have been confirmed worldwide with over 6.3 million deaths as a result. Artificial Intelligence (AI) solutions [...] Read more.
Coronavirus disease (COVID-19) has had a significant impact on global health since the start of the pandemic in 2019. As of June 2022, over 539 million cases have been confirmed worldwide with over 6.3 million deaths as a result. Artificial Intelligence (AI) solutions such as machine learning and deep learning have played a major part in this pandemic for the diagnosis and treatment of COVID-19. In this research, we review these modern tools deployed to solve a variety of complex problems. We explore research that focused on analyzing medical images using AI models for identification, classification, and tissue segmentation of the disease. We also explore prognostic models that were developed to predict health outcomes and optimize the allocation of scarce medical resources. Longitudinal studies were conducted to better understand COVID-19 and its effects on patients over a period of time. This comprehensive review of the different AI methods and modeling efforts will shed light on the role that AI has played and what path it intends to take in the fight against COVID-19. Full article
(This article belongs to the Special Issue Machine Learning Applications for COVID-19 and Its Complications: Screening, Diagnosis, Treatment, and Prognosis)
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