Objectives There exists a wide gap in the availability of mechanical ventilator devices and their acute need in the context of the COVID-19 pandemic. An initial triaging method that accurately identifies the need for mechanical ventilation in hospitalised patients with COVID-19 is needed. We aimed to investigate if a potentially deteriorating clinical course in hospitalised patients with COVID-19 can be detected using all X-ray images taken during hospitalisation.
Methods We exploited the well-established DenseNet121 deep learning architecture for this purpose on 663 X-ray images acquired from 528 hospitalised patients with COVID-19. Two Pulmonary and Critical Care experts blindly and independently evaluated the same X-ray images for the purpose of validation.
Results We found that our deep learning model predicted the need for mechanical ventilation with a high accuracy, sensitivity and specificity (90.06%, 86.34% and 84.38%, respectively). This prediction was done approximately 3 days ahead of the actual intubation event. Our model also outperformed two Pulmonary and Critical Care experts who evaluated the same X-ray images and provided an incremental accuracy of 7.24%–13.25%.
Conclusions Our deep learning model accurately predicted the need for mechanical ventilation early during hospitalisation of patients with COVID-19. Until effective preventive or treatment measures become widely available for patients with COVID-19, prognostic stratification as provided by our model is likely to be highly valuable.
- critical care
Data availability statement
Data and code are available from the author on reasonable request.
This article is made freely available for use in accordance with BMJ’s website terms and conditions for the duration of the covid-19 pandemic or until otherwise determined by BMJ. You may use, download and print the article for any lawful, non-commercial purpose (including text and data mining) provided that all copyright notices and trade marks are retained.https://bmj.com/coronavirus/usage
Statistics from Altmetric.com
What are the new findings?
Artificial intelligence techniques can be used to accurately predict the need for mechanical ventilation in patients with COVID-19.
Deep leaning–based prediction of the need for mechanical ventilation outperforms predictions offered by subject experts.
How might it impact on healthcare in the future?
Triaging of hospital resources for admitted patients with COVID-19 is paramount. Our tool can play an important role in this regard.
Conceptually, our tool can therefore help in a rational and optimal use of resources for management of patients with COVID-19.
The COVID-19 global pandemic has caused almost 50 million infections and over 1.2 million deaths within a span of just over 10 months.1 Strikingly, the cumulative COVID-19 hospitalisation rate is 137.6 per 100 000 infections.2 A significant number of patients with COVID-19 need supportive care such as intravenous fluid administration and supplemental oxygen. Further, as many as 32% of hospitalised patients with COVID-19 need admission to an intensive care unit3 and respiratory support through mechanical ventilation.4 5 This has caused a great strain in hospital resources in certain geographical regions with high rates of COVID-19 infection. For example, at the height of COVID-19 pandemic in Wuhan and New York, there were concerns of the health system being overwhelmed from the sheer number of patients requiring hospitalisation. In Wuhan, a temporary COVID-19 facility was built, and in New York, a United States Navy hospital ship was dispatched to help cope with the number of patients requiring hospitalisation.6 Since then, COVID-19 has now spread globally and has, in many instances, severely tested healthcare system capacity to handle the sheer number of patients that have continued to flood healthcare facilities. Considering inadequate vaccination resources and suboptimal antiviral treatments, hospital systems will need to be prepared for an increase in hospitalisation rates, ICU admissions and need for mechanical ventilation.
It has been observed that many patients with COVID-19 experience a worsening of shortness of breath and need for supplemental oxygen or mechanical ventilation during the second week of the illness.7 However, not every patient who is hospitalised with COVID-19 infection needs mechanical ventilation or ICU level of care. Thus, a tool that can effectively predict the potential need for mechanical ventilation would ensure a better triage at initial point of contact with healthcare system and enable better allocation of healthcare resources by avoiding unnecessary hospitalisations. This was the motivation for the present study.
