key: cord-0701537-1kjkwe3x
authors: Hu, Zongsheng; Yang, Zhenyu; Lafata, Kyle J.; Yin, Fang‐Fang; Wang, Chunhao
title: A radiomics‐boosted deep‐learning model for COVID‐19 and non‐COVID‐19 pneumonia classification using chest x‐ray images
date: 2022-03-15
journal: Med Phys
DOI: 10.1002/mp.15582
sha: 053b0273d8a94314c75b570675f7325b23408627
doc_id: 701537
cord_uid: 1kjkwe3x

PURPOSE: To develop a deep learning model design that integrates radiomics analysis for enhanced performance of COVID‐19 and non‐COVID‐19 pneumonia detection using chest x‐ray images. METHODS: As a novel radiomics approach, a 2D sliding kernel was implemented to map the impulse response of radiomic features throughout the entire chest x‐ray image; thus, each feature is rendered as a 2D map in the same dimension as the x‐ray image. Based on each of the three investigated deep neural network architectures, including VGG‐16, VGG‐19, and DenseNet‐121, a pilot model was trained using x‐ray images only. Subsequently, two radiomic feature maps (RFMs) were selected based on cross‐correlation analysis in reference to the pilot model saliency map results. The radiomics‐boosted model was then trained based on the same deep neural network architecture using x‐ray images plus the selected RFMs as input. The proposed radiomics‐boosted design was developed using 812 chest x‐ray images with 262/288/262 COVID‐19/non‐COVID‐19 pneumonia/healthy cases, and 649/163 cases were assigned as training‐validation/independent test sets. For each model, 50 runs were trained with random assignments of training/validation cases following the 7:1 ratio in the training‐validation set. Sensitivity, specificity, accuracy, and ROC curves together with area‐under‐the‐curve (AUC) from all three deep neural network architectures were evaluated. RESULTS: After radiomics‐boosted implementation, all three investigated deep neural network architectures demonstrated improved sensitivity, specificity, accuracy, and ROC AUC results in COVID‐19 and healthy individual classifications. VGG‐16 showed the largest improvement in COVID‐19 classification ROC (AUC from 0.963 to 0.993), and DenseNet‐121 showed the largest improvement in healthy individual classification ROC (AUC from 0.962 to 0.989). The reduced variations suggested improved robustness of the model to data partition. For the challenging non‐COVID‐19 pneumonia classification task, radiomics‐boosted implementation of VGG‐16 (AUC from 0.918 to 0.969) and VGG‐19 (AUC from 0.964 to 0.970) improved ROC results, while DenseNet‐121 showed a slight yet insignificant ROC performance reduction (AUC from 0.963 to 0.949). The achieved highest accuracy of COVID‐19/non‐COVID‐19 pneumonia/healthy individual classifications were 0.973 (VGG‐19)/0.936 (VGG‐19)/ 0.933 (VGG‐16), respectively. CONCLUSIONS: The inclusion of radiomic analysis in deep learning model design improved the performance and robustness of COVID‐19/non‐COVID‐19 pneumonia/healthy individual classification, which holds great potential for clinical applications in the COVID‐19 pandemic.

