ANC Workshop - Oisin Mac Aodha, Yuelin Yao
Tuesday, 30th April 2024
High order expression dependencies finely resolve cell states and subtypes in single cell data - Yuelin Yao
Abstract: Single cells are typically typed by clustering in reduced dimensional transcriptome space. Here we introduce Stator, a novel method, workflow and app that reveals cell types, subtypes and states without relying on local proximity of cells in gene expression space. Rather, Stator derives higher-order gene expression dependencies from a sparse gene-by-cell expression matrix. From these dependencies the method multiply labels the same single cell according to type, sub-type and state (activation, differentiation or cell cycle sub-phase). By applying the method to data from mouse embryonic brain, and human healthy or diseased liver, we show how Stator first recapitulates other methods’ cell type labels, and then reveals combinatorial gene expression markers of cell type, state, and disease at higher resolution. By allowing multiple state labels for single cells we reveal cell type fates of embryonic progenitor cells and liver cancer states associated with patient survival.
Learning in Fine-Grained Visual Domains - Oisin Mac Aodha
Abstract: The visual concepts depicted in images from domains such as medicine, biodiversity monitoring, and biological imaging are inherently “fine-grained”. By this, we mean that distinct visual concepts may appear very similar to the untrained eye. Learning these subtle differences can be very challenging in low data regimes where expert annotations are not easily available. In this talk, I will provide an overview of recent research from my group on this topic. I will present work on learning 3D representations of images without requiring explicit 3D supervision, new methods for automatically discovering visual concepts in data, models for estimating the spatial distribution of fine-grained categories, and ongoing work to develop a new dataset for text-based retrieval of fine-grained visual concepts.
Event type: Workshop
Date: Tuesday, 30th April
Time: 11:00
Location: G.03
Speaker(s): Oisin Mac Aodha, Yuelin Yao
Chair/Host: Saber Mirzaee Bafti