Toward Foundation Models of Cellular Morphology, Juan C. Caicedo

Speaker: Juan C. Caicedo, PhD, Morgridge Investigator and Assistant Professor, Biostatistics and Medical Informatics, UW-Madison

Date: Tuesday, March 19th, 2024

Time: 10:00 AM Central Time

Location: WIMR 2409 and Zoom

Title: Toward Foundation Models of Cellular Morphololgy

Abstract: Cellular morphology can reveal the response of cells under a diverse set of experimental conditions, including chemical and genetic perