Skip to content Skip to navigation

Data denoising and transfer learning in single cell transcriptomics

Tuesday, May 26, 2020 - 4:30pm

Speaker:   Nancy Zhang, University of Pennsylvania

Abstract:   Cells are the basic biological units of multicellular organisms. The development of single-cell RNA sequencing (scRNA-seq) technologies have enabled us to study the diversity of cell types in tissue and to elucidate the roles of individual cell types in disease. Yet, scRNA-seq data are noisy and sparse, with only a small proportion of the transcripts that are present in each cell represented in the final data matrix. We propose a transfer learning framework based on deep neural nets to borrow information across related single cell data sets for denoising and expression recovery. Our goal is to leverage the expanding resources of publicly available scRNA-seq data, for example, the Human Cell Atlas which aims to be a comprehensive map of cell types in the human body. Our method is based on a Bayesian hierarchical model coupled to a deep autoencoder, the latter trained to extract transferable gene expression features across studies coming from different labs, generated by different technologies, and/or obtained from different species. Through this framework, we explore the limits of data sharing: How much can be learned across cell types, tissues, and species? How useful are data from other technologies and labs in improving the estimates from your own study? If time allows, I will also discuss the implications of such data denoising to downstream statistical inference.