Development and validation of bone-suppressed deep learning classification of COVID-19 presentation in chest radiographs
Original Article

Development and validation of bone-suppressed deep learning classification of COVID-19 presentation in chest radiographs

Ngo Fung Daniel Lam1^, Hongfei Sun1^, Liming Song1^, Dongrong Yang1^, Shaohua Zhi1^, Ge Ren1^, Pak Hei Chou1, Shiu Bun Nelson Wan2, Man Fung Esther Wong2^, King Kwong Chan3, Hoi Ching Hailey Tsang3, Feng-Ming (Spring) Kong4^, Yì Xiáng J. Wáng5^, Jing Qin6, Lawrence Wing Chi Chan1^, Michael Ying1^, Jing Cai1^

1Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; 2Department of Radiology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China; 3Department of Radiology and Imaging, Queen Elizabeth Hospital, Hong Kong, China; 4Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; 5Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Hong Kong, China; 6School of Nursing, The Hong Kong Polytechnic University, Hong Kong, China

Contributions: (I) Conception and design: NFD Lam, J Cai, G Ren; (II) Administrative support: SBN Wan, MFE Wong, KK Chan, HCH Tsang, FS Kong, YXJ Wáng, J Qin, LWC Chan, M Ying, J Cai; (III) Provision of study materials or patients: PH Chou, KK Chan, HCH Tsang; (IV) Collection and assembly of data: NFD Lam, H Sun, L Song, PH Chou; (V) Data analysis and interpretation: NFD Lam, H Sun; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

^ORCID: Ngo Fung Daniel Lam, 0000-0002-8575-7162; Hongfei Sun, 0000-0002-3995-7251; Liming Song, 0000-0002-8522-2352; Dongrong Yang, 0000-0002-4559-5701; Shaohua Zhi, 0000-0003-3151-9713; Ge Ren, 0000-0003-2049-2682; Man Fung Esther Wong, 0000-0001-6961-3890; Feng-Ming Kong, 0000-0003-2652-098X; Yì Xiáng J. Wáng, 0000-0001-5697-0717; Lawrence Wing Chi Chan, 0000-0001-6451-2273; Michael Ying, 0000-0001-5979-6072; Jing Cai, 0000-0001-6934-0108.

Correspondence to: Jing Cai, PhD; Michael Ying, PhD. Department of Health Technology and Informatics, The Hong Kong Polytechnic University. Hong Kong, China. Email: jing.cai@polyu.edu.hk; michael.ying@polyu.edu.hk.

Background: Coronavirus disease 2019 (COVID-19) is a pandemic disease. Fast and accurate diagnosis of COVID-19 from chest radiography may enable more efficient allocation of scarce medical resources and hence improved patient outcomes. Deep learning classification of chest radiographs may be a plausible step towards this. We hypothesize that bone suppression of chest radiographs may improve the performance of deep learning classification of COVID-19 phenomena in chest radiographs.

Methods: Two bone suppression methods (Gusarev et al. and Rajaraman et al.) were implemented. The Gusarev and Rajaraman methods were trained on 217 pairs of normal and bone-suppressed chest radiographs from the X-ray Bone Shadow Suppression dataset (https://www.kaggle.com/hmchuong/xray-bone-shadow-supression). Two classifier methods with different network architectures were implemented. Binary classifier models were trained on the public RICORD-1c and RSNA Pneumonia Challenge datasets. An external test dataset was created retrospectively from a set of 320 COVID-19 positive patients from Queen Elizabeth Hospital (Hong Kong, China) and a set of 518 non-COVID-19 patients from Pamela Youde Nethersole Eastern Hospital (Hong Kong, China), and used to evaluate the effect of bone suppression on classifier performance. Classification performance, quantified by sensitivity, specificity, negative predictive value (NPV), accuracy and area under the receiver operating curve (AUC), for non-suppressed radiographs was compared to that for bone suppressed radiographs. Some of the pre-trained models used in this study are published at (https://github.com/danielnflam).

Results: Bone suppression of external test data was found to significantly (P<0.05) improve AUC for one classifier architecture [from 0.698 (non-suppressed) to 0.732 (Rajaraman-suppressed)]. For the other classifier architecture, suppression did not significantly (P>0.05) improve or worsen classifier performance.

