| Literature DB >> 33934177 |
Eduardo J Mortani Barbosa1,2, Bogdan Georgescu3, Shikha Chaganti3, Gorka Bastarrika Aleman4, Jordi Broncano Cabrero5, Guillaume Chabin6, Thomas Flohr7, Philippe Grenier8, Sasa Grbic3, Nakul Gupta9, François Mellot8, Savvas Nicolaou10, Thomas Re3, Pina Sanelli11, Alexander W Sauter12, Youngjin Yoo3, Valentin Ziebandt7, Dorin Comaniciu3.
Abstract
OBJECTIVES: To investigate machine learning classifiers and interpretable models using chest CT for detection of COVID-19 and differentiation from other pneumonias, interstitial lung disease (ILD) and normal CTs.Entities:
Keywords: COVID-19; Classification; Deep learning; Tomography; Viral pneumonia
Mesh:
Year: 2021 PMID: 33934177 PMCID: PMC8088310 DOI: 10.1007/s00330-021-07937-3
Source DB: PubMed Journal: Eur Radiol ISSN: 0938-7994 Impact factor: 5.315
Fig. 1Selection criteria for the COVID-19 and control cohorts in the study
Data-split table by classes and categories into training, validation, and test datasets
| 2 classes | 4 categories | Training | Validation | Test |
|---|---|---|---|---|
| Positive | COVID-19 | 1011 | 50 | 100 |
| Negative | Pneumonia (non-COVID-19) | 189 | 16 | 33 |
| ILD | 388 | 16 | 33 | |
| No pathology | 559 | 17 | 34 |
Fig. 2Overview of the deep learning–based COVID-19 classifier. Preprocessing consists of lung segmentation and opacities probability distribution computation [12] followed by a 3D deep neural network trained to distinguish between the COVID-19 class and non-COVID-19 class
Fig. 3Heat map of hierarchical clustering. This illustrates the unsupervised hierarchical clustering of the seven metrics along with cohort membership (COVID-19, other pneumonia, ILD, and no pathologies) from the entire training set of 1800 cases. The metric values are standardized and rescaled to a value between 0 and 1. a Training dataset; b Test dataset
Fig. 4a Bootstrapped ROCs for discriminating COVID-19 from ILD, other pneumonia, and no pathology control by the models proposed in this study. The models M1, M2, and M3 and CO-RADS scoring [16] were evaluated with 100 COVID-19 positive, 33 ILD, 33 other pneumonia, and 34 healthy without pathologies on CTs. The 95% confidence intervals (shown as a band) are computed by bootstrapping over 1000 samples with replacement from the predicted scores. b Bootstrapped ROCs for our 3D DL classifier (M3), the model proposed by Li et al [10], and the model proposed by Harmon et al [15]. For the model proposed by Li et al, we trained and tested on our dataset using the code provided by the authors. The 95% confidence intervals (shown as a band) are computed by bootstrapping over 1000 samples with replacement from the predicted scores
Metrics-based classifier confusion matrices. the models were evaluated with 100 covid-19, 33 ILD, 33 other pneumonia, and 34 no pathologies CT scans. The operating point was chosen as the closest point to the top left corner on the ROC computed over the test dataset (without bootstrapping). Note: the table shows the prediction vs ground truth for each of the negative class categories (ILD, other pneumonia, no pathology). M1, metrics-based random forest classifier; M2, metrics-based logistic regression classifier; M3, Deep learning–based classifier; CO-RADS, SCORING system [16]
| Ground truth | |||||
|---|---|---|---|---|---|
| Positive | Negative | ||||
| COVID-19 | ILD | Pneumonia (non-COVID-19) | No pathology | ||
| Predicted (M1) | Positive | 86 | 21 | 19 | 0 |
| Negative | 14 | 12 | 14 | 34 | |
| Predicted (M2) | Positive | 74 | 11 | 10 | 0 |
| Negative | 26 | 22 | 23 | 34 | |
| Predicted (M3) | Positive | 90 | 3 | 12 | 2 |
| Negative | 10 | 30 | 21 | 32 | |
| Predicted (CO-RADS) | Positive | 74 | 8 | 15 | 0 |
| Negative | 26 | 19 | 18 | 34 | |
Fig. 5Examples of correctly classified COVID-19-positive patients from both methods. Red marks abnormalities associated with COVID-19
Fig. 6Examples of incorrectly classified samples by both methods: top-row COVID-19 (false negative), middle-row ILD (false positive), bottom-row other pneumonia (false positive). Red marks abnormalities associated with COVID-19 (top-row), associated with ILD (middle-row), or associated with other pneumonia (bottom-row), respectively
Confusion matrix for the model from Li et al and Harmon et al. The operating point was chosen as the closest point to the top left corner on the ROC computed over the test dataset (without bootstrapping)
| Ground truth | |||||
|---|---|---|---|---|---|
| Positive | Negative | ||||
| COVID-19 | ILD | Pneumonia | No pathology | ||
| Predicted (Li et al) | Positive | 86 | 6 | 14 | 0 |
| Negative | 14 | 27 | 19 | 34 | |
| Predicted (Harmon et al) | Positive | 64 | 14 | 7 | 1 |
| Negative | 36 | 19 | 26 | 33 | |