Since its first discovery in 2019, the coronavirus disease has affected more than 100 million people globally, and more than 5 million deaths related to COVID-19 were reported by the end of 2021. 1 Accurate and efficient diagnosis of COVID-19 is crucial to interrupt disease transmission and to start treatments of affected individuals. Currently, reverse transcriptionpolymerase chain reaction (RT-PCR) has been recognized as the gold standard for COVID-19 diagnosis for its high specificity. 2 While RT-PCR test may have limited sensitivity and long time of processing (a few hours to 2 days), 3 radiographic procedures, including chest x-ray and CT exams, have been adopted clinically as alternative diagnosis tools. 4 While COVID-19 related abnormalities could be more easily found in volumetric CT images, 5 planar chest x-ray has its unique advantages in COVID-19 diagnosis. Specifically, the short imaging time on a more accessible X-ray unit enables rapid COVID-19 exams, which can be critical in areas with highvolume patients and/or limited-resource medical facilities. To date, pilot studies have revealed that certain xray image features, including peripheral consolidations and ground-glass opacities, have been widely observed in COVID-19 infected patients. [4] [5] [6] [7] [8] [9] However,the prevalent application of chest x-ray imaging in COVID-19 diagnosis is challenged by relatively limited sensitivity and specificity. 5 Additionally, radiographic exams including chest x-rays may not be optimal for radiologists' reading in the differentiation of non-COVID-19 pneumonia from COVID-19, which is important for early patient stratification that can lower COVID-19 mortality rate with more targeted treatments. 10, 11 Computed aided diagnosis systems (CAD) may have the potential to solve the aforementioned problem with high throughput quantitative analysis. In the last several months under the COVID-19 pandemic, studies revealed that CAD systems outperformed radiologists in radiographic-based COVID-19 diagnosis; with CAD information as reference information, radiologist reading results could be significantly improved. [11] [12] [13] One approach for such a CAD system is radiomics-based image analysis, which first extracts radiomics features as computation image biomarkers and then uses the extracted features in hand-made or machine learning classifier tasks. Although handcrafted radiomics features are commonly used in medical image analysis with possible qualitative image interpretability, the reported accuracy (75%-80%) of COVID-19 diagnosis is still limited in the representative radiomics-based CAD works. [14] [15] [16] Driven by recent theoretical developments and access to massive computation power, deep learning has demonstrated its great potential in CAD developments. It has been reported that deep learning solutions based on artificial neural network deployment could achieve high (>90%) specificities in COVID-19 diagnosis against healthy individuals 17, 18 ; moreover, decent specificities (>85%) of differentiating COVID-19 from non-COVID-19 pneumonia have been achieved. 11, [19] [20] [21] Nevertheless, like all other deep learning applications in medical image analysis, the hyperparameters in the neural network are generated without explicit human knowledge intervention. Thus, the "black box" nature of deep learning-based CAD inhibits their interpretability, and potential clinical applications of these CADs could be impaired by limited interpretability by clinicians.

In this work, we aim to develop a radiomics-boosted deep learning CAD design for chest x-ray based COVID-19 diagnosis. Because hand-crafted radiomics and deep learning are complementary approaches to image representation, their integration may facilitate better model performance and interpretation. 22 Innovative implementation of radiomics analysis was included to analyze deep features from 3 custom-trained neural networks for COVID-19, non-COVID-19 pneumonia, and healthy individuals classification, and such radiomics analysis results were then incorporated as additional imagebased input sources for 3 improved neural network designs. The proposed methodology may enhance deep learning interpretability for COVID-19 diagnosis from a current radiomics knowledge perspective.

In this IRB-waived retrospective study, a total of 812 chest x-ray images were collected from three public databases, 23-25 including 262/288/262 images of COVID-19/non-COVID-19 pneumonia/healthy individuals, respectively. The image numbers from the three categories were approximately the same for eliminating categorical bias during deep learning training. All collected images were verified by experienced medical physicists with proper lung x-ray display settings and with absences of the overlaid image reading annotations. To unify image data size, all images were resized to a 256 × 256 matrix grid size using b-spine interpolation and were normalized to 256 gray levels. 649 and 163 images (8:2) were assigned for the model training set and the independent test set, respectively.

