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Kang H, Kim N, Ryu J. Attentional decoder networks for chest X-ray image recognition on high-resolution features. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 251:108198. [PMID: 38718718 DOI: 10.1016/j.cmpb.2024.108198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/31/2024] [Accepted: 04/21/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND AND OBJECTIVE This paper introduces an encoder-decoder-based attentional decoder network to recognize small-size lesions in chest X-ray images. In the encoder-only network, small-size lesions disappear during the down-sampling steps or are indistinguishable in the low-resolution feature maps. To address these issues, the proposed network processes images in the encoder-decoder architecture similar to U-Net families and classifies lesions by globally pooling high-resolution feature maps. However, two challenging obstacles prohibit U-Net families from being extended to classification: (1) the up-sampling procedure consumes considerable resources, and (2) there needs to be an effective pooling approach for the high-resolution feature maps. METHODS Therefore, the proposed network employs a lightweight attentional decoder and harmonic magnitude transform. The attentional decoder up-samples the given features with the low-resolution features as the key and value while the high-resolution features as the query. Since multi-scaled features interact, up-sampled features embody global context at a high resolution, maintaining pathological locality. In addition, harmonic magnitude transform is devised for pooling high-resolution feature maps in the frequency domain. We borrow the shift theorem of the Fourier transform to preserve the translation invariant property and further reduce the parameters of the pooling layer by an efficient embedding strategy. RESULTS The proposed network achieves state-of-the-art classification performance on the three public chest X-ray datasets, such as NIH, CheXpert, and MIMIC-CXR. CONCLUSIONS In conclusion, the proposed efficient encoder-decoder network recognizes small-size lesions well in chest X-ray images by efficiently up-sampling feature maps through an attentional decoder and processing high-resolution feature maps with harmonic magnitude transform. We open-source our implementation at https://github.com/Lab-LVM/ADNet.
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Affiliation(s)
- Hankyul Kang
- Department of Artificial Intelligence, Ajou University, Suwon, Republic of Korea
| | - Namkug Kim
- Department of Convergence Medicine, Ulsan University, Seoul, Republic of Korea
| | - Jongbin Ryu
- Department of Artificial Intelligence, Ajou University, Suwon, Republic of Korea; Department of Software and Computer Engineering, Ajou University, Suwon, Republic of Korea.
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Abbasi Habashi S, Koyuncu M, Alizadehsani R. A Survey of COVID-19 Diagnosis Using Routine Blood Tests with the Aid of Artificial Intelligence Techniques. Diagnostics (Basel) 2023; 13:1749. [PMID: 37238232 PMCID: PMC10217633 DOI: 10.3390/diagnostics13101749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing a disease called COVID-19, is a class of acute respiratory syndrome that has considerably affected the global economy and healthcare system. This virus is diagnosed using a traditional technique known as the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. However, RT-PCR customarily outputs a lot of false-negative and incorrect results. Current works indicate that COVID-19 can also be diagnosed using imaging resolutions, including CT scans, X-rays, and blood tests. Nevertheless, X-rays and CT scans cannot always be used for patient screening because of high costs, radiation doses, and an insufficient number of devices. Therefore, there is a requirement for a less expensive and faster diagnostic model to recognize the positive and negative cases of COVID-19. Blood tests are easily performed and cost less than RT-PCR and imaging tests. Since biochemical parameters in routine blood tests vary during the COVID-19 infection, they may supply physicians with exact information about the diagnosis of COVID-19. This study reviewed some newly emerging artificial intelligence (AI)-based methods to diagnose COVID-19 using routine blood tests. We gathered information about research resources and inspected 92 articles that were carefully chosen from a variety of publishers, such as IEEE, Springer, Elsevier, and MDPI. Then, these 92 studies are classified into two tables which contain articles that use machine Learning and deep Learning models to diagnose COVID-19 while using routine blood test datasets. In these studies, for diagnosing COVID-19, Random Forest and logistic regression are the most widely used machine learning methods and the most widely used performance metrics are accuracy, sensitivity, specificity, and AUC. Finally, we conclude by discussing and analyzing these studies which use machine learning and deep learning models and routine blood test datasets for COVID-19 detection. This survey can be the starting point for a novice-/beginner-level researcher to perform on COVID-19 classification.
