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1.
Front Med (Lausanne) ; 9: 861680, 2022.
Article in English | MEDLINE | ID: covidwho-1911057

ABSTRACT

As the COVID-19 pandemic devastates globally, the use of chest X-ray (CXR) imaging as a complimentary screening strategy to RT-PCR testing continues to grow given its routine clinical use for respiratory complaint. As part of the COVID-Net open source initiative, we introduce COVID-Net CXR-2, an enhanced deep convolutional neural network design for COVID-19 detection from CXR images built using a greater quantity and diversity of patients than the original COVID-Net. We also introduce a new benchmark dataset composed of 19,203 CXR images from a multinational cohort of 16,656 patients from at least 51 countries, making it the largest, most diverse COVID-19 CXR dataset in open access form. The COVID-Net CXR-2 network achieves sensitivity and positive predictive value of 95.5 and 97.0%, respectively, and was audited in a transparent and responsible manner. Explainability-driven performance validation was used during auditing to gain deeper insights in its decision-making behavior and to ensure clinically relevant factors are leveraged for improving trust in its usage. Radiologist validation was also conducted, where select cases were reviewed and reported on by two board-certified radiologists with over 10 and 19 years of experience, respectively, and showed that the critical factors leveraged by COVID-Net CXR-2 are consistent with radiologist interpretations.

2.
Front Artif Intell ; 5: 827299, 2022.
Article in English | MEDLINE | ID: covidwho-1809634

ABSTRACT

Tuberculosis (TB) remains a global health problem, and is the leading cause of death from an infectious disease. A crucial step in the treatment of tuberculosis is screening high risk populations and the early detection of the disease, with chest x-ray (CXR) imaging being the most widely-used imaging modality. As such, there has been significant recent interest in artificial intelligence-based TB screening solutions for use in resource-limited scenarios where there is a lack of trained healthcare workers with expertise in CXR interpretation. Motivated by this pressing need and the recent recommendation by the World Health Organization (WHO) for the use of computer-aided diagnosis of TB in place of a human reader, we introduce TB-Net, a self-attention deep convolutional neural network tailored for TB case screening. We used CXR data from a multi-national patient cohort to train and test our models. A machine-driven design exploration approach leveraging generative synthesis was used to build a highly customized deep neural network architecture with attention condensers. We conducted an explainability-driven performance validation process to validate TB-Net's decision-making behavior. Experiments on CXR data from a multi-national patient cohort showed that the proposed TB-Net is able to achieve accuracy/sensitivity/specificity of 99.86/100.0/99.71%. Radiologist validation was conducted on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, and showed consistency between radiologist interpretation and critical factors leveraged by TB-Net for TB case detection for the case where radiologists identified anomalies. The proposed TB-Net not only achieves high tuberculosis case detection performance in terms of sensitivity and specificity, but also leverages clinically relevant critical factors in its decision making process. While not a production-ready solution, we hope that the open-source release of TB-Net as part of the COVID-Net initiative will support researchers, clinicians, and citizen data scientists in advancing this field in the fight against this global public health crisis.

3.
Front Med (Lausanne) ; 8: 729287, 2021.
Article in English | MEDLINE | ID: covidwho-1775688

ABSTRACT

The COVID-19 pandemic continues to rage on, with multiple waves causing substantial harm to health and economies around the world. Motivated by the use of computed tomography (CT) imaging at clinical institutes around the world as an effective complementary screening method to RT-PCR testing, we introduced COVID-Net CT, a deep neural network tailored for detection of COVID-19 cases from chest CT images, along with a large curated benchmark dataset comprising 1,489 patient cases as part of the open-source COVID-Net initiative. However, one potential limiting factor is restricted data quantity and diversity given the single nation patient cohort used in the study. To address this limitation, in this study we introduce enhanced deep neural networks for COVID-19 detection from chest CT images which are trained using a large, diverse, multinational patient cohort. We accomplish this through the introduction of two new CT benchmark datasets, the largest of which comprises a multinational cohort of 4,501 patients from at least 16 countries. To the best of our knowledge, this represents the largest, most diverse multinational cohort for COVID-19 CT images in open-access form. Additionally, we introduce a novel lightweight neural network architecture called COVID-Net CT S, which is significantly smaller and faster than the previously introduced COVID-Net CT architecture. We leverage explainability to investigate the decision-making behavior of the trained models and ensure that decisions are based on relevant indicators, with the results for select cases reviewed and reported on by two board-certified radiologists with over 10 and 30 years of experience, respectively. The best-performing deep neural network in this study achieved accuracy, COVID-19 sensitivity, positive predictive value, specificity, and negative predictive value of 99.0%/99.1%/98.0%/99.4%/99.7%, respectively. Moreover, explainability-driven performance validation shows consistency with radiologist interpretation by leveraging correct, clinically relevant critical factors. The results are promising and suggest the strong potential of deep neural networks as an effective tool for computer-aided COVID-19 assessment. While not a production-ready solution, we hope the open-source, open-access release of COVID-Net CT-2 and the associated benchmark datasets will continue to enable researchers, clinicians, and citizen data scientists alike to build upon them.

