Covid - Mtnet: Covid-19 Detection With Multi-Task Deep Learning Approaches
Covid - Mtnet: Covid-19 Detection With Multi-Task Deep Learning Approaches
Covid - Mtnet: Covid-19 Detection With Multi-Task Deep Learning Approaches
Approaches
Md Zahangir Alom, M M Shaifur Rahman, Mst Shamima Nasrin, Tarek M. Taha, and Vijayan K. Asari
Department of Electrical and Computer Engineering, University of Dayton, Dayton, OH, USA
Emails: {alomm1, rahmanm24, nasrinm1, ttaha1, asari1}@udayton.edu
Abstract
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Figure 2: COVID-Det_Xray: End-to-end system for pneumonia detection in the top row and COVID-19 detection with TL learning
from pneumonia detection at the bottom. Bottom row shows the training phase for COVID-19 which include inputs, data
augmentation, training model with TL and outputs (N: normal and C: COVID-19).
high architectural diversity and selective long-range deep learning-based method shows around 86.7% testing
connectivity. The model experimented on two open access accuracy from CT images [17].
data repositories, one for COVID-19 detection dataset and
another for pneumonia detection dataset. The experimental According to the literature studies, the X-ray and CT scans
results show around 83.5% testing accuracy. In this case, have been used very often to recognize the patients with
both databases were merged for performing training and COVID-19. Hence, we present here an end-to-end deep
testing of the proposed method [15]. However, in our learning-based system for COVID-19 detection and
proposed approach, we have trained a model with a infected regions detection from both X-ray and CT images.
pneumonia dataset and used Transfer Learning (TL) for
training the same model with a COVID-19 dataset. 3. Methodology
In this implementation, we have used multiple models
A deep learning-based detection for COVID-19 from Chest for different tasks where the classification model is for
3D CT volumes with weak labeled samples has been COVID-19 detection and the segmentation model is used
proposed recently. For each patient, a pretrained UNet for Region of Interest (ROI) detection for COVID-19. The
model was applied for 3D lung region segmentation and Inception Recurrent Residual Neural Network (IRRCNN)
then a 3D-CNN model was applied for predicting the model is used for the COVID-19 detection task [18]. The
probability of COVID-19 infections. The model was NABLA-N network is applied for infected region
trained on 499 CT volumes and tested on 131 CT volumes segmentation from X-ray and CT images.
and obtained 0.959 ROC AUC with 0.907 and 0.911
sensitivity and specificity respectively. Overall, this model COVID-19 Detection from X-ray-Image
shows around 90% accuracy [16]. In addition, the recent (COVID-Det_Xray): first, we have used the IRRCNN
study shows very promising accuracy for pneumonia model to classify the normal and pneumonia detection from
detection tasks where the model developed grouped three chest X-ray images. Then, the Transfer Learning (TL)
different categories: COVID-19, Influenza-A viral method is used to train with samples to determine
pneumonia, and healthy cases from CT images. The VNet COVID-19 and normal images from Chest X-ray images.
based VNET-IR-RPN is used for region of interest The end-to-end training method is shown in Figure 2. The
segmentation for pulmonary tuberculosis. The proposed IRRCNN model is used for this implementation where five
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Figure 3: Chest segmentation model for X-ray (Chest-Seg_Xray): the top row of the figure shows the training method and bottom
row demonstrates the different steps for testing phase.
Inception Recurrent Residual Unit (IRRUs) are used [18]. China. For COVID-Det_CT, we have used the IRRCNN
The IRRUs are shown for unit 3 in the top of Figure classification model, which is trained on our own datasets.
2. After successfully training the model for COVID-19 The database samples are collected from normal CT and
detection, the system has been tested with completely new CT scan with COVID-19. From this implementation, the
samples collected from new patients. same methods are followed as described for
COVID-19 segmentation from X-ray-Image COVID-Det_Xray.
(COVID-Seg_Xray): another system is developed for
detecting infected regions for COVID-19 in X-ray images. COVID-19 segmentation from CT scans
In this case, the NABLA-N model is applied for only chest (COVID-Seg_CT): for mining the specific infected region
segmentation [19]. The end to end training and testing of COVID-19 virus in lung region, we have developed an
method for chest segmentation method (Chest-Seg_Xray) end to end system for segmentation of lung region from 2D
is shown in Figure 3. Mathematical morphological
approaches are applied for selecting the refinement and
selecting appropriate contours for chest region extraction,
which is shown in the last column of the second row in
Figure 3. In the testing phase, precise chest regions are
extracted. After generating segmentation masks for the
chest regions, the mask is used to extract only the chest (a) (b) (c)
regions from the input images, which is shown in Figure Figure 4: The pipeline processing for COVID-19 infected
4(a). A classical image processing method and adaptive region detection: (a) chest regions, (d) mask for COVID-19
thresholding approach are applied for extracting the infected regions and (c) final heatmap image.