In this context, a deep learning analysis of chest radiograph was able to identify patients with COVID-19 infection with more than 90% accuracy.8 Also, Wang et al 9 were able to stratify patients in high-risk and low-risk groups by a deep learning analysis of lung CT images. In this study, we focused on using the information contained within chest X-ray images to predict the need for mechanical ventilation. A chest radiograph has practical advantages over CT scans in being more readily available especially in resource-challenged scenarios and less risk of equipment contamination. Indeed, a chest radiograph was performed for every patient with COVID-19 evaluated in our hospital emergency room. Here, we present a deep learning analysis of chest radiograph of patients with COVID-19 to predict need for mechanical ventilation.
The clinical and image data for this study were collected at the John H. Stroger, Jr Hospital of Cook County, Chicago, IL. All patients with COVID-19 who were admitted to the study centre between 15 March 2020 and 31 May 2020 and followed up until the censoring date of 16 June 2020 were included. The study cohort was identified in two: first, all confirmed COVID-19 cases were identified, and second, only the new inpatients were selected from those identified in step 1. COVID-19 positivity was confirmed for all patients using PCR for the RdRp and N genes of the SARS-CoV-2 virus. Clinical data of these patients were collected by chart reviews. The study did not require informed consent from the patients as the data were retrospectively collected after de-identification.
Chest X-ray images
All patients with symptoms suggestive of a possible infection with SARS-CoV-2 underwent portable antero-posterior chest X-ray assessment at the study centre. Chest X-ray images were acquired using the GE Healthcare Optima XR240-amx system rated at 90 kV and 1.5 mA. The protocol followed was as follows: Ensuring appropriate isolation and distancing practices, the X-ray images were acquired in upright or near-upright posture. Images were saved in dicom and jpg format and were manually scrubbed to remove all identifiable information.
The acquired X-ray images were first resized to 224×224 pixels and then centre cropped as required for many deep learning networks that use convolutional layers to parse out image features. To ensure robustness in training and validation of the deep learning network, we undertook two steps in data preprocessing. First, we augmented each image using a random combination of right or left rotation (maximum 30°), random cropping and random lighting. These augmentations permitted us to use different variations of the original image for training the deep learning algorithm thereby reducing the potential overfitting. Second, since the patients who needed mechanical ventilation in the study dataset represented a minority class, for training the network we first oversampled the number of ventilated patients so as to achieve a class balance of ~50% of X-ray images for ventilated and non-ventilated patients in the training sample. Combination of the first and second steps in data preprocessing yielded a set of 1320 X-ray images from the ventilated patients and 1200 X-ray images from non-ventilated patients. This set of 2520 images was used for network training.
The established and validated CheXNeXt deep learning algorithm10 as well as the PXR network11 are based on the DenseNet12112 architecture. While the CheXNeXt predicts one or more of 14 lung pathologies from an X-ray image of the chest, the PXR network scores an X-ray image for severity of acute respiratory distress syndrome (ARDS). We used the same backbone for our proposed prognosticator algorithm. The architecture of a DenseNet121 network is shown in figure 1B. Briefly, the DenseNet121 represents a series of convolutional operations on the image array (size 224×224 pixels) and is characterised by a serial combination of four dense blocks (D1–D4, figure 1B) interspersed with three transitional blocks (T1–T3, figure 1B). Each dense block is, in turn, a serial combination of densely connected convolutional layers such that each succeeding layer receives inputs from all preceding layers. The total number of hidden layers in a DenseNet121 network are 121 (hence the name) and the output is typically given as a multi-probability array which is subjected to a softmax function to obtain likely classifications. In our case, since the outcome (need for mechanical ventilation) was binary, we changed the last layer to a sigmoid function (equivalent to a logit function in logistic regression) as shown in figure 1B. We used this modified DenseNet121 network architecture in our study.