To investigate radiomics-boosted deep learning as a general methodology, we studied three deep neural networks, VGG-16 (Figure 1a ), VGG-19 (Figure 1b) , and DenseNest-121 (Figure 1c ), for COVID-19/non-COVID-19 pneumonia/healthy individual classification. Based on pre-trained deep learning schemes, 26,27 the investigated three deep neural networks share the same two-part design: the 1 st part is the convolutional base: In VGG-16 and VGG-19, the convolutional bases consist of five convolutional blocks. Each convolutional block is stacked by two to four convolutional layers and a max-pooling layer. In each convolutional layer, the filter size is 3 × 3 with padding and stride of 1. Max-pooling is performed over a 2 × 2-pixel window with a stride of 2. In DenseNet-121, the convolutional base consists of one convolutional block and four dense blocks. The convolutional block consists of 7 × 7 convolutional layers with a stride of 2 and a 3 × 3 Max-pooling with a stride of 2. The dense blocks consist of 6, 12, 24, and 16 convolutional units, respectively. Each unit is stacked by a 1 × 1 and a 3 × 3 convolutional layer. The first three dense blocks are followed by three transition layers, which consist of a 1 × 1 convolutional layer with stride 1 and a 2 × 2 average pool with stride 2; the 2 nd part is the Dense part, which is the stack of dense layers. pneumonia, and healthy results, respectively. To deal with relatively small data size in this work, the convolutional bases loaded the weights that were pre-trained on ImageNet as a transfer learning scheme. 28 In addition, in order to make the models more relevant for the problem at hand, fine-tune technique was used with the last few convolutional layers (marked * in Figure 1 : the last convolutional blocks in VGG-16 and VGG-19, as well as the last dense block in DenseNet121) being set as free parameters for task-specific training. To avoid the occurrence of overfitting, a dropout layer was added between the first two dense layers with a dropout possibility of 0.5, and soft-max activation was used in the output layer.

Classic radiomics analysis calculates radiomic features as scalar values from a pre-defined region-of -interest (ROI) in image space. While this approach has been widely adopted to capture the overall textures in ROI, it cannot capture the anatomy-driven subtle texture variations within the ROI. As such, we implement a RFM calculation workflow, 29 which is summarized in Figure 2 .

For RFM generation, a 2D kernel (13 × 13 matrix size) was adopted to form a ROI, and 37 radiomic features were extracted as a 1 × 37 vector within this ROI following classic GLCOM 30 (21 features) and GLRLM 31 (16 features) feature extraction methods using 32 grey levels. For each feature, the calculated feature value was assigned as the pixel value centered at the ROI. By moving this 2D kernel across the x-ray image as a sliding window operation, 37 feature maps were formed in the same dimension as original x-ray images. All radiomic analysis was done using custom code that was benchmarked with digital phantoms 32 and complies with the imaging biomarker standardization initiative. 33

