LuMiRa: An Integrated Lung Deformation Atlas and 3D-CNN Model of Infiltrates for COVID-19 Prognosis

Although, recently convolutional neural networks (CNNs) based prognostic models have been developed for COVID-19 severity prediction, most of these studies have analyzed characteristics of lung infiltrates (ground-glass opacities and consolidations) on chest radiographs or CT. However, none of the studies have explored the possible lung deformations due to the disease. Our hypothesis is that more severe disease results in more pronounced deformation. The key contributions of this work are three-fold: (1) A new lung deformation based biomarker analyzing regions of differential distensions between COVID-19 patients with mild and severe disease. (2) Integrating 3D-CNN characterization of lung deformation regions and lung infiltrates on lung CT into a novel framework (LuMiRa) for prognosticating COVID-19 severity. (3) Validating LuMiRa on one of the largest multi-institutional cohort till date (N = 948 patients). We found that majority of the shape deformations were observed in the mediastinal surface of both the lungs and in left interior lobe. On a testing cohort based on two institutions, Av (N = 419) and Bv (N = 113), LuMiRa yielded an area under the receiver operating characteristic curve (AUC) of 0.89 and 0.77 respectively showing significant improvement over a 3D-CNN trained over just lung infiltrates (AUC = 0.85 (p < 0.001), AUC = 0.75 (p = 0.01)). Additionally, LuMiRa performed significantly better than machine learning models trained on clinical and radiomic features (0.82, 0.78 and 0.72, 0.72 on Av and Bv respectively).