TY - JOUR AU - Sehanobish, Arijit AU - Ravindra, Neal AU - van Dijk, David PY - 2021/05/18 Y2 - 2024/03/29 TI - Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks JF - Proceedings of the AAAI Conference on Artificial Intelligence JA - AAAI VL - 35 IS - 6 SE - AAAI Technical Track Focus Area on AI Responses to the COVID-19 Pandemic DO - 10.1609/aaai.v35i6.16619 UR - https://ojs.aaai.org/index.php/AAAI/article/view/16619 SP - 4864-4873 AB - A molecular and cellular understanding of how SARS-CoV-2 variably infects and causes severe COVID-19 remains a bottleneck in developing interventions to end the pandemic. We sought to use deep learning (DL) to study the biology of SARS-CoV-2 infection and COVID-19 severity by identifying transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity. To do this, we developed a new approach to generating self-supervised edge features. We propose a model that builds on Graph Attention Networks (GAT), creates edge features using self-supervised learning, and ingests these edge features via a Set Transformer. This model achieves significant improvements in predicting the disease state of individual cells, given their transcriptome. We apply our model to single-cell RNA sequencing datasets of SARS-CoV-2 infected lung organoids and bronchoalveolar lavage fluid samples of patients with COVID-19, achieving state-of-the-art performance on both datasets with our model. We then borrow from the field of explainable AI (XAI) to identify the features (genes) and cell types that discriminate bystander vs. infected cells across time and moderate vs. severe COVID-19 disease. To the best of our knowledge, this represents the first application of DL to identifying the molecular and cellular determinants of SARS-CoV-2 infection and COVID-19 severity using single-cell omics data. ER -