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Affiliation(s)
| | - Murat Koyuncu
- Department of Information Systems Engineering, Atilim University, 06830 Ankara, Turkey;
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Waurn Ponds, Geelong, VIC 3216, Australia
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Yagin FH, Cicek İB, Alkhateeb A, Yagin B, Colak C, Azzeh M, Akbulut S. Explainable artificial intelligence model for identifying COVID-19 gene biomarkers. Comput Biol Med 2023; 154:106619. [PMID: 36738712 PMCID: PMC9889119 DOI: 10.1016/j.compbiomed.2023.106619] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
AIM COVID-19 has revealed the need for fast and reliable methods to assist clinicians in diagnosing the disease. This article presents a model that applies explainable artificial intelligence (XAI) methods based on machine learning techniques on COVID-19 metagenomic next-generation sequencing (mNGS) samples. METHODS In the data set used in the study, there are 15,979 gene expressions of 234 patients with COVID-19 negative 141 (60.3%) and COVID-19 positive 93 (39.7%). The least absolute shrinkage and selection operator (LASSO) method was applied to select genes associated with COVID-19. Support Vector Machine - Synthetic Minority Oversampling Technique (SVM-SMOTE) method was used to handle the class imbalance problem. Logistics regression (LR), SVM, random forest (RF), and extreme gradient boosting (XGBoost) methods were constructed to predict COVID-19. An explainable approach based on local interpretable model-agnostic explanations (LIME) and SHAPley Additive exPlanations (SHAP) methods was applied to determine COVID-19- associated biomarker candidate genes and improve the final model's interpretability. RESULTS For the diagnosis of COVID-19, the XGBoost (accuracy: 0.930) model outperformed the RF (accuracy: 0.912), SVM (accuracy: 0.877), and LR (accuracy: 0.912) models. As a result of the SHAP, the three most important genes associated with COVID-19 were IFI27, LGR6, and FAM83A. The results of LIME showed that especially the high level of IFI27 gene expression contributed to increasing the probability of positive class. CONCLUSIONS The proposed model (XGBoost) was able to predict COVID-19 successfully. The results show that machine learning combined with LIME and SHAP can explain the biomarker prediction for COVID-19 and provide clinicians with an intuitive understanding and interpretability of the impact of risk factors in the model.
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Affiliation(s)
- Fatma Hilal Yagin
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey.
| | - İpek Balikci Cicek
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey.
| | - Abedalrhman Alkhateeb
- Software Engineering Department, King Hussein School for Computing Sciences, Amman, Jordan.
| | - Burak Yagin
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey.
| | - Cemil Colak
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey.
| | - Mohammad Azzeh
- Data Science Department, King Hussein School for Computing Sciences, Amman, Jordan.
| | - Sami Akbulut
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey; Inonu University, Faculty of Medicine, Department of Surgery, 44280, Malatya, Turkey; Inonu University, Faculty of Medicine, Department of Public Health, 44280, Malatya, Turkey.