For each of the three investigated deep neural network architecture, two model versions were trained: in the 1 st pilot model, the x-ray image is the sole model input. To accommodate the input shape of pre-trained neural networks, the grayscale x-ray images were broadcast to three channels as a network input variable. This model serves as the benchmarking deep learning model in this work; in the 2 nd version as a radiomics-boosted model, the grayscale x-ray image and two derived RFMs were stacked as the 3-channel neural network input variable. These two RFMs were selected based on the analysis of the 1 st model's saliency map (SM), which indicates how important each pixel is with respect to the final classification results of the neural network in the benchmarking model. It is calculated as the absolute gradient of class activation which is defined as the dot product of prediction output and target divided by the input image 34 : a pixel with a higher intensity value in SM indicates higher importance of that pixel in neural network's attention for diagnosis. The two RFMs with the highest average cross-correlation (CC) values against the SM results in training data were selected. This action amplifies certain pixels (and regions) with potentially high importance of disease diagnosis in the image space, which could improve the overall diagnostic accuracy of the proposed radiomics-boosted model in comparison with the 1 st pilot model. To investigate model robustness, 50 runs of each model version were trained using the training data set (649 images). In each run, the training and validation samples were randomly selected following a 7:1 ratio. During deep learning training within the TensorFlow environment using a Nvidia™ (Santa Clara, CA) Tesla V100 graphic card, the loss function was categorical cross-entropy, and Adam optimizer was selected. For model evaluation, sensitivity, specificity, accuracy, and Table 1 summarizes the quantitative comparisons of sensitivity, specificity, accuracy, and ROC AUC between pilot models and radiomics-boosted models. For the VGG-16 architecture,the radiomics-boosted deep learning model achieved statistical improvements in all parameters with p < 0.05. The largest improvements were observed in non-COVID-19 pneumonia diagnosis. Additionally, the reduced standard deviations of the reported statistics indicated the enhanced robustness of the radiomics-boosted deep learning design. These quantitative results highlight the superiority of the proposed radiomics-boosted deep learning model in the context of VGG-16 architecture. The standard deviation of 50 runs is less than 3%, reaching a high level of robustness. For VGG-19 architecture, the mean values of all parameters were higher in the radiomics-boosted model than the pilot model; however, the observed numerical improvements were small, and only a few improvements were found with statistical significance in COVID-19 and healthy class results. The standard deviations were also reduced as indicators of improved model robustness. Results from DenseNet-121 architecture were similar to VGG-16 and VGG-19 results except for non-COVID-19 pneumonia classification, in which mixed impacts in the radiomics-boosted model were presented; nevertheless, the radiomics-boosted model did improve COVID-19 and healthy individual classification performance and increased model robustness in the healthy individual classification. As a summary, the radiomics-boosted design achieved best performance in COVID-19 diagnosis in both VGG-16 and VGG-19 architecture applications, while it achieved the best performance in healthy individual classification in DenseNet-121 architecture application. Figure 4 summarizes the ROC analysis results of the three studied architectures. The blue and red solid lines represent the average ROC results of 50 runs of two deep model versions (x-ray only vs. x-ray + RFM), and the colored bands represent the model performance variation as ±1 standard deviation. For VGG-16 architecture (Figure 4a) , radiomics-boosted design improved ROC results of all three classification tasks, and the largest performance improvement was observed in non-COVID-19 pneumonia diagnosis. Additionally, the radiomics-boosted deep learning model has narrower ROC bandwidth, which suggests the enhanced robustness of its design under different data sample uses. The same improvements were also observed in VGG-19 results (Figure 4b ),but the improvements' magnitudes were smaller than ones in VGG-16 results, which was mainly contributed by the higher performance of VGG-19 prior to radiomics-boosted implementation. In Figure 4c of DenseNet-121 results, while the ROC improvement by radiomics-boosted design was prominent in healthy individual classification, the improvement in COVID-19 diagnosis was limited. As reported in Table 1 , the ROC result in non-COVID-19pneumonia showed a slightly decreased performance after radiomics-boosted design, though such decrease has found no statistical significance.

As an example of saliency map visualization, the SM results of the VGG-16 architecture are illustrated in the last column of Figure 3 . The pixel values in SM can be interpreted as the attention of the deep learning model. As seen, the attention patterns, that is, colored hot regions distribution in SMs, demonstrated prominent spatial heterogeneity across the image field-of -view. In addition, the current SM illustration suggests potential class-specific spatial patterns of deep network attention: more attention might be drawn to lateral lung regions for COVID-19 detection, while mediastinum regions might be attention focus for non-COVID-19 pneumonia detection. In order to quantitatively analyze the attention patterns across different patient cohorts, we calculated the CC matrix for SMs of all three radiomics-boosted architectures in the test set in Figure 5 , which includes all the CCs between paired SM results from the test set. For VGG-16 and VGG-19 results, CCs within each cohort were relatively higher than those calculated across different cohorts. This result suggests that the developed deep learning model captured cohort-specific features for the classification task. Additionally, the mean CC result of COVID-19 versus non-COVID-19 pneumonia (VGG-16:0.12; VGG-19: 0.10) cohort was slightly higher than the result of COVID-19 versus healthy cohorts (VGG-16:0.07; VGG-19: 0.08) and non-COVID-19 pneumonia versus healthy cohorts (VGG-16:0.09; VGG-19: 0.09). This observed COVID-19/non-COVID-19 pneumonia similarity supports the clinical reports of challenges in COVID-19/non-COVID-19 pneumonia differentiation. 10, 11 For the DenseNet-121, however, all reported CCs were very small and were an order smaller than those in VGG-16 and VGG-19 results. These results suggest that SM from DenseNet-121 architecture did not capture meaningful class-specific spatial patterns.

To our best knowledge, this work is the first of its kind for combining radiomic analysis and deep neural network implementation. achieved a sensitivity of 88% and a specificity of 79% in COVID-19/non-COVID-19 pneumonia diagnosis with a dataset of 2060 patients. Nishio et al. 19 achieved an accuracy of 83.7% for three categories of classification (healthy/non-COVID-19 pneumonia/COVID-19) using the VGG-16 model trained on 1248 images. Tulin et al. 21 achieved an accuracy of 87.0% for tri-class classification (healthy/non-COVID-19 pneumonia/COVID-19) using the Darknet-19. In this work, we studied a total of 812 chest x-ray images from three public datasets, 23-25 which were not curated by the typical medical image study protocols. As a result, proper image processing is necessary for streamlined deep learning implementation. In particular, we resized all images to 256 × 256 grid size and normalized all images to 256 gray levels as uint8 format. These operations are standard in digital image processing which will facilitate the data reproducibility of this work. In addition, the robustness of the developed model was systematically analyzed. For each model design, we trained 50 runs of models using randomly selected training and validation samples following a ratio of 7:1. The small standard deviation (< 0.06) of selected metrics and ROC results revealed the enhanced robustness of the developed model, which further demonstrates the potential of the radiomics-boosted deep learning design in clinical situations using different x-ray image data sources.

The deep learning implementations in this work adopted three commonly used deep neural network architectures based on a transfer learning scheme. VGG-16 was first selected for the following reason: (1) it has been widely studied for medical image analysis tasks as a transfer learning scheme; (2) in comparison with other prevalent candidates, VGG-16 possesses a smaller number of trainable parameters under the transfer learning scheme and thus leads to reduced calculation workload for network training; and (3) previous studies 19 reported that VGG-16 achieved the highest accuracy in COVID-19 diagnosis tasks in comparison with several other pre-trained deep neural network architectures. In addition to VGG-16,we studied VGG-19 and DenseNet-121 for the proposed radiomics-boosted design. As reported in Figures 3 and 4 , results of VGG-19 after the radiomics-boosted design were similar to the ones in VGG-16 implementation, which can be attributed to the high similarity of network architecture shown in Figure 1 . 26 On the other hand, the performance improvement after the radiomics-boosted design was higher in VGG-16 application than in VGG-19 application: this can be explained by the fact that classification performance from VGG-19 using x-ray image only was higher than ones from VGG-16. Although the total trainable parameter numbers under the transfer learning scheme were approximately the same in VGG-16 and VGG-19, VGG-19 has a larger dimension with more total parameters due to the three additional convolutional layers. Overall, the proposed radiomics-boosted design still improved VGG-19 performance in terms of the 4 classification evaluators as well as model robustness.

In the DenseNet-121 study, the improvements after radiomics-boosted design were rather limited. While radiomics-boosted design improved healthy individual classification results with statistical significance, ROC results in non-COVID-19 pneumonia classification showed a slight performance decrease. A plausible explanation is the fact that DenseNet-121 has a larger dimension with more trainable parameters (>70 m) than VGG-16 and VGG-19 (∼40 m) under the transfer learning scheme.In addition,DenseNet-121 has more parameters in total (>75 m) than VGG-19 (∼55 m). As such, a larger x-ray image set might be necessary to exploit the full potential of the proposed radiomics-boosted design in the DenseNet-121 application. Nevertheless, the current results, especially the prominent performance improvement in healthy individual classification, are sufficient to support the benefit of radiomics-boosted design in the DenseNet-121 application.

The inclusion of RFMs is a key technical innovation. Instead of calculating radiomic features as scalar values from selected volumes in image space, RFMs capture the anatomy-driven subtle texture variations within ROIs. It has been demonstrated that radiomics are associated with pulmonary function 35 and lung ventilation measurements 29 ; as such, the potential functional information in RFMs contributes to the enhanced COVID-19 diagnosis accuracy. The selection of two RFMs from 37 RFMs is more than a trivial task. While direct comparisons of all possible RFM combinations are feasible, it requires a high computational cost without the potential of transferring this technique to other clinical applications. Driven by the hypothesis that certain RFMs can be related to neural network hyperparameters, we selected RFMs based on similarity metrics between RFMs and neural network saliency maps which measure the attention pattern of the network implementation. Such a pattern can be used as an auxiliary tool for radiologists in image reading, that is, highlighting specific regions as visual clues for human reading. This potential human-aid tool can be important in accurate COVID-19/non-COVID-19 pneumonia differentiation, which can be a challenging task for radiologists using chest x-ray images without volumetric information. 11 RFMs with higher similarities to SMs could emphasize regional information to enhance neural network attention, which increases synchronously with SM results. It is worth mentioning that both VGG-16 and VGG-19 results identified GLCOM Entropy based on SM results, which emphasizes the similarity of the two deep learning architectures. In addition to the current design, it would be of interest to investigate other RFM selection mechanisms that can be complementary to the SM results (i.e., based on "dissimilarity") for potential performance improvement. DenseNet-121 SM results in Figure 5 , however, did not show recognized class-specific SM spatial patterns in comparison with VGG-16 and VGG-19. The absence of such patterns may stem from the potentially limited sample size due to large variable numbers of DenseNet-121.Additionally, ImageNet-based transfer learning may affect SM calculation results as well. Future works of DenseNet-121 analysis, based on full training from scratch or transfer learning from an x-ray-specific dataset, are of our interest to continue SM-based deep learning interpretability studies.

The presented design of combining radiomics analysis and deep neural network implementation may create a new paradigm of the CAD system. The implemented RFM calculation workflow may also enhance neural network performance in other tasks, particularly those where multi-channel imaging data are required as input. 36 Additionally, the proposed method provides a radiomics perspective of deep learning interpretability. The hyperparameters in the neural network are trained without explicit human knowledge intervention and thus are hard to interpret by empirical knowledge. For deep learning-based CAD systems, the "black box" nature impaired the clinical deployments of such systems without clinicians' confidence. As a step towards deep learning interpretability, we investigated neural network attention information using a radiomics-based analysis. Radiomics has been widely studied as computational imaging biomarkers for disease detection and outcome monitoring, 37 and it has been demonstrated that radiomic feature spaces can be mathematically decomposed to provide interpration. 38 Following the saliency map analysis approach in this work, additional parameters can be used to enhance deep learning interpretability, such as histology sample images from biopsy and anatomy contours from radiation therapy. These directions will be studied in future works when appropriate datasets become available.

In this study, we proposed a radiomics-boosted deep learning design for x-ray based COVID-19 diagnosis and non-COVID-19 pneumonia diagnosis. An innovative RFM calculation workflow was implemented to generate additional input sources for deep neural networks, and such design was tested using three deep neural network architectures. Results showed that the proposed radiomics-boosted deep learning design improved the performance and robustness of COVID-19/non-COVID-19 pneumonia/healthy individual classification in concurrence with a radiomics viewpoint of deep learning interpretation. It holds great potential for clinical applications for COVID-19 diagnosis and generalization in other diagnosis tasks.

We would like to thank Mr. Randall Grimes for his administrative support of this research work.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Image data in this work come from publically available datasets; the developed radiomics feature map calculation tool and the presented deep neural network implementations can be shared upon request to the corresponding author.

The authors have no conflicts to disclose.

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A radiomics-boosted deep-learning model for COVID-19 and non-COVID-19 pneumonia classification using chest x-ray images