Differential privacy preserved federated learning for prognostic modeling in COVID-19 patients using large multi-institutional chest CT dataset.

BACKGROUND: Notwithstanding the encouraging results of previous studies reporting on the efficiency of deep learning (DL) in COVID-19 prognostication, clinical adoption of the developed methodology still needs to be improved. To overcome this limitation, we set out to predict the prognosis of a large multi-institutional cohort of patients with COVID-19 using a DL-based model. PURPOSE: This study aimed to evaluate the performance of deep privacy-preserving federated learning (DPFL) in predicting COVID-19 outcomes using chest CT images. METHODS: After applying inclusion and exclusion criteria, 3055 patients from 19 centers, including 1599 alive and 1456 deceased, were enrolled in this study. Data from all centers were split (randomly with stratification respective to each center and class) into a training/validation set (70%/10%) and a hold-out test set (20%). For the DL model, feature extraction was performed on 2D slices, and averaging was performed at the final layer to construct a 3D model for each scan. The DensNet model was used for feature extraction. The model was developed using centralized and FL approaches. For FL, we employed DPFL approaches. Membership inference attack was also evaluated in the FL strategy. For model evaluation, different metrics were reported in the hold-out test sets. In addition, models trained in two scenarios, centralized and FL, were compared using the DeLong test for statistical differences. RESULTS: The centralized model achieved an accuracy of 0.76, while the DPFL model had an accuracy of 0.75. Both the centralized and DPFL models achieved a specificity of 0.77. The centralized model achieved a sensitivity of 0.74, while the DPFL model had a sensitivity of 0.73. A mean AUC of 0.82 and 0.81 with 95% confidence intervals of (95% CI: 0.79-0.85) and (95% CI: 0.77-0.84) were achieved by the centralized model and the DPFL model, respectively. The DeLong test did not prove statistically significant differences between the two models (p-value = 0.98). The AUC values for the inference attacks fluctuate between 0.49 and 0.51, with an average of 0.50 ± 0.003 and 95% CI for the mean AUC of 0.500 to 0.501. CONCLUSION: The performance of the proposed model was comparable to centralized models while operating on large and heterogeneous multi-institutional datasets. In addition, the model was resistant to inference attacks, ensuring the privacy of shared data during the training process.

Deep Learning-based calculation of patient size and attenuation surrogates from localizer Image: Toward personalized chest CT protocol optimization.

PURPOSE: Extracting water equivalent diameter (DW), as a good descriptor of patient size, from the CT localizer before the spiral scan not only minimizes truncation errors due to the limited scan field-of-view but also enables prior size-specific dose estimation as well as scan protocol optimization. This study proposed a unified methodology to measure patient size, shape, and attenuation parameters from a 2D anterior-posterior localizer image using deep learning algorithms without the need for labor-intensive vendor-specific calibration procedures. METHODS: 3D CT chest images and 2D localizers were collected for 4005 patients. A modified U-NET architecture was trained to predict the 3D CT images from their corresponding localizer scans. The algorithm was tested on 648 and 138 external cases with fixed and variable table height positions. To evaluate the performance of the prediction model, structural similarity index measure (SSIM), body area, body contour, Dice index, and water equivalent diameter (DW) were calculated and compared between the predicted 3D CT images and the ground truth (GT) images in a slicewise manner. RESULTS: The average age of the patients included in this study (1827 male and 1554 female) was 53.8 ± 17.9 (18-120) years. The DW, tube current ,and CTDIvol measured on original axial images in the external 138 cases group were significantly larger than those of the external 648 cases (P < 0.05). The SSIM and Dice index calculated between the prediction and GT for body contour were 0.998 ± 0.001 and 0.950 ± 0.016, respectively. The average percentage error in the calculation of DW was 2.7 ± 3.5 %. The error in the DW calculation was more considerable in larger patients (p-value < 0.05). CONCLUSIONS: We developed a model to predict the patient size, shape, and attenuation factors slice-by-slice prior to spiral scanning. The model exhibited remarkable robustness to table height variations. The estimated parameters are helpful for patient dose reduction and protocol optimization.

COVID-19 prognostic modeling using CT radiomic features and machine learning algorithms: Analysis of a multi-institutional dataset of 14,339 patients.

BACKGROUND: We aimed to analyze the prognostic power of CT-based radiomics models using data of 14,339 COVID-19 patients. METHODS: Whole lung segmentations were performed automatically using a deep learning-based model to extract 107 intensity and texture radiomics features. We used four feature selection algorithms and seven classifiers. We evaluated the models using ten different splitting and cross-validation strategies, including non-harmonized and ComBat-harmonized datasets. The sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were reported. RESULTS: In the test dataset (4,301) consisting of CT and/or RT-PCR positive cases, AUC, sensitivity, and specificity of 0.83 ± 0.01 (CI95%: 0.81-0.85), 0.81, and 0.72, respectively, were obtained by ANOVA feature selector + Random Forest (RF) classifier. Similar results were achieved in RT-PCR-only positive test sets (3,644). In ComBat harmonized dataset, Relief feature selector + RF classifier resulted in the highest performance of AUC, reaching 0.83 ± 0.01 (CI95%: 0.81-0.85), with a sensitivity and specificity of 0.77 and 0.74, respectively. ComBat harmonization did not depict statistically significant improvement compared to a non-harmonized dataset. In leave-one-center-out, the combination of ANOVA feature selector and RF classifier resulted in the highest performance. CONCLUSION: Lung CT radiomics features can be used for robust prognostic modeling of COVID-19. The predictive power of the proposed CT radiomics model is more reliable when using a large multicentric heterogeneous dataset, and may be used prospectively in clinical setting to manage COVID-19 patients.

COLI-Net: Deep learning-assisted fully automated COVID-19 lung and infection pneumonia lesion detection and segmentation from chest computed tomography images.

We present a deep learning (DL)-based automated whole lung and COVID-19 pneumonia infectious lesions (COLI-Net) detection and segmentation from chest computed tomography (CT) images. This multicenter/multiscanner study involved 2368 (347'259 2D slices) and 190 (17 341 2D slices) volumetric CT exams along with their corresponding manual segmentation of lungs and lesions, respectively. All images were cropped, resized, and the intensity values clipped and normalized. A residual network with non-square Dice loss function built upon TensorFlow was employed. The accuracy of lung and COVID-19 lesions segmentation was evaluated on an external reverse transcription-polymerase chain reaction positive COVID-19 dataset (7'333 2D slices) collected at five different centers. To evaluate the segmentation performance, we calculated different quantitative metrics, including radiomic features. The mean Dice coefficients were 0.98 ± 0.011 (95% CI, 0.98-0.99) and 0.91 ± 0.038 (95% CI, 0.90-0.91) for lung and lesions segmentation, respectively. The mean relative Hounsfield unit differences were 0.03 ± 0.84% (95% CI, -0.12 to 0.18) and -0.18 ± 3.4% (95% CI, -0.8 to 0.44) for the lung and lesions, respectively. The relative volume difference for lung and lesions were 0.38 ± 1.2% (95% CI, 0.16-0.59) and 0.81 ± 6.6% (95% CI, -0.39 to 2), respectively. Most radiomic features had a mean relative error less than 5% with the highest mean relative error achieved for the lung for the range first-order feature (-6.95%) and least axis length shape feature (8.68%) for lesions. We developed an automated DL-guided three-dimensional whole lung and infected regions segmentation in COVID-19 patients to provide fast, consistent, robust, and human error immune framework for lung and pneumonia lesion detection and quantification.

Deep learning-based fully automated Z-axis coverage range definition from scout scans to eliminate overscanning in chest CT imaging.

BACKGROUND: Despite the prevalence of chest CT in the clinic, concerns about unoptimized protocols delivering high radiation doses to patients still remain. This study aimed to assess the additional radiation dose associated with overscanning in chest CT and to develop an automated deep learning-assisted scan range selection technique to reduce radiation dose to patients. RESULTS: A significant overscanning range (31 ± 24) mm was observed in clinical setting for over 95% of the cases. The average Dice coefficient for lung segmentation was 0.96 and 0.97 for anterior-posterior (AP) and lateral projections, respectively. By considering the exact lung coverage as the ground truth, and AP and lateral projections as input, The DL-based approach resulted in errors of 0.08 ± 1.46 and - 1.5 ± 4.1 mm in superior and inferior directions, respectively. In contrast, the error on external scout views was - 0.7 ± 4.08 and 0.01 ± 14.97 mm for superior and inferior directions, respectively.The ED reduction achieved by automated scan range selection was 21% in the test group. The evaluation of a large multi-centric chest CT dataset revealed unnecessary ED of more than 2 mSv per scan and 67% increase in the thyroid absorbed dose. CONCLUSION: The proposed DL-based solution outperformed previous automatic methods with acceptable accuracy, even in complicated and challenging cases. The generizability of the model was demonstrated by fine-tuning the model on AP scout views and achieving acceptable results. The method can reduce the unoptimized dose to patients by exclunding unnecessary organs from field of view.