Conclusions: Rajaraman suppression significantly improved classification performance in one classification architecture, and did not significantly worsen classifier performance in the other classifier architecture. This research could be extended to explore the impact of bone suppression on classification of different lung pathologies, and the effect of other image enhancement techniques on classifier performance.

Keywords: Classification; bone suppression; deep learning; chest radiography; coronavirus disease 2019 (COVID-19)


Submitted Aug 09, 2021. Accepted for publication Mar 21, 2022.

doi: 10.21037/qims-21-791


Introduction

Coronavirus Disease 2019 (COVID-19) is a pandemic disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can result in alveolar damage and respiratory failure (1) and has a fatality rate of 2% (2). New variants of SARS-CoV-2 are associated with increased transmissibility (3), decreased vaccine effectiveness and increased hospital admissions rates (4) than previous variants. In general, the clinical standard for confirmed diagnosis of the disease is reverse-transcriptase polymerase chain reaction (RT-PCR) testing of nasopharyngeal swabs (1,5), with radiology generally being used as a fast auxiliary diagnostic methodology alongside RT-PCR testing (6). Chest X-ray (CXR) imaging is an economical and accessible method for imaging the patient lung (7,8), with mobile systems capable of imaging at patient bedside with less risk of cross-contamination. Rapid and accurate methods to diagnose COVID-19 from CXRs could assist healthcare systems in controlling the spread of the disease.

Deep learning methods—in particular, convolutional neural networks—have shown great success (9) in general image processing applications (10). Such methods have recently been developed as a potential step towards automated diagnosis of COVID-19 from CXRs (8,11-15). Many efforts have been made to improve the diagnostic accuracy of deep learning classification methods, including but not limited to architectural improvements (16) and multi-modality classification (17). Concurrently, many methods for medical image enhancement have been developed, including those for CXR bone suppression (18-25). In this context, bone suppression is the removal of the bone shadows caused by increased attenuation of X-rays in the ribs and clavicles. Bone suppression of CXRs has been demonstrated to improve automated classification and manual diagnosis of lung pathologies (19,26-28). Manji et al. (28) demonstrated that radiologists diagnosed lung nodules in bone-free images acquired from dual energy subtraction radiography faster and more accurately than from standard CXRs. However, dual energy subtraction radiography requires specialized hardware, which may be unavailable for many institutions, and increased patient dose (25). Hence there is interest in the development and use of software-based bone-suppression techniques that could be applied to standard CXRs. Freedman et al. (27) demonstrated that radiologists performed significantly better in detecting lung nodules in CXRs when aided with proprietary visualization software that suppressed the clavicle and ribs, filtered noise and adjusted contrast. Baltruschat et al. (26) found that an ensemble of lung pathology classification models trained on software-based bone-suppressed and lung-cropped images resulted in improved performance when identifying lung pathologies in CXRs compared to an ensemble trained on non-suppressed images. Rajaraman et al. (19) demonstrated that deep learning-based bone suppression of CXRs improved the sensitivity, specificity and accuracy of a tuberculosis classification model significantly by 7%, 4% and 5% respectively for an internal test set.

In this retrospective study, we hypothesize that bone suppression could be used to improve the classification of COVID-19 phenomena in CXRs. The study develops and validates a classification workflow, in which input radiographs are bone-suppressed before classification. The major contributions from this study include: (I) application of bone suppression to improve classification of COVID-19 phenomena; (II) use of an external test set to assess the impact of bone suppression on classification models trained on non-suppressed and bone-suppressed CXRs. This study provides insight into the possibility of further improving deep learning classifier performance via image enhancement. We present the following article in accordance with the TRIPOD reporting checklist (available at https://qims.amegroups.com/article/view/10.21037/qims-21-791/rc).


Methods

Overview

The workflow for the study is as follows: first, input images were resized using nearest-neighbor interpolation; second, bone suppression was applied; third, classification was performed. Bone suppression was performed with two methods described in Section Bone suppression of Methods. The methods [‘Gusarev’ (18) and ‘Rajaraman’ (19)] were trained from chest radiographs. These methods are feedforward neural networks, and were chosen for training stability in preliminary work. To examine the effect of bone suppression on image classification performance, two deep learning-based image classification methods [the pre-trained ‘COVID-Net CXR2’ (11) method and the ‘VGG16- Modified’ (19) method] were implemented and used as described in Section Classification of Methods, to classify the images as “COVID” or “Non-COVID”. The performance of the classification models for non-suppressed test CXRs was compared to that for bone-suppressed test CXRs. All bone suppression and classification models were trained and tested on a workstation with a RTX2080Ti GPU (NVIDIA, Santa Clara, CA, USA) using CUDA 11.0. This study was conducted in accordance with the Declaration of Helsinki (as revised in 2013) and with ethics approval from The Hong Kong Polytechnic University Faculty Research Committee (No. HSEARS20201107001). Since only anonymized data was acquired in this study, individual consent for this retrospective study was waived.

Datasets

This retrospective study makes use of anonymized image datasets collected previously for other purposes. Frontal chest radiograph datasets were collected for the purposes of training the bone suppression methods, training the VGG16-Modified classification method, and testing the trained methods. Acquired images included both anteroposterior (AP) and posteroanterior (PA) cases. Imaging methodology included computed radiography and digital radiography from both static and mobile X-ray machines. The Gusarev and Rajaraman bone suppression methods employed in this study were trained using a publicly available dataset of PA chest radiographs (Digital Image Database) from the Japanese Society of Radiological Technology (JSRT) (29). The JSRT dataset was acquired from 13 institutions in Japan and 1 institution in the United States around 1997–1998. Juhász et al. (30) had applied in-house bone suppression algorithms to the JSRT images and publicly released the resulting dataset, which was used in this study as the bone-suppressed “target” dataset to train the bone suppression models. The JSRT and Juhász datasets had been combined and published as the X-ray Bone Shadow Suppression dataset (31) (https://www.kaggle.com/hmchuong/xray-bone-shadow-supression). To the authors’ knowledge, this is the only publicly available set of co-registered non-suppressed and bone-suppressed chest radiographs. A total of 241 non-suppressed and bone-suppressed image pairs were acquired (31), each pair derived from a unique patient, of which 148 images contained at least one lung nodule and 93 images were without nodules. To train the bone suppression models, the dataset was cleaned by removing image pairs where poor suppression (defined as observing at least 1 rib or clavicle with edges visible across the lung tissue) and image artifacts were observed. A total of 217 image pairs (131 with nodule, 86 without nodule) remained after data cleaning. Of those, 20 images (9%) were retained for internal testing; the remaining 197 images were used for 10-fold cross-validation of the bone suppression models.

Second, to train the VGG16-Modified classification model, CXRs from COVID-19 and non-COVID-19 datasets were acquired. A total of 996 CXR images of COVID-19 positive patients were extracted from the publicly available RICORD-1c dataset (32,33), consisting of PA, AP and portable acquisitions from three institutions. Data accrual began in April 2020 and ended before March 5, 2021. A total of 1,125 CXR images of patients with no lung pathology (‘normal’), and 100 CXR images of patients with non-COVID-19 pneumonia, were randomly extracted from the publicly available RSNA Pneumonia Challenge dataset [National Institute of Health Clinical Center, United States (34-36)], which contained patient data that had been acquired between 1992 and 2015. The data was split into an 8-fold cross-validation set (896 COVID, 1,025 normal), and internal testing (100 COVID, 200 non-COVID) sets. Non-COVID pneumonia data was used exclusively in the internal test set to assess the generalizability of the trained models.

Third, an external test dataset was created to test the classification models. An anonymized dataset consisting of 524 COVID-19-positive patients was obtained from Queen Elizabeth Hospital (Hong Kong, China) with ethics approval from the relevant ethics committee (KC/KE-20-0337/ER-4), and combined with a separate anonymized dataset of 564 COVID-19-negative patients that was obtained from Pamela Youde Nethersole Eastern Hospital (Hong Kong, China) with ethics approval from the relevant ethics committee (HKECREC-2020-119). After data cleaning to remove low-resolution, non-AP/PA, and non-chest radiographs, 320 COVID-19 and 518 non-COVID radiographs remained. The earliest CXR from each patient was used for external testing in this study, under the assumption that this was acquired within a day of patient admission. Potentially eligible patients were identified from hospital admissions, forming a consecutive series. Inclusion criteria for this dataset are as follows: patients with age 18 years or older, clinically diagnosed with COVID-19 (using PCR testing), had received chest radiography for COVID-19, and had radiographs acquired between 1st January 2020 and 31st December 2020. Exclusion criteria were patients who had previous pulmonary pneumonia and previous treatment for lung diseases. The proportions of potentially eligible patients who were included or excluded were unavailable due to limitations in the ethical review. Furthermore, due to limitations in the ethical review, this dataset is not available to the public.