4.
Front Med (Lausanne) ; 8: 821120, 2021.
Article in English | MEDLINE | ID: covidwho-1731791

ABSTRACT

Medical image analysis continues to hold interesting challenges given the subtle characteristics of certain diseases and the significant overlap in appearance between diseases. In this study, we explore the concept of self-attention for tackling such subtleties in and between diseases. To this end, we introduce, a multi-scale encoder-decoder self-attention (MEDUSA) mechanism tailored for medical image analysis. While self-attention deep convolutional neural network architectures in existing literature center around the notion of multiple isolated lightweight attention mechanisms with limited individual capacities being incorporated at different points in the network architecture, MEDUSA takes a significant departure from this notion by possessing a single, unified self-attention mechanism with significantly higher capacity with multiple attention heads feeding into different scales in the network architecture. To the best of the authors' knowledge, this is the first "single body, multi-scale heads" realization of self-attention and enables explicit global context among selective attention at different levels of representational abstractions while still enabling differing local attention context at individual levels of abstractions. With MEDUSA, we obtain state-of-the-art performance on multiple challenging medical image analysis benchmarks including COVIDx, Radiological Society of North America (RSNA) RICORD, and RSNA Pneumonia Challenge when compared to previous work. Our MEDUSA model is publicly available.

5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-324065

ABSTRACT

Background: Tuberculosis (TB) remains a global health problem, and is the leading cause of death from an infectious disease. A crucial step in the treatment of tuberculosis is screening high risk populations and the early detection of the disease, with chest x-ray (CXR) imaging being the most widely-used imaging modality. As such, there has been significant recent interest in artificial intelligence-based TB screening solutions for use in resource-limited scenarios where there is a lack of trained healthcare workers with expertise in CXR interpretation. Motivated by this pressing need and the recent recommendation by the World Health Organization (WHO) for the use of computer-aided diagnosis of TB in place of a human reader, we introduce TB-Net, a self-attention deep convolutional neural network tailored for TB case screening. Methods: : We used CXR data from a multi-national patient cohort to train and test our models. A machine-driven design exploration approach leveraging generative synthesis was used to build a highly customized deep neural network architecture with attention condensers. Results: : We conducted an explainability-driven performance validation process to validate TB-Net's decision-making behaviour. Experiments on CXR data from a multi-national patient cohort showed that the proposed TB-Net is able to achieve accuracy/sensitivity/specificity of 99.86%/100.0%/99.71%. Radiologist validation was conducted on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, and showed consistency between radiologist interpretation and critical factors leveraged by TB-Net for TB case detection for the case where radiologists identified anomalies. Conclusion: The proposed TB-Net not only achieves high tuberculosis case detection performance in terms of sensitivity and specificity, but also leverages clinically relevant critical factors in its decision making process. While not a production-ready solution, we hope that the open-source release of TB-Net as part of the COVID-Net initiative will support researchers, clinicians, and citizen data scientists in advancing this eld in the ght against this global public health crisis.