Network training and validation
We used the Tensorflow 2.2.0 (https://www.tensorflow.org/) and Keras 2.3.0-tf framework (https://keras.io/) for model training and evaluation. The Jupyter notebook containing all the Python code is available with the authors and will be shared on receipt of reasonable request. Training of the model was done on all the layers of DenseNet121 (ie, no layers were frozen) with the following pre-specifications: batch size: 32, optimizer: stochastic gradient descent (SGD), loss function: binary cross-entropy, learning rate: 0.003, epochs per cycle length: 4 (with plateaued loss) and cycle length: 10. The model that provided the best validation accuracy was selected as the final model.
X-Ray evaluation by Pulmonary and Critical Care (PCC) experts
Two experienced (3 years beyond Fellowship) experts from the field of PCC evaluated all the X-ray images included in the independent test set (153 images on 118 patients). This evaluation by the PCC experts was done retrospectively, conducted blindly and independently, and was based on clinical gestalt. Both the PCC experts answered the following question for each X-ray image evaluated: “Based on this X-ray image, do you think that this COVID-19 patient will need to be mechanically ventilated during the index hospitalisation?” These evaluations were done in a blinded fashion, independent of the knowledge of the prediction by the DL algorithm as well as to other clinical characteristics like age, sex and comorbidities at the time of admission.
Descriptive statistics included mean and SD for continuous variables and proportions for categorical variables. Agreement between PCC experts’ evaluation and the DL algorithm’s prediction with the ground truth was assessed using Cohen’s kappa. Performance metrics for the image classification task were precision (synonymous with positive predictive value as used in epidemiology), recall (synonymous with sensitivity), accuracy and F1 score (which was estimated as the harmonic mean of precision and recall). In addition, area under a receiver operating characteristic curve (AUROC) was estimated for the DL predictions. Predictive performance of the DL model was assessed at the level of the image as well as at the level of the patient. To summarise the performance at the level of a patient, we considered the prediction to be ‘mechanical ventilation needed’ if any of the multiple X-ray images on the same patient had indicated a high likelihood of ventilation need by the DL model. Correspondingly, the maximum probability estimated by the DL model for multiple X-rays on a given patient was considered as the predicted probability of the need for mechanical ventilation at the level of the patient.
Prognostic value of the predictions from the deep learning model and evaluations from the PCC experts was conducted using Kaplan-Meier plots and Cox proportional-hazards models. Incremental performance attributable to the deep learning model was estimated using Harrell’s C statistic for survival models13 14 and compared for statistical significance using the likelihood χ2 test. All statistical analyses were conducted in Stata V.12.0 (Stata Corp, College Station, TX) software package. A global type I error rate of 0.05 was used to test statistical significance.
Patient and public involvement
Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.
Data and images for this study come from 528 COVID-19 positive, hospitalised patients and a total of 663 X-ray images (figure 2). On the last day, 7 (1.3%) of the patients were still in hospital all of whom had completed at least 16 days of inpatient follow-up. Of the 528 patients, 79 (~15%) required mechanical ventilation. Clinical characteristics of the study participants based on the need for mechanical ventilation are shown in table 1. None of the sociodemographic and comorbidity variables were statistically significantly different in patients who received mechanical ventilation as compared with those who did not. Also, the average time interval between symptom onset and hospital admission was comparable in patients who did or did not require mechanical ventilation (6–7 days in both groups of patients). However, in general, those who received mechanical ventilation were more likely to be aged over 60 years and have hypertension, obesity, diabetes or chronic kidney disease as a comorbidity. Interestingly, those patients who eventually required mechanical ventilation had been ordered ~2 radiographs on an average as compared with a single radiograph ordered in most patients who did not require mechanical ventilation. The death rate in those who were mechanically ventilated was very high (~66%) as compared with those who did not need mechanical ventilation (~4%) as shown in table 1.
Model training results
The results of training of the proposed model are shown in figure 1E. The loss function monotonically decreased (except for cycle length 7) in both the training and the validation subsets and, conversely, the accuracy of prediction increased in a mirror-image fashion in both subsets. The model achieved convergence quickly. At the end of 10 cycle lengths, the training set and test set accuracy was very high—almost 100% in the training set and 100% in the validation set. As shown in figure 1F, the model perfectly predicted the need for mechanical ventilation in the validation set.