The external test dataset for the bone suppression methods and the classification methods was created by combining the data from the two abovementioned Hong Kong hospitals, totaling 518 non-COVID-19 and 320 COVID-19 CXRs from unique patients. From the literature, a test set of this size is suitable (11,19). Known clinical information about the image datasets used in this study is summarized in Table 1.

Table 1

Clinical information of the datasets used in this study

Dataset Geographic region Male/female Age (years, mean ± SD) Number of non-pathological/non-COVID pneumonia/COVID-19 patients
RSNA Pneumonia Challenge North America NA NA 1,125/100/0
RICORD-1c North America 208/143 55±18 0/0/996
JSRT (all) Japan 116/125 58±14 93/NA/NA
JSRT (for bone suppression) Japan 104/113 NA 86/NA/NA
Hong Kong Hospitals (all) Hong Kong (China) 260/264 (QEH);
280/284 (PYNEH)
46±22 (QEH);
57±25 (PYNEH)
0/0/524 (QEH);
564/0/0 (PYNEH)
Hong Kong Hospitals (for external test set) Hong Kong (China) 152/168 (QEH);
265/253 (PYNEH)
NA 0/0/320 (QEH);
518/0/0 (PYNEH)

The authors could not identify the age and sex information of the subjects in the RSNA Pneumonia Challenge dataset. All patients in the JSRT dataset who were not non-pathological had lung nodules. Mean and standard deviation of the patient ages in the PYNEH dataset were derived from 478 out of the 564 unique patients used. SD, standard deviation; JSRT, Japanese Society of Radiological Technology; NA, not applicable/no information found; QEH, Queen Elizabeth Hospital; PYNEH, Pamela Youde Nethersole Eastern Hospital.

Bone suppression

Classification performance on non-suppressed test images was compared to that on bone-suppressed test images. In this study, bone suppression was performed using the following published neural network architectures.

The Gusarev method was modified from that introduced by Gusarev et al. (18), and was instead implemented as shown in Figure 1. Convolutional layer weights were initialized with a normal distribution with a mean of 0 and standard deviation of 0.02, whilst batch normalization weights were initialized with the same standard deviation and a mean of 1. The training batch size was 5, and the network was trained for 400 epochs. An Adam optimizer (38) was used, with an initial learning rate of 0.001 and β1,β2 of 0.9, 0.999 respectively. The learning rate was decreased by 25% every 100 epochs. The loss LGusarev to be minimized was defined in Eq. [1]:

LGusarev=0.16×MSE+0.84×(1MSSSIM)

Figure 1 The Gusarev network for bone suppression used in this study. It is modified from that described by Gusarev et al. (18) by the addition of the batch normalization (37) layer in the ConvBlock. Every 2D convolutional layer (“Conv2d”) uses a filter size (f) of 5×5, a stride (s) of 1 and a padding (p) of 2. The final layer uses a sigmoid activation function to generate the bone-suppressed output image.

where MSSSIM is the multiscale structural similarity index measure (SSIM) (39) and MSE is the mean-squared error between the predicted bone-suppressed image and the target image.

The Rajaraman method was implemented as described by Rajaraman et al. (19) and as shown in Figure 2. Convolutional layer weights were initialized with a normal distribution with a mean of 0 and standard deviation of 0.02. An Adam optimizer (38) was used, with an initial learning rate of 0.001 and β1,β2 of 0.9, 0.999 respectively, to train the model for 200 epochs with a batch size of 8. The learning rate was reduced on plateau by a factor of 0.5 after 10 epochs with no improvement (defined as a change of 0.0001 in the loss). The loss LRajaraman to be minimized was defined in Eq. [2]:

LRajaraman=0.16×MAE+0.84×(1MSSSIM)

Figure 2 The Rajaraman network for bone suppression used in this study. Every 2D convolutional layer (“Conv2d”) uses a filter size (f) of 3×3, a stride (s) of 1 and a padding (p) of 1. Arrows denote skip connections. Elementwise addition is used to combine tensors both in ResBlocks and in the larger network. In the ResBlock scaling layer, the input tensor is elementwise multiplied by 0.1. The final layer uses a sigmoid activation function to generate the bone-suppressed output image.

where MAE is the mean absolute error.