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Ramírez-del Real T, Martínez-García M, Márquez MF, López-Trejo L, Gutiérrez-Esparza G, Hernández-Lemus E. Individual Factors Associated With COVID-19 Infection: A Machine Learning Study. Front Public Health 2022; 10:912099. [PMID: 35844896 PMCID: PMC9279686 DOI: 10.3389/fpubh.2022.912099] [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: 04/04/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
The fast, exponential increase of COVID-19 infections and their catastrophic effects on patients' health have required the development of tools that support health systems in the quick and efficient diagnosis and prognosis of this disease. In this context, the present study aims to identify the potential factors associated with COVID-19 infections, applying machine learning techniques, particularly random forest, chi-squared, xgboost, and rpart for feature selection; ROSE and SMOTE were used as resampling methods due to the existence of class imbalance. Similarly, machine and deep learning algorithms such as support vector machines, C4.5, random forest, rpart, and deep neural networks were explored during the train/test phase to select the best prediction model. The dataset used in this study contains clinical data, anthropometric measurements, and other health parameters related to smoking habits, alcohol consumption, quality of sleep, physical activity, and health status during confinement due to the pandemic associated with COVID-19. The results showed that the XGBoost model got the best features associated with COVID-19 infection, and random forest approximated the best predictive model with a balanced accuracy of 90.41% using SMOTE as a resampling technique. The model with the best performance provides a tool to help prevent contracting SARS-CoV-2 since the variables with the highest risk factor are detected, and some of them are, to a certain extent controllable.
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Affiliation(s)
- Tania Ramírez-del Real
- Cátedras Conacyt, National Council on Science and Technology, Mexico City, Mexico
- Center for Research in Geospatial Information Sciences, Mexico City, Mexico
| | - Mireya Martínez-García
- Clinical Research Division, National Institute of Cardiology “Ignacio Chávez”, Mexico City, Mexico
| | - Manlio F. Márquez
- Clinical Research Division, National Institute of Cardiology “Ignacio Chávez”, Mexico City, Mexico
| | - Laura López-Trejo
- Institute for Security and Social Services of State Workers, Mexico City, Mexico
| | - Guadalupe Gutiérrez-Esparza
- Cátedras Conacyt, National Council on Science and Technology, Mexico City, Mexico
- Clinical Research Division, National Institute of Cardiology “Ignacio Chávez”, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Abayomi-Alli OO, Damaševičius R, Maskeliūnas R, Misra S. An Ensemble Learning Model for COVID-19 Detection from Blood Test Samples. SENSORS 2022; 22:s22062224. [PMID: 35336395 PMCID: PMC8955536 DOI: 10.3390/s22062224] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023]
Abstract
Current research endeavors in the application of artificial intelligence (AI) methods in the diagnosis of the COVID-19 disease has proven indispensable with very promising results. Despite these promising results, there are still limitations in real-time detection of COVID-19 using reverse transcription polymerase chain reaction (RT-PCR) test data, such as limited datasets, imbalance classes, a high misclassification rate of models, and the need for specialized research in identifying the best features and thus improving prediction rates. This study aims to investigate and apply the ensemble learning approach to develop prediction models for effective detection of COVID-19 using routine laboratory blood test results. Hence, an ensemble machine learning-based COVID-19 detection system is presented, aiming to aid clinicians to diagnose this virus effectively. The experiment was conducted using custom convolutional neural network (CNN) models as a first-stage classifier and 15 supervised machine learning algorithms as a second-stage classifier: K-Nearest Neighbors, Support Vector Machine (Linear and RBF), Naive Bayes, Decision Tree, Random Forest, MultiLayer Perceptron, AdaBoost, ExtraTrees, Logistic Regression, Linear and Quadratic Discriminant Analysis (LDA/QDA), Passive, Ridge, and Stochastic Gradient Descent Classifier. Our findings show that an ensemble learning model based on DNN and ExtraTrees achieved a mean accuracy of 99.28% and area under curve (AUC) of 99.4%, while AdaBoost gave a mean accuracy of 99.28% and AUC of 98.8% on the San Raffaele Hospital dataset, respectively. The comparison of the proposed COVID-19 detection approach with other state-of-the-art approaches using the same dataset shows that the proposed method outperforms several other COVID-19 diagnostics methods.
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Affiliation(s)
- Olusola O. Abayomi-Alli
- Department of Software Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
| | - Robertas Damaševičius
- Department of Software Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
- Correspondence:
| | - Rytis Maskeliūnas
- Department of Multimedia Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania;
| | - Sanjay Misra
- Department of Computer Science and Communication, Ostfold University College, 3001 Halden, Norway;
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