CAD-RADS scoring of coronary CT angiography with Multi-Axis Vision Transformer: a clinically-inspired deep learning pipeline

The standard non-invasive imaging technique used to assess the severity and extent of Coronary Artery Disease (CAD) is Coronary Computed Tomography Angiography (CCTA). However, manual grading of each patient's CCTA according to the CAD-Reporting and Data System (CAD-RADS) scoring is time-consuming and operator-dependent, especially in borderline cases. This work proposes a fully automated, and visually explainable, deep learning pipeline to be used as a decision support system for the CAD screening procedure. The pipeline performs two classification tasks: firstly, identifying patients who require further clinical investigations and secondly, classifying patients into subgroups based on the degree of stenosis, according to commonly used CAD-RADS thresholds. The pipeline pre-processes multiplanar projections of the coronary arteries, extracted from the original CCTAs, and classifies them using a fine-tuned Multi-Axis Vision Transformer architecture. With the aim of emulating the current clinical practice, the model is trained to assign a per-patient score by stacking the bi-dimensional longitudinal cross-sections of the three main coronary arteries along channel dimension. Furthermore, it generates visually interpretable maps to assess the reliability of the predictions. When run on a database of 1873 three-channel images of 253 patients collected at the Monzino Cardiology Center in Milan, the pipeline obtained an AUC of 0.87 and 0.93 for the two classification tasks, respectively. According to our knowledge, this is the first model trained to assign CAD-RADS scores learning solely from patient scores and not requiring finer imaging annotation steps that are not part of the clinical routine.

Rapid quantification of COVID-19 pneumonia burden from computed tomography with convolutional LSTM networks

Quantitative lung measures derived from computed tomography (CT) have been demonstrated to improve prognostication in coronavirus disease (COVID-19) patients, but are not part of the clinical routine since required manual segmentation of lung lesions is prohibitively time-consuming. We propose a new fully automated deep learning framework for rapid quantification and differentiation between lung lesions in COVID-19 pneumonia from both contrast and non-contrast CT images using convolutional Long Short-Term Memory (ConvLSTM) networks. Utilizing the expert annotations, model training was performed 5 times with separate hold-out sets using 5-fold cross-validation to segment ground-glass opacity and high opacity (including consolidation and pleural effusion). The performance of the method was evaluated on CT data sets from 197 patients with positive reverse transcription polymerase chain reaction test result for SARS-CoV-2. Strong agreement between expert manual and automatic segmentation was obtained for lung lesions with a Dice score coefficient of 0.876 $\pm$ 0.005; excellent correlations of 0.978 and 0.981 for ground-glass opacity and high opacity volumes. In the external validation set of 67 patients, there was dice score coefficient of 0.767 $\pm$ 0.009 as well as excellent correlations of 0.989 and 0.996 for ground-glass opacity and high opacity volumes. Computations for a CT scan comprising 120 slices were performed under 2 seconds on a personal computer equipped with NVIDIA Titan RTX graphics processing unit. Therefore, our deep learning-based method allows rapid fully-automated quantitative measurement of pneumonia burden from CT and may generate results with an accuracy similar to the expert readers.