The Rajaraman and Gusarev bone suppression networks were trained and evaluated using 10-fold cross validation. The models with the best results were used for further processing. The training images were resized to 256×256 to alleviate the computational cost. Data augmentation operations, performed during training, included: random rotations of up to 10° clockwise and counterclockwise; random translations of up to 10% of image dimensions horizontally and vertically; scaling by a random factor ranging from 0.9 to 1.1; horizontal flipping at a 50% chance; intensity flipping (black to white and white to black) at a 50% chance; contrast stretching (where a random percentage, up to 10%, of the lowest and highest intensity voxels are set to the minimum and maximum intensity allowable for the image, and the remaining pixel intensities in the image are rescaled to fit the range). The bone suppression models were implemented in Python 3.6 and PyTorch 1.10.

The performance of the bone suppression methods was quantified using the peak signal-to-noise ratio (PSNR), SSIM (40) and root-mean-squared error (RMSE) for the internal test set, and was qualitatively assessed using the Hong Kong hospitals external test set. The paired Student t-test was used to assess the statistical significance of the bone suppression methods.

Classification

To identify the effect of bone suppression on classification, two classification models were implemented. The COVID-Net CXR2 model, a publicly available, pre-trained 2-class (‘Not COVID’ and ‘COVID’) classification model (11), was implemented. As shown in the published paper and code (11), all images input into the classifier were processed as follows: (I) the topmost 8% of the image was removed in order to remove metadata in the image; (II) the image was center-cropped by removing both ends of the longer side of the image, such that the remaining image is square; (III) the image was resized using bilinear interpolation to 480×480 pixels; (IV) the image was input into the model’s neural network for classification. This model had been trained on the ImageNet (41) natural image database, then on the COVIDx8B dataset which consisting of approximately 8,700 non-pathological CXRs, 5,900 non-COVID pneumonia CXRs, and 4,600 COVID-19 CXRs obtained from public datasets (32,33,36,42-45). No bone suppression of the dataset had been performed prior to training. The model had then been modified using a proprietary deep learning-based generative synthesis process to create the final model, which was used in this study without modification. COVID-Net had been implemented in TensorFlow 2.6.

COVID-Net had been trained on datasets generated by crowd-sourcing (11). This is noted to be problematic (46), since the submitted images may have been mislabeled, and images may have been submitted to multiple crowd-sourced datasets resulting in duplication within the training data. Therefore, we trained a classification network using datasets sourced from medical archives [RSNA Pneumonia Detection Challenge dataset (36), a subset of the ChestX-ray8 dataset released by the National Institutes of Health Clinical Center, and RICORD-1C (33)]. The network architecture used in this study is inspired by that introduced by Rajaraman et al. (19), and is as follows: a VGG-16 (47) network pretrained on ImageNet (41) was truncated after the last convolutional block to be used as a feature extractor. A global average pooling (48) layer, a dropout layer (49) (50% dropout chance), and then a fully connected output layer with two output nodes was appended in that order. VGG16 had been chosen because it had been used in previous chest disease classification studies (19,50) and had demonstrated improved results over alternatives such as DenseNet-121 (51) and ResNet-50 (52). In this study, our model is denoted “VGG16-Modified”. It was trained as described: (I) all VGG-16 parameters are frozen; (II) the whole network is trained using the Adam optimizer (learning rate = 0.001, beta1 = 0.9, beta2 = 0.999) for 5 epochs; (III) the parameters of the final three convolutional layers of the VGG16 feature extractor are unfrozen; (IV) the network is fine-tuned by training using stochastic gradient descent (learning rate = 5e-6, weight decay = 0.01) for 40 epochs. The training batch size was 8. The network was trained using 8-fold cross-validation.

Three VGG16-Modified models were independently trained using three cross-validation datasets. The first cross-validation dataset consisted of the 896 COVID-19 CXR images and 1,025 non-pathological CXR images introduced in Section Datasets of Methods. The second dataset was generated by Gusarev suppression of the first dataset. The third dataset was generated by Rajaraman suppression of the first dataset. The COVID and non-pathological image data for all three datasets were augmented by four and three times respectively (18), using the same data augmentation operations as those used for bone suppression model training (Section Bone suppression of Methods), resulting in final dataset sizes of 3,584 COVID and 3,075 non-pathological CXR images for each dataset. No augmentation was performed during training. The fold with the best average accuracy was used for further processing. Prior to model input, images were resized and center-cropped to 224×224 pixels (to fit the VGG16 input) using nearest-neighbor interpolation. The VGG16-Modified model was implemented in Python 3.6, PyTorch 1.10 and torchvision 0.11.