features to identify the infected regions of COVID-19 from
the segmented chest region in Figure 4(b). Finally, the images where the same NABLA-N model is used as
output heatmap image with COVID-19 infected regions are mentioned in COVID-Seg_Xray. First, we have trained the
shown in Figure (c). model on publicly available 2D lung images, which is
COVID-19 detection from CT scans (COVID-Det_CT): called Lung_Seg_CT. Then the trained Lung_Seg_CT
CT scans are also used for detecting coronavirus which is model is directly applied to segment the lung region from
very effective to detect the infection of COVID-19 within a the entire set of CT images. Classical image processing and
couple of days after infection. This is stated according to morphological analysis are then applied to extract infected
the assessment system followed by the expert in Wuhan, regions with COVID-19. The entire system is named
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“COVID-Seg_CT”. For the testing phase, the same number of samples, 80% of samples are used for training
processing pipeline CT is used, which is demonstrated for and the remaining 20% are used for validation and testing
X-ray, as demonstrated in Figure 3 and 4. of the COVID-Seg_Xray model. This is the first step of
infected regions extraction from input chest X-ray
Architecture details: The IRRCNN model consists of an images. The randomly selected X-ray images and
input layer, five IRRUs, a Global Average Pooling (GAP) corresponding masks are shown in Figure 6.
layer, and a Softmax output layer. For this model, we have
applied 1×1, and 3×3 kernels for IRRU. The entire model
utilizes around 34M network parameters. On the other
hand, the NABLA-N network consists of an encoding and
three decoding units. The model architecture is as followed:
3→16×(3×3) →32×(3×3) →64×(3×3) →128×(3×3)
→256×(3×3) →512×(3×3) →256×(3×3) →128×(3×3)
→64×(3×3) →32×(3×3) →16×(3×3) →1. The general
notation of FN× (M×N) where FN represents the number of Figure 5: Randomly selected samples without pneumonia in first
feature maps and (M×N) represents the kernel size which is row and second row shows the X-ray image with pneumonia.
(3×3) kernels used in each layer except the last layer. The
Rectified Linear Unit (ReLU) activation function is used all In addition, for COVID-19 detection from CT images, there
through the network in this implementation. At the end, a is no labeled dataset available for this specific task. Hence,
1×1 convolutional layer is used to reduce the dimension of we have collected samples from different sources for
the feature maps to the single channel outputs with a normal CT scans. The COVID-19 CT images are
sigmoid activation function. In addition, we have utilized considered from different CT scans from confirmed
the up-sampled feature maps from 3 different encoding patients. A total of 420 samples are collected where 247
layers including the bottleneck layer. Therefore, we named samples are for normal and 178 samples are for COVID-19.
the model NABLA-3 network. The NABLA-3 model We have observed the variant sizes of the samples, the
utilizes totally 18.98 Million (M) network parameters. The lowest dimension of the images 450×338 pixels and highest
network is initialized with the He initialization method 630×630 pixels.
[21].
4. Experiments
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(a) (b) (c) (d) (e)
Figure 11: Chest segmentation (Chest-Seg_Xray) results: (a) input chest images (b) Ground Truth (c) Model outputs (d) Refined
outputs and (e) Final outputs with contours where the green and red contour represent the ground truth and detection respectively.
The experimental results for the segmentation model for column, the percentage of infection is around 51.23%,
COVID-19 X-ray samples are shown in Figure 12. The first 27.66%, and 47.89% respectively.
column shows the inputs images, the second column shows
the outputs from COVID-Seg_Xray, the third column COVID-Seg_Xray outputs for COVID-19 from
shows the polished segmentation masks, the fourth column Abdominal CT: We have also observed that for some
represents outputs for only chest regions, and the fifth cases, patients have been confirmed with COVID-19 after
column shows the final outputs with COVID-19 infected analysis of the abdominal CT images. Thus, we have
regions. The qualitative results clearly demonstrate that the evaluated the same model for X-ray as has been tested on
proposed model is able to segment and detect contaminated abdominal CT images. The outputs for abdominal CT
regions of COVID-19 accurately from the chest X-ray images are shown in Figure 13. The first column shows the
images. input images, the second column represents the refined
segmented mask, where only large regions have been
In addition, for quantitative justification, we have selected among a set of segmented regions, and the fourth
calculated the total number of pixels of the lung regions and column shows the extracted lung region with respect to the
the total number of pixels for infected regions with refined mask in Figure 13(b). The classical image
COVID-19. The percentage is calculated with respect to the processing method and adaptive thresholding method are
total areas of the lung, which can be used for measuring the applied to extract the pixels to represent COVID-19, and
contingency and severeness of corona-virus patients. For the sixth column demonstrates the heatmaps for the
the first row and third column in Figure 12, the number of infected regions for COVID-19. For the first row, the total
total pixels for lung is 6696 and total number of infected number of pixels for the lung regions is 5184 and the total
pixels with COVID-19 is 2245. Thus, the percentage of number of infected pixels with COVID-19 is 1599. Hence,
infection is 33.52% with respect to the total pixels of lung the percentage of infection is 30.84%. For the second and
regions. In the last row of Figure 12, the total number of third row, the percentage of infection is 80.39% and
pixels for lung regions is 9601 and the total number of 23.18% respectively. The quantitative and qualitative
infected pixels with COVID-19 is 3609.Thus the results clearly show that the proposed classification and
percentage of infection is 37.58%. This quantitative segmentation for X-ray images demonstrate promising
analysis can be applied to define the severeness of the detection and infected region extraction.