6.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-311693

ABSTRACT

The COVID-19 pandemic continues to rage on, with multiple waves causing substantial harm to health and economies around the world. Motivated by the use of CT imaging at clinical institutes around the world as an effective complementary screening method to RT-PCR testing, we introduced COVID-Net CT, a neural network tailored for detection of COVID-19 cases from chest CT images as part of the open source COVID-Net initiative. However, one potential limiting factor is restricted quantity and diversity given the single nation patient cohort used. In this study, we introduce COVID-Net CT-2, enhanced deep neural networks for COVID-19 detection from chest CT images trained on the largest quantity and diversity of multinational patient cases in research literature. We introduce two new CT benchmark datasets, the largest comprising a multinational cohort of 4,501 patients from at least 15 countries. We leverage explainability to investigate the decision-making behaviour of COVID-Net CT-2, with the results for select cases reviewed and reported on by two board-certified radiologists with over 10 and 30 years of experience, respectively. The COVID-Net CT-2 neural networks achieved accuracy, COVID-19 sensitivity, PPV, specificity, and NPV of 98.1%/96.2%/96.7%/99%/98.8% and 97.9%/95.7%/96.4%/98.9%/98.7%, respectively. Explainability-driven performance validation shows that COVID-Net CT-2's decision-making behaviour is consistent with radiologist interpretation by leveraging correct, clinically relevant critical factors. The results are promising and suggest the strong potential of deep neural networks as an effective tool for computer-aided COVID-19 assessment. While not a production-ready solution, we hope the open-source, open-access release of COVID-Net CT-2 and benchmark datasets will continue to enable researchers, clinicians, and citizen data scientists alike to build upon them.

7.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-304710

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 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 patient cases into a custom network architecture for severity assessment. Experimental results with a multi-national patient cohort curated by the Radiological Society of North America (RSNA) RICORD initiative 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.

8.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318846

ABSTRACT

As the COVID-19 pandemic continues to devastate globally, the use of chest X-ray (CXR) imaging as a complimentary screening strategy to RT-PCR testing continues to grow given its routine clinical use for respiratory complaint. As part of the COVID-Net open source initiative, we introduce COVID-Net CXR-2, an enhanced deep convolutional neural network design for COVID-19 detection from CXR images built using a greater quantity and diversity of patients than the original COVID-Net. To facilitate this, we also introduce a new benchmark dataset composed of 19,203 CXR images from a multinational cohort of 16,656 patients from at least 51 countries, making it the largest, most diverse COVID-19 CXR dataset in open access form. The COVID-Net CXR-2 network achieves sensitivity and positive predictive value of 95.5%/97.0%, respectively, and was audited in a transparent and responsible manner. Explainability-driven performance validation was used during auditing to gain deeper insights in its decision-making behaviour and to ensure clinically relevant factors are leveraged for improving trust in its usage. Radiologist validation was also conducted, where select cases were reviewed and reported on by two board-certified radiologists with over 10 and 19 years of experience, respectively, and showed that the critical factors leveraged by COVID-Net CXR-2 are consistent with radiologist interpretations. While not a production-ready solution, we hope the open-source, open-access release of COVID-Net CXR-2 and the respective CXR benchmark dataset will encourage researchers, clinical scientists, and citizen scientists to accelerate advancements and innovations in the fight against the pandemic.

9.
Diagnostics (Basel) ; 12(1)2021 Dec 23.
Article in English | MEDLINE | ID: covidwho-1580952

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 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.

10.
Clin Epidemiol Glob Health ; 10: 100673, 2021.
Article in English | MEDLINE | ID: covidwho-956963

ABSTRACT

BACKGROUND/OBJECTIVE: It is important to predict the COVID-19 patient's prognosis, particularly in countries with lack or deficiency of medical resource for patient's triage management. Currently, WHO guideline suggests using chest imaging in addition to clinicolaboratory evaluation to decide on triage between home-discharge versus hospitalization. We designed our study to validate this recommendation to guide clinicians. This study providing some suggestions to guide clinicians for better decision making in 2020. METHODS: In this retrospective study, patients with RT-PCR confirmed COVID-19 (N = 213) were divided in different clinical and management scenarios: home-discharge, ward hospitalization and ICU admission. We reviewed the patient's initial chest CT if available. We evaluated quantitative and qualitative characteristics of CT as well as relevant available clinicolaboratory data. Chi-square, One-Way ANOVA and Paired t-test were used for analysis. RESULTS: The finding showed that most patients with mixed patterns, pleural effusion, 5 lobes involved, total score ≥10, SpO2% ≤ 90, ESR (mm/h) ≥ 60 and WBC (103/µL) ≥ 8000 were hospitalized. Most patients with Ground-glass opacities only, ≤3 lobes involvement, peripheral distribution, SpO2% ≥ 95, ESR (mm/h) < 30 and WBC(103/µL) < 6000 were home-discharged. CONCLUSIONS: This study suggests the use of initial chest CT (qualitative and quantitative evaluation) in addition to initial clinicolaboratory data could be a useful supplementary method for clinical management and it is an excellent decision making tool (home-discharge versus ICU/Ward admission) for clinicians.

