Deep Learning for Enhancing Precision Medicine

Most medical treatments have been developed aiming at the best-on-average efficacy for large populations, resulting in treatments successful for some patients but not for others. It necessitates the need for precision medicine that tailors medical treatment to individual patients. Omics data holds comprehensive genetic information on individual variability at the molecular level and hence the potential to be translated into personalized therapy. However, the attempts to transform omics data-driven insights into clinically actionable models for individual patients have been limited. Meanwhile, advances in deep learning, one of the most promising branches of artificial intelligence, have produced unprecedented performance in various fields. Although several deep learning-based methods have been proposed to predict individual phenotypes, they have not established the state of the practice, due to instability of selected or learned features derived from extremely high dimensional data with low sample sizes, which often results in overfitted models with high variance. To overcome the limitation of omics data, recent advances in deep learning models, including representation learning models, generative models, and interpretable models, can be considered. The goal of the proposed work is to develop deep learning models that can overcome the limitation of omics data to enhance the prediction of personalized medical decisions. To achieve this, three key challenges should be addressed: 1) effectively reducing dimensions of omics data, 2) systematically augmenting omics data, and 3) improving the interpretability of omics data.