Latent Space Inference For Spatial Transcriptomics

Abstract

In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art methods, namely single-cell RNA sequencing and image based spatial transcriptomics can only recover a subset of this information, either full genetic expression with loss of spatial information, or spatial information with loss of resolution in sequencing data. In this project, we investigate a probabilistic machine learning method to obtain the full genetic expression information for tissues samples while also preserving their spatial coordinates. This is done through mapping both datasets to a joint latent space representation with the use of variational machine learning methods. From here, the full genetic and spatial information can be decoded and to give us greater insights on the understanding of cellular processes and pathways.