After the bone suppression models and VGG16-Modified classifier models had been trained, the performance of the COVID-Net CXR2 and VGG16-Modified classifier models were quantified by sensitivity, specificity, negative predictive value (NPV), accuracy, and area under the receiver operating curve (AUC) on the Hong Kong hospitals external test set. NPV is important because the public health consequences of missing a COVID-19 diagnosis was deemed to be greater than that of mistakenly identifying someone as infected. The performance of COVID-Net CXR2 when classifying a non-suppressed, a Gusarev-suppressed and a Rajaraman-suppressed external test set was compared. The VGG16-Modified model trained on non-suppressed data was assessed using the non-suppressed external test set; the model trained on Gusarev-suppressed data, on the Gusarev-suppressed external test set; and the model trained on Rajaraman-suppressed data, on the Rajaraman-suppressed external test set.

The 95% confidence intervals for AUC were calculated using the DeLong test (53) to assess statistical significance in differences between classifier performance. Due to the nature of this study, the classifiers were not blind-tested. The trained bone suppression models and VGG16-Modified models used in this study are available for use from (https://github.com/danielnflam).


Results

Clinical information

The clinical information of patients whose datasets were used in this study is shown in Table 1. Patients in the JSRT dataset were either non-pathological or had lung nodules.

Bone suppression

Internal test set

Qualitative bone suppression results for a subset of the internal test set of 20 image pairs are shown in Figures 3,4 for Gusarev and Rajaraman suppression, respectively. Quantitative results for all methods are given in Table 2. For both Gusarev and Rajaraman suppression, the suppressed images were significantly (P<0.05) more similar to the target images than the non-suppressed images.

Figure 3 Representative examples of the non-suppressed original (A), target (C) and Gusarev-suppressed (B) CXRs from the internal (JSRT) test set. The white rectangles at the edges of the original image had been generated during image anonymization to remove metadata. CXR, chest X-ray; JSRT, Japanese Society of Radiological Technology.
Figure 4 Representative examples of the non-suppressed original (A), target (C) and Rajaraman-suppressed (B) CXRs from the internal (JSRT) test set. The white rectangles at the edges of the original image had been generated during image anonymization to remove metadata. CXR, chest X-ray; JSRT, Japanese Society of Radiological Technology.

Table 2

Internal test results for the bone suppression methods used in this study

Bone suppression method PSNR (higher is better, mean ± SD) SSIM (higher is better, mean ± SD) RMSE (lower is better, mean ± SD)
None 32.9±3.0 0.982±0.005 0.024±0.010
Gusarev 33.8±2.9 0.984±0.004 0.022±0.010
Rajaraman 34.0±3.7 0.986±0.004 0.021±0.010

PSNR, peak signal-to-noise ratio; SD, standard deviation; SSIM, structural similarity index measure; RMSE, root-mean-squared error.

External test set

Representative examples of non-suppressed and bone-suppressed CXRs from the Hong Kong hospitals dataset are shown in Figures 5,6 for Gusarev and Rajaraman suppression respectively. As no ground-truth CXR existed for this dataset, no quantitative results could be shown.

Figure 5 Representative examples of the CXRs from the Hong Kong hospitals external test set, before (A) and after (B) Gusarev bone suppression. The top row shows radiographs from a non-COVID patient; the bottom row, those from a COVID-positive patient. CXR, chest X-ray.
Figure 6 Representative examples of the CXRs from the Hong Kong hospitals external test set, before (A) and after (B) Rajaraman bone suppression. The top row shows radiographs from a non-COVID patient; the bottom row, those from a COVID-positive patient. CXR, chest X-ray.

Classification

The sensitivity, specificity, NPV, accuracy and AUC results for both classifier architectures processing external test data sets are shown in Table 3.

