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.2020 Dec;24(12):3595-3605.
doi: 10.1109/JBHI.2020.3037127. Epub 2020 Dec 4.

COVIDGR Dataset and COVID-SDNet Methodology for Predicting COVID-19 Based on Chest X-Ray Images

COVIDGR Dataset and COVID-SDNet Methodology for Predicting COVID-19 Based on Chest X-Ray Images

S Tabik et al. IEEE J Biomed Health Inform.2020 Dec.

Abstract

Currently, Coronavirus disease (COVID-19), one of the most infectious diseases in the 21st century, is diagnosed using RT-PCR testing, CT scans and/or Chest X-Ray (CXR) images. CT (Computed Tomography) scanners and RT-PCR testing are not available in most medical centers and hence in many cases CXR images become the most time/cost effective tool for assisting clinicians in making decisions. Deep learning neural networks have a great potential for building COVID-19 triage systems and detecting COVID-19 patients, especially patients with low severity. Unfortunately, current databases do not allow building such systems as they are highly heterogeneous and biased towards severe cases. This article is three-fold: (i) we demystify the high sensitivities achieved by most recent COVID-19 classification models, (ii) under a close collaboration with Hospital Universitario Clínico San Cecilio, Granada, Spain, we built COVIDGR-1.0, a homogeneous and balanced database that includes all levels of severity, from normal with Positive RT-PCR, Mild, Moderate to Severe. COVIDGR-1.0 contains 426 positive and 426 negative PA (PosteroAnterior) CXR views and (iii) we propose COVID Smart Data based Network (COVID-SDNet) methodology for improving the generalization capacity of COVID-classification models. Our approach reaches good and stable results with an accuracy of [Formula: see text], [Formula: see text], [Formula: see text] in severe, moderate and mild COVID-19 severity levels. Our approach could help in the early detection of COVID-19. COVIDGR-1.0 along with the severity level labels are available to the scientific community through this link https://dasci.es/es/transferencia/open-data/covidgr/.

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Figures

Fig. 1.
Fig. 1.
The stratification of radiological severity of COVID-19. Examples of how RALE index is calculated.
Fig. 2.
Fig. 2.
Flowchart of the proposed COVID-SDNet methodology.
Fig. 3.
Fig. 3.
The segmentation-based cropping pre-processing applied to the input X-ray image.
Fig. 4.
Fig. 4.
Class-inherent transformations applied to a negative sample. a) Original negative sample; b) Negative transformation; c) Positive transformation.
Fig. 5.
Fig. 5.
Heatmap showing the parts of the input image that triggered the positive prediction (b) and counterfactual explanation (c).
Fig. 6.
Fig. 6.
Heatmap showing the parts of the input image that triggered the positive prediction (b) and counterfactual explanation (c).
Fig. 7.
Fig. 7.
Heatmap showing the parts of the input image that triggered the positive prediction (b) and counterfactual explanation (c).
Fig. 8.
Fig. 8.
Heatmap that explains the parts of the input image that triggered the counterfactual explanation (b) and the negative actual prediction (c).
See this image and copyright information in PMC

References

    1. Kissler S. M. et al. , “Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period,” Science, vol. 368, no. 6493, pp. 860–868, 2020. - PMC - PubMed
    1. Wong H. et al. , “Frequency and distribution of chest radiographic findings in COVID-19 positive patients,” Radiology, 2020, Art. no. 201160. - PMC - PubMed
    1. Li Y. et al. , “Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19,” J. Med. Virol., vol. 92, no. 7 pp. 903–908, Jul. 2020, doi: 10.1002/jmv.25786. - DOI - PMC - PubMed
    1. Fang Y. et al. , “Sensitivity of chest CT for COVID-19: Comparison to RT-PCR,” Radiology, 2020, Art. no. 200432. - PMC - PubMed
    1. Weinstock M. et al. , “Chest X-ray findings in 636 ambulatory patients with COVID-19 presenting to an urgent care center: A normal chest X-ray is no guarantee,” J. Urgent Care Med., vol. 14, no. 7, pp. 13–18, 2020.

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