11.
Pol Arch Intern Med ; 130(7-8): 629-634, 2020 08 27.
Article in English | MEDLINE | ID: covidwho-761202

ABSTRACT

INTRODUCTION: Currently, there are known contributing factors but no comprehensive methods for predicting the mortality risk or intensive care unit (ICU) admission in patients with novel coronavirus disease 2019 (COVID­19). OBJECTIVES: The aim of this study was to explore risk factors for mortality and ICU admission in patients with COVID­19, using computed tomography (CT) combined with clinical laboratory data. PATIENTS AND METHODS: Patients with polymerase chain reaction-confirmed COVID­19 (n = 63) from university hospitals in Tehran, Iran, were included. All patients underwent CT examination. Subsequently, a total CT score and the number of involved lung lobes were calculated and compared against collected laboratory and clinical characteristics. Univariable and multivariable proportional hazard analyses were used to determine the association among CT, laboratory and clinical data, ICU admission, and in­hospital death. RESULTS: By univariable analysis, in­hospital mortality was higher in patients with lower oxygen saturation on admission (below 88%), higher CT scores, and a higher number of lung lobes (more than 4) involved with a diffuse parenchymal pattern. By multivariable analysis, in­hospital mortality was higher in those with oxygen saturation below 88% on admission and a higher number of lung lobes involved with a diffuse parenchymal pattern. The risk of ICU admission was higher in patients with comorbidities (hypertension and ischemic heart disease), arterial oxygen saturation below 88%, and pericardial effusion. CONCLUSIONS: We can identify factors affecting in­hospital death and ICU admission in COVID-19. This can help clinicians to determine which patients are likely to require ICU admission and to inform strategic healthcare planning in critical conditions such as the COVID­19 pandemic.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Real-Time Polymerase Chain Reaction , Adult , Age Distribution , Aged , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Female , Humans , Iran , Male , Middle Aged , Pandemics , Pneumonia, Viral/epidemiology , Poland/epidemiology , SARS-CoV-2 , Sex Distribution , Tomography, X-Ray Computed , Young Adult
12.
SN Compr Clin Med ; 2(9): 1366-1376, 2020.
Article in English | MEDLINE | ID: covidwho-718568

ABSTRACT

We investigated significant predictors of poor in-hospital outcomes for patients admitted with viral pneumonia during the COVID-19 outbreak in Tehran, Iran. Between February 22 and March 22, 2020, patients who were admitted to three university hospitals during the COVID-19 outbreak in Tehran, Iran were included. Demographic, clinical, laboratory, and chest CT scan findings were gathered. Two radiologists evaluated the distribution and CT features of the lesions and also scored the extent of lung involvement as the sum of three zones in each lung. Of 228 included patients, 45 patients (19.7%) required ICU admission and 34 patients (14.9%) died. According to regression analysis, older age (OR = 1.06; P < 0.001), blood oxygen saturation (SpO2) < 88% (OR = 2.88; P = 0.03), and higher chest CT total score (OR = 1.10; P = 0.03) were significant predictors for in-hospital death. The same three variables were also recognized as significant predictors for invasive respiratory support: SpO2 < 88% (OR = 3.97, P = 0.002), older age (OR = 1.05, P < 0.001), and higher CT total score (OR = 1.13, P = 0.008). Potential predictors of invasive respiratory support and in-hospital death in patients with viral pneumonia were older age, SpO2 < 88%, and higher chest CT score.

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