Table 3

Quantitative results for the classification models when evaluating the external test dataset for classification (Hong Kong hospitals dataset)

Bone suppression of external test data None Gusarev Rajaraman
COVID-Net CXR2
   Sensitivity (%) 80.93 77.81 71.25
   Specificity (%) 56.18 60.42 67.95
   NPV (%) 82.67 81.51 79.28
   Accuracy (%) 65.63 67.06 69.21
   AUC ± SE95% 0.686±0.031 0.691±0.031 0.696±0.032
VGG16-Modified
   Sensitivity (%) 52.81 61.88 61.88
   Specificity (%) 86.87 78.76 84.56
   NPV (%) 74.88 76.98 78.21
   Accuracy (%) 73.87 72.32 75.90
   AUC ± SE95% 0.698±0.031 0.703±0.032 0.732±0.031*

For the COVID-Net CXR2 architecture, the same model was tested with non-suppressed, Gusarev-suppressed and Rajaraman-suppressed external testing data. For the VGG16-Modified architecture, separate models trained on non-suppressed, Gusarev-suppressed and Rajaraman-suppressed data were each tested with their correspondingly suppressed external test data (e.g., non-suppressed training data model with non-suppressed test data). *, denotes a significant (P<0.05) difference from the non-suppressed external test data. NPV, negative predictive value; AUC, area under the receiver operating curve; SE95%, the error associated with a 95% confidence interval.

For the VGG16-Modified classifier, the AUC (±95% confidence interval) results for the internal test set were 0.887±0.033, 0.828±0.037 and 0.838±0.035 for the non-suppressed, Gusarev-suppressed and Rajaraman-suppressed models respectively. Interestingly, bone suppression resulted in significantly (P<0.05) worse results than no suppression. For the external test set (320 COVID and 518 non-COVID patients), bone suppression improved classifier performance from 0.698±0.031 (no suppression) to 0.703±0.032 (Gusarev suppression) and 0.732±0.031 (Rajaraman suppression). Rajaraman suppression resulted in significantly (P<0.05) improved AUC scores compared to no suppression. NPV increased after bone suppression (from 74.88% to a maximum of 78.21% for Rajaraman suppression).

For COVID-Net CXR2, no significant difference in classifier performance was observed between non-suppressed (0.686±0.031), Gusarev-suppressed (0.691±0.031) and Rajaraman-suppressed (0.696±0.032) external test data sets. NPV decreased after bone suppression (from 82.67% to a minimum of 79.28% for Rajaraman suppression). Interestingly, the AUC for COVID-Net CXR2 did not differ significantly from that for VGG16-Modified, for the non-suppressed external test data set.


Discussion

The Rajaraman-suppressed and Gusarev-suppressed images were significantly (P<0.05) more similar to the target images than the non-suppressed images, suggesting that the bone suppression methods are fit for purpose. Qualitative examination of the Gusarev- and Rajaraman-suppressed radiographs (Figures 5,6, respectively) in this study suggest that rib shadows are reduced post-suppression, albeit imperfectly. A limitation of the bone suppression performed in this study was that the target images were themselves derived from a method by Juhász et al. (30), instead of acquired directly from dual-energy subtraction radiography. Hence, the bone suppression models could have learnt to reproduce the errors produced by Juhász suppression. Published studies have been performed using the JSRT and Juhász et al. datasets to pursue bone suppression of CXRs (19,54), and, to the authors’ knowledge, no other publicly available co-registered non-suppressed and bone-suppressed chest radiograph dataset exists.

The main purpose of the study was to examine whether bone suppression improved the performance of COVID-19 classification models. For the external test set, results demonstrate that Rajaraman suppression significantly (P<0.05) improved AUC for the VGG16-Modified classifier architecture compared to no suppression, whereas no significant improvement was observed for COVID-Net CXR2. This difference may have been because COVID-Net had been trained on a larger and more varied dataset of non-suppressed CXRs (4,600 COVID + 14,600 non-COVID) than VGG16-Modified (896 COVID + 1,025 non-COVID before augmentation). Hence, the COVID-Net CXR2 model could have learned to disregard bone shadow when classifying CXRs. It is interesting to note that, for VGG16-Modified, internal test set results significantly worsened after bone suppression, whilst external test set results demonstrated either no significant change (Gusarev suppression) or significant improvement (Rajaraman suppression). This difference was suspected to arise from minor overfitting in the non-suppressed classifier model. Ultimately, the results suggest that bone suppression could be applied to improve the performance of classifier models, with the worst-case scenario being a statistically insignificant change in performance. Further work could involve acquiring more CXRs to improve classifier performance, and examining the effect of bone suppression on more classifier architectures. Furthermore, it is plausible that, as demonstrated by the research of Rajaraman et al. (19), this technique could be applied to lung pathologies outside of COVID-19 such as lung carcinomas.