COVID-19 disease. For the second, third and fourth
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Figure 12: Experimental results of COVID-Seg_Xray model: first column represents the input images, second column shows the
predicted segmentation masks, third column shows the refined outputs with chest regions, fourth column represent only chest
regions, and fifth column represent the heatmap in the infected regions.
COVID-Det_CT outputs: From the literature survey, we which is named COVID-Det_CT. The system is trained and
have observed that CT scans are used to identify the tested on our own dataset. The COVID-Det_CT shows
COVID-19 detection directly. In some critical cases, around 98.78% testing accuracy for 45 samples.
Doctors fail to take a decision directly from the X-ray
analysis. Instead, the CT scans are used to take final COVID-Seg_CT outputs: For extracting infected regions
decisions on the patients. Different studies have claimed with COVID-19, the NABLA-N network-based
that CT is most efficient to confirm the COVID-19 patients. segmentation model is trained and tested on a publicly
Thus, we have included a detection model for CT images available 2D lung segmentation dataset. This model is
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(a) (b) (c) (d) (e)
Figure 13: Experimental results of COVID-Seg_Xray model for abdominal CT: (a)inputs, (b) segmented masks, (c) lung regions,
(d) extracted pixels for COVID-19, and (d)final heat with heatmap.
Since, we did not have any label samples for COVID-19 for
segmentation tasks, the COVID-Seg_CT model is directly (a) (b) (c)
applied to segment the lung regions from the samples with Figure 14: COVID-Seg_CT outputs for testing samples:
COVID-19. After segmenting the lung region from CT (a) inputs (b) Ground Truth (GT) and (c) model outputs.
images, mathematical morphological operations are
performed to refine the segmentation masks. Lung regions cases, we have observed false detection, as shown in the
are then extracted with respect to the mask. The second row in Figure 15(d).
segmentation results of COVID-Seg_CT model for
COVID-19 samples are shown in Figure 15. The first 6. Discussions
column shows the input images, the second column shows
The proposed pneumonia detection method shows
the lung segmentation results, the third column represents
around 87.26% testing accuracy whereas the recently
lung regions, and the fourth column represents the result
published paper shows 84.67% testing accuracy in [15].
with heatmap. In most of the cases, the proposed model
Thus, our IRRCNN based detection model shows around
provides good accuracy of detection. However, in some
3.76% better testing accuracy for pneumonia detection
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(a) (b) (c) (d)
Figure 15: The COVID-19 infected region detection results from lung CT images: (a) inputs images, (b) segmented and refined masks
with TL learning approach, and (d) infected region with heatmaps.
tasks. In addition, most of the COVID-19 infected region detection shown in the second row in Figure 15 (d). This
detection methods proposed are based on patch-based needs to be improved.
detection methods for infected region extraction, where
there is a big possibility to have false positive and false 8. Conclusion
negative detection as the decision is taken based on the In this study, we propose an end-to-end system for
class [17]. On the other hand, we proposed an infected COVID-19 detection and infected region localization from
region with different level of evaluation for pixel level two different modalities of medical imaging. For
analysis. Thus, the qualitative results clearly demonstrated classification, and segmentation tasks, our improved
the infected region from the lung part and the proposed Inception Recurrent Residual Neural Network (IRRCNN)
COVID-19 detection significantly reduces the possibility and NABLA-3 network models are applied. The models are
of false positive and false negative detection for tested on X-ray, abdominal CT, and full body CT images
COVID-19. on publicly available datasets. The observed results show
very promising detection results with 84.67% and 98.78%
7. Limitations testing accuracy for COVID-19 from X-ray and CT images
Both detection and segmentation methods for X-ray respectively. In addition, the qualitative results clearly
images provide very promising accuracy. However, there demonstrate high accuracy in the segmentation and
are some limitations of this study which need to be detection of infected regions by COVID-19 in both X-ray
addressed in the near future. First, the COVID-Det_Xray and CT images. In the near future, we would like to collect
model needs to be trained and tested with more COVID-19 more samples of COVID-19 affected subjects to develop a
samples. Second, as the COVID-Det_CT model is trained robust and more accurate system.
and tested on only 300 samples in the initial
implementation, the model provides very good detection References
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