Predictive performance of the model in the test set
The predictive performance of the model was assessed at two levels—at the level of X-ray images (n=153) and at the level of an individual patient (n=118). These results are shown in figure 3 (panels A–B for image-level analyses and panels E–F for patient-level analyses). The ROC curve using mechanical ventilation (22 patients, 43 X-ray images) as the ground truth and the probability estimates from the DL model as predictor (figure 3A) showed an AUROC of 79.34% at the image level. The optimum cut-off point on this ROC had a sensitivity and specificity of 70% and 84%, respectively. The confusion matrix (figure 3B) showed that the performance of the DL model was good with a high accuracy (0.7974), good recall, precision and F1 score (0.6976, 0.6250 and 0.6593) as well as a good Cohen’s kappa (0.5158).
We replicated these analyses at the level of the patient with the maximum predicted probability (from multiple X-ray images). We observed (figure 3E) that the AUROC increased to 90.06% with an optimum sensitivity and specificity of 86.34% and 84.38%, respectively. Comparing these estimates with the corresponding image-level estimates (figure 3A), we found that analyses at the level of the patient yielded substantially higher sensitivity without loss of specificity. The confusion matrix for comparison of the patient-level prediction with ground truth (figure 3F) showed a markedly improved predictive performance: accuracy (0.8474), recall (0.8636), precision (0.5588), F1 score (0.6786) and Cohen’s kappa (0.5845).
Independent evaluation by PCC experts
Independent evaluations by the two PCC experts are shown as confusion matrices for image-level analyses (figure 3C,D) and patient-level analyses (figure 3G,H). Performance of both PCC experts was relatively lower as compared with the DL model at the image level as well as at the patient level. At the image level, the performance characteristics of PCC expert 1 were accuracy (0.7451), recall (0.6744), precision (0.5370), F1 score (0.5979) and Cohen’s kappa (0.4148). Similarly, the performance characteristics of PCC expert 2 at the level of images were accuracy (0.7059), recall (0.8140), precision (0.4861), F1 score (0.6087) and Cohen’s kappa (0.3962). Like the DL model performance, the performance characteristics improved when the analyses were done at the level of patients (figure 3G,H). For example, the performance characteristics of PCC expert 1 at the level of patient were accuracy (0.8051), recall (0.8636), precision (0.4872), F1 score (0.6230) and Cohen’s kappa (0.5049). For PCC expert 2, the performance characteristics were accuracy (0.7119), recall (0.9090), precision (0.3846), F1 score (0.5405) and Cohen’s kappa (0.3774). Despite these improved estimates at the level of the patient and with the exception of recall for PCC expert 2, all the performance characteristics of both the PCC experts were either on par or below the corresponding estimates for the DL model.
Incremental predictive performance of DL model
To assess the incremental predictive performance of the DL model, we conducted survival analyses with time to mechanical ventilation as the outcome of interest. These results are shown in figure 4. Kaplan-Meier plots (figure 4A–C) showed that patients predicted to need mechanical ventilation by the DL model or the PCC experts rapidly progressed to mechanical ventilation (red curves in figure 4A–C). However, the relative hazards of progressing to mechanical ventilation were highest for the DL model (15.3) as compared with those of PCC experts 1 (11.3) and PCC expert 2 (9.9) indirectly implying better prognostic stratification by the DL model. To directly assess the incremental value of the DL model over the stratification done by the PCC experts, we conducted pairwise comparisons of a series of Cox proportional-hazards models using Harrell’s C-statistic. This statistic was estimated to be 0.7454 for stratification offered by PCC expert 1 but increased to 0.8331 (improvement 0.0877, p<0.001) on addition of DL model prediction as a covariate in the Cox model (compare models 1 and 1A in figure 4D). Similarly, the addition of DL model prediction to the stratification offered by PCC expert 2 improved Harrell’s C-statistic from 0.6921 to 0.8246 (improvement 0.1325, p<0.001). Lastly, when stratifications offered by both the PCC experts were simultaneously used as covariates, Harrel’s C-statistic was estimated to be 0.7685 which increased to 0.8382 on addition of the DL model prediction as a covariate (improvement 0.0724, p=0.001). Together, the results in figure 4 demonstrate that the DL model significantly and incrementally contributed to an improved prediction of the need for and time to mechanical ventilation over and beyond the predictions obtained from two PCC experts.
Time gained by early prediction using the DL model
Lastly, we examined the time gained by using the DL model predictions for the need of mechanical ventilation. These analyses were done at the level of the patient with start point defined as the time at which the DL model first predicted the need for mechanical ventilation. Using this strategy, we observed that the median time to mechanical ventilation was 2.98 (95% CI 1.63 to 4.32) days. Thus, the DL model developed in this study predicted mechanical ventilation early at the time of or during index hospitalisation.
We have developed a novel, X-ray image-based, deep learning model to predict the need for mechanical ventilation early during hospitalisation of patients with COVID-19. Our model was accurate (90% at the level of the patient), externally validated in an independent test set and provided improved prediction as compared with the prognostic performance of stratification provided by two PCC experts. Considering the urgent need for effective rationalisation of healthcare resources for patients with COVID-19, especially the ventilators, we believe that our DL model can have an important role in critical care of patients with COVID-19. This anticipation is contingent on the observation that our DL model was able to predict the need for mechanical ventilation approximately 3 days on average ahead of the actual intubation event. It needs to be mentioned, however, that we do not anticipate that clinicians will use our DL model to make clinical decisions—rather, the DL model is intended to be used as an aid for patient triaging and informed resource allocation by hospitals.
We conducted the analyses both at the level of the images and at the level of the individual patient. This distinction is important to understand. The training of the model was indeed done using all available images, but to translate the DL predictions to clinical situations, we needed to determine whether a selected patient (rather than an X-ray image) would need mechanical ventilation. To that end, when any of the X-ray images for a patient was classified by the DL algorithm as high risk (that is likely needing mechanical ventilation), we considered that the patient should be classified as in need of mechanical ventilation. Operationally, this strategy of patient-level classification can be expected to improve the sensitivity of prediction for two reasons. First, the average per-patient X-rays ordered was higher for the patients who required mechanical ventilation as compared with those who did not (table 1). At the level of the patient, therefore, combining information from multiple X-rays is likely to predict the need for mechanical ventilation in those who eventually required mechanical ventilation. Second, the option to use any indicative X-ray as diagnostic for a patient will likely lower the diagnostic threshold making the algorithm more sensitive. A comparison of the ROC curves shown in figure 3A,E demonstrates that there indeed was a substantial improvement in sensitivity (from 70% to 86%) without loss of specificity when those analyses were done at the level of the patient rather than at the level of each X-ray image.
Previously, the CheXNeXT system10 has been used to predict 14 pathologies based on chest X-rays but not in the context of COVID-19 infection. There have been several studies15–19 to detect or diagnose COVID-19 based on chest radiographs, but deep learning attempts to prognosticate COVID-19 disease course have been few and far between. Cohen et al 20 developed an algorithm to predict patients at high risk of mortality; Zhu et al 21 have developed a deep learning method to stage disease severity, the CheXNeXt deep learning; and, recently, Li et al 22 have developed a deep-learning Siamese network to predict the Radiographic Assessment of Lung Edema (RALE) scores23 used to quantify severity of ARDS in patients with COVID-19. These landmark studies have proffered definitive directions for the potential use of chest X-rays in clinical care of critical patients. However, a direct application of these systems to predict actionable outcomes like the need for mechanical ventilation is currently lacking. Existing studies have tended to focus on different aspects of chest X-ray images for COVID-19 prognostication. For example, the primary purpose of RALE score is quantification of pulmonary oedema23 while the algorithms developed by Zhu et al 21 and Cohen et al 20 focus on identification of ground-glass opacities and the geographical extent. Considering the novelty of COVID-19 pathophysiology, we aimed to include all possible and detectable abnormalities and therefore used the CheXNeXT system that can accurately identify 14 different pathologies. In this context, it is noteworthy that using cytokine/chemokine data on hospitalised patients with COVID-19, Donlan et al 11 have shown that circulating concentration of interleukin-13 (IL-13) can predict the need for mechanical ventilation. Since IL-13 can contribute to pulmonary eosinophilia and tissue remodelling, it is thus possible that radiographically detectable texture alterations that are neither captured by the RALE score nor the CheXNeXT system may accompany these cytokine profiles. This hypothesis is, in part, supported by investigations in COVID-19 negative patients.24 25 Whether such a correlation exists within the context of COVID-19 is currently unknown. In totality, these previous studies provide a possible biological explanation as to why chest radiographs can predict the need for mechanical ventilation in immediate future.
The results of our study should be considered in the light of some limitations. First, this was a retrospective, observational evaluation and the confounding and bias implicit in such an investigation will remain a limitation. Second, the data for this study were derived from a single centre and the generalisability of this approach to other settings needs to be established in further studies. Third, we restricted our model to the use of chest radiographs only. However, additional clinical parameters at the time of hospital admission such as respiratory rate, oxygenation status (eg, the ROX index)26 and altered mental status27 along with sociodemographic characteristics, comorbidity profile and laboratory investigations can potentially further improve the prediction. Future studies need to evaluate these possibilities, but our focus was to use an objective measure such as a chest radiograph and provide a tool to the critical care provider with a reasonable expectation of the future course of disease in a given patient. Fourth, we used Harrel’s C statistic as a measure of the predictive accuracy of the Cox regression models. In the setting of a binary outcome, Harrell’s C statistic behaves statistically similar to the AUROC curve. This behaviour of the statistic is however influenced by censoring in the context of survival analyses. This is generally considered as a limitation of Harrell’s C statistic for Cox models.28 Alternative methods like Uno’s C statistic28 and time-dependent receiver operating characteristic curves29 are available for the survival analysis framework. Notwithstanding these methodological nuances, since comparison of two models on the same set of patients with the same censoring characteristics was undertaken in our study, a comparison in Harrell’s C statistics did provide us with an estimate of the improved prediction by the DL model over that of the PCC experts. Fifth, the evaluation of the X-rays by the PCC experts was done retrospective solely for the purpose of this research and not as a part of routine patient care. Also, currently there are no clinical protocols in place to predict the need for mechanical ventilation based on chest radiography. Therefore, whether the DL model supersedes the PCC experts in terms of the time gained in advance cannot be answered based on this study. Future studies need to address that question specifically.
Until effective preventive and management options for patients with COVID-19 become widely available, consorted efforts that reduce the risks to the patient and thus the burden on healthcare system are needed. To that end, our study demonstrates a proof-of-principle that chest X-ray images acquired early during hospitalisation can accurately predict the need for mechanical ventilation in patients with COVID-19. Such a tool can be valuable in effectively triaging patients with COVID-19 at the time of initial healthcare contact.
Data availability statement
Data and code are available from the author on reasonable request.
The study was approved by the Institutional Review Board of the Cook County Health, Chicago, IL (Approval No. 20-038 x).
ARK and AMA contributed equally.
Contributors AMA and HK conceptualised the study; ARK and HK conceptualised the deep learning solution; ARK wrote Python scripts, trained and tested the model; AsS and SS provided expertise in pulmonary and critical care; AbS, MI, SZ, JV, MA, AJ, AA and JR participated in data collection along with AMA; HK conducted statistical analyses; AMA, ARK and HK wrote the first draft of the manuscript; all authors reviewed and approved the final manuscript. AMA and HK are the guarantors of this manuscript and take responsibility for data integrity, analytical accuracy and draft writing.
Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
Competing interests None declared.
If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.