Limitations of the study are as follows. Only two classifier architectures were tested in this study, so it is difficult to definitively conclude that bone suppression improves classification performance. In the future, the effect of bone suppression could be tested on a wider variety of classifiers, particularly those based on novel architectures (16) or those using inputs from different imaging modalities (17). Furthermore, bone suppression of the test data has only been tested for two-class classification models. The impact of bone suppression on the performance of three-class models (that classify CXRs into non-pathological, non-COVID-19 pneumonia and COVID-19) (11,12) remains to be seen. The demographics of the training data and external test set are also of interest. The patients of the external test dataset in this study are mostly of East Asian descent, compared to the North American patient data used to train VGG-Rajaraman and the North American and South Asian patient data used to train COVID-Net (11,32-34,36,42,43,45). Possible biological variability in COVID-19 radiological presentation between different demographics may have contributed to poor classifier performance (55,56). Furthermore, standard imaging protocols may differ between nations. Acquisition of patient data from a wider range of institutions could enable further research into whether the results in this study are generalizable.

In general, future work could be pursued in several other ways. Other classification architectures could be tested to see whether bone suppression improved their performance. More image data could be acquired to improve both the classifier performance and the generality of the external test set. Other image enhancement techniques beyond bone suppression could be pursued to improve classification performance for other clinical conditions imaged using other modalities. Radiomics analysis of the enhanced images, and analysis of other non-deep learning features (57), could be combined with deep learning features to further improve classification performance.


Conclusions

Rajaraman bone suppression of external test data was found to significantly (P<0.05) improve the AUC of the VGG16-Modified classifier. In general, bone suppression significantly improved, or did not worsen, classifier performance for an external test data set. Further research into bone suppression and other image enhancement techniques could significantly improve deep learning image classification performance.


Acknowledgments

We would like to acknowledge the patients and staff of Pamela Youde Nethersole Eastern Hospital and Queen Elizabeth Hospital for providing the data with which this study was performed.

Funding: This work was supported by Health and Medical Research Fund (No. HMRF COVID190211), the Food and Health Bureau, The Government of the Hong Kong Special Administrative Region.


Footnote

Reporting Checklist: The article is presented in accordance with the TRIPOD reporting checklist. Available at https://qims.amegroups.com/article/view/10.21037/qims-21-791/rc

Conflicts of Interest: All authors have completed the ICMJE Uniform Disclosure Form (Available at https://qims.amegroups.com/article/view/10.21037/qims-21-791/coif). FMK has research grants from Varian Medical Systems, Merck Pharmaceutical (through Chinese Society of Clinical Oncology), and speaker’s honorarium from AstraZeneca. NFDL was employed by an institution and worked under a supervisor that received money from the Health and Medical Research Fund (No. HMRF COVID190211), the Food and Health Bureau, The Government of the Hong Kong Special Administrative Region. JC has received research grant (No. HMRF COVID190211) for this study. YXJW serves as the Editor-In-Chief of Quantitative Imaging in Medicine and Surgery. The other authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. This study was conducted in accordance with the Declaration of Helsinki (as revised in 2013) and with ethics approval from The Hong Kong Polytechnic University Faculty Research Committee (No. HSEARS20201107001). Since only anonymized data was acquired and used in this study, individual consent for this retrospective study was waived. Data from Queen Elizabeth Hospital was acquired with ethics approval from the Kowloon Central/Kowloon East Research Ethics Committee (No. KC/KE-20-0337/ER-4). Data from Pamela Youde Nethersole Eastern Hospital was acquired with ethics approval from the Hong Kong East Cluster Research Ethics Committee (No. HKECREC-2020-119).

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.


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Cite this article as: Lam NFD, Sun H, Song L, Yang D, Zhi S, Ren G, Chou PH, Wan SBN, Wong MFE, Chan KK, Tsang HCH, Kong FM(, Wáng YXJ, Qin J, Chan LWC, Ying M, Cai J. Development and validation of bone-suppressed deep learning classification of COVID-19 presentation in chest radiographs. Quant Imaging Med Surg 2022;12(7):3917-3931. doi: 10.21037/qims-21-791

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