Deep generative models for single-cell and spatial genomics by Ajita Shree

Speaker: Ms. Ajita Shree is a PhD student in the Department of Computer Science and Engineering at IIT Kanpur and will be joining EMBL-EBI, UK, as a postdoctoral researcher.

Abstract: Recent advances in large-scale genomic assays, including single-cell and spatial transcriptomics (ST), have provided unprecedented insights into the biological mechanisms underlying development, disease, and therapeutic response. However, these datasets pose significant computational challenges.

One of the major challenges is the integration of heterogeneous single-cell datasets across donors, time points, and experimental conditions to create a unified resource for downstream analysis. In this talk, I will present scDREAMER, a novel deep generative model that can perform integration of multi-batch single-cell datasets in unsupervised, semi-supervised and supervised settings. Using real benchmarking datasets, we demonstrate that scDREAMER can overcome critical challenges including skewed cell type distribution among batches, nested batch-effects, large number of batches and enables integration of millions of cells across species.

Further, I will discuss the emerging field of spatial genomics, which enables the study of gene expression at a spatial level, but its spot-level resolution poses challenges in resolving cell-type contributions in situ. This has spurred extensive development of deconvolution methods, yet evaluation remains lacking. In this work, we present a novel graph attention auto-encoder for simulating spatial cell type distributions from three major tissue types including brain, cancer and organs, and performed a comprehensive benchmarking.

Bio: Ajita Shree is a PhD student in the Department of Computer Science and Engineering at IIT Kanpur and will be joining EMBL-EBI, UK, as a postdoctoral researcher. Previously, she worked for three years as a Data Scientist at GE Aerospace and GE Global Research, and was a graduate of GE’s Global Leadership Program. She earned her M.Tech. in Computer Science and Engineering from IIT Delhi in 2017 and holds a B.Tech. in Computer Science and Engineering.