COVID-19 prognostic modeling using CT radiomic features and machine learning algorithms: Analysis of a multi-institutional dataset of 14,339 patients

We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and...

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Published in:Computers in biology and medicine Vol. 145; p. 105467
Main Authors: Shiri, Isaac, Salimi, Yazdan, Pakbin, Masoumeh, Hajianfar, Ghasem, Avval, Atlas Haddadi, Sanaat, Amirhossein, Mostafaei, Shayan, Akhavanallaf, Azadeh, Saberi, Abdollah, Mansouri, Zahra, Askari, Dariush, Ghasemian, Mohammadreza, Sharifipour, Ehsan, Sandoughdaran, Saleh, Sohrabi, Ahmad, Sadati, Elham, Livani, Somayeh, Iranpour, Pooya, Kolahi, Shahriar, Khateri, Maziar, Bijari, Salar, Atashzar, Mohammad Reza, Shayesteh, Sajad P., Khosravi, Bardia, Babaei, Mohammad Reza, Jenabi, Elnaz, Hasanian, Mohammad, Shahhamzeh, Alireza, Foroghi Ghomi, Seyaed Yaser, Mozafari, Abolfazl, Teimouri, Arash, Movaseghi, Fatemeh, Ahmari, Azin, Goharpey, Neda, Bozorgmehr, Rama, Shirzad-Aski, Hesamaddin, Mortazavi, Roozbeh, Karimi, Jalal, Mortazavi, Nazanin, Besharat, Sima, Afsharpad, Mandana, Abdollahi, Hamid, Geramifar, Parham, Radmard, Amir Reza, Arabi, Hossein, Rezaei-Kalantari, Kiara, Oveisi, Mehrdad, Rahmim, Arman, Zaidi, Habib
Format: Journal Article
Language:English
Published: United States Elsevier Ltd 01.06.2022
Elsevier Limited
The Authors. Published by Elsevier Ltd
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ISSN:0010-4825, 1879-0534, 1879-0534
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Abstract We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81–0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81–0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients. [Display omitted] •CT images of 14′339 COVID-19 patients with known outcome from 19 centers were enrolled.•28 combinations of feature selection and classification approaches were implemented.•The models were evaluated using 10 different splitting and cross-validation strategies.•Lung CT radiomics features are promising for generalizable prognostic modeling.
AbstractList Image 1
We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients.BACKGROUNDWe aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients.Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported.METHODSWhole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported.In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81-0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81-0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance.RESULTSIn the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81-0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81-0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance.Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.CONCLUSIONLung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.
BackgroundWe aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients.MethodsWhole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported.ResultsIn the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81–0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81–0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance.ConclusionLung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.
We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81-0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81-0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.
We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81–0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81–0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients. [Display omitted] •CT images of 14′339 COVID-19 patients with known outcome from 19 centers were enrolled.•28 combinations of feature selection and classification approaches were implemented.•The models were evaluated using 10 different splitting and cross-validation strategies.•Lung CT radiomics features are promising for generalizable prognostic modeling.
AbstractBackgroundWe aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. MethodsWhole lung segmentations were performed automatically using a deep learning-based model to extract 105 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. ResultsIn the test dataset (4301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81–0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81–0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. ConclusionLung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.
ArticleNumber 105467
Author Mostafaei, Shayan
Sharifipour, Ehsan
Kolahi, Shahriar
Saberi, Abdollah
Radmard, Amir Reza
Movaseghi, Fatemeh
Besharat, Sima
Jenabi, Elnaz
Pakbin, Masoumeh
Mansouri, Zahra
Ahmari, Azin
Sadati, Elham
Shahhamzeh, Alireza
Ghasemian, Mohammadreza
Livani, Somayeh
Bijari, Salar
Bozorgmehr, Rama
Salimi, Yazdan
Shirzad-Aski, Hesamaddin
Mortazavi, Nazanin
Shayesteh, Sajad P.
Khateri, Maziar
Zaidi, Habib
Shiri, Isaac
Akhavanallaf, Azadeh
Goharpey, Neda
Afsharpad, Mandana
Hajianfar, Ghasem
Mortazavi, Roozbeh
Geramifar, Parham
Karimi, Jalal
Teimouri, Arash
Arabi, Hossein
Khosravi, Bardia
Sohrabi, Ahmad
Rahmim, Arman
Babaei, Mohammad Reza
Hasanian, Mohammad
Sanaat, Amirhossein
Abdollahi, Hamid
Atashzar, Mohammad Reza
Askari, Dariush
Foroghi Ghomi, Seyaed Yaser
Iranpour, Pooya
Avval, Atlas Haddadi
Oveisi, Mehrdad
Sandoughdaran, Saleh
Rezaei-Kalantari, Kiara
Mozafari, Abolfazl
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Keywords COVID-19
X-ray CT
Prognosis
Machine learning
Radiomics
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Snippet We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. Whole lung segmentations were performed...
AbstractBackgroundWe aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. MethodsWhole lung segmentations...
BackgroundWe aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients.MethodsWhole lung segmentations were...
We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients.BACKGROUNDWe aimed to analyze the prognostic power...
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StartPage 105467
SubjectTerms Algorithms
Artificial intelligence
Classifiers
Coronaviruses
COVID-19
COVID-19 - diagnostic imaging
Datasets
Deep learning
Feature extraction
Humans
Internal Medicine
Lung Neoplasms
Lungs
Machine Learning
Medical prognosis
Modelling
Other
Patients
Polymerase chain reaction
Prognosis
Radiomics
Retrospective Studies
Sensitivity
Statistical analysis
Tomography, X-Ray Computed - methods
Variance analysis
X-ray CT
Title COVID-19 prognostic modeling using CT radiomic features and machine learning algorithms: Analysis of a multi-institutional dataset of 14,339 patients
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