LogGENE: A smooth alternative to check loss for Deep Healthcare Inference Tasks

High-throughput Genomics is ushering a new era in personalized health care, and targeted drug design and delivery. Mining these large datasets, and obtaining calibrated predictions is of immediate relevance and utility. In our work, we develop methods for Gene Expression Inference based on Deep neural networks. However, unlike typical Deep learning methods, our inferential technique, while achieving state-of-the-art performance in terms of accuracy, can also provide explanations, and report uncertainty estimates. We adopt the Quantile Regression framework to predict full conditional quantiles for a given set of house keeping gene expressions. Conditional quantiles, in addition to being useful in providing rich interpretations of the predictions, are also robust to measurement noise. However, check loss, used in quantile regression to drive the estimation process is not differentiable. We propose log-cosh as a smooth-alternative to the check loss. We apply our methods on GEO microarray dataset. We also extend the method to binary classification setting. Furthermore, we investigate other consequences of the smoothness of the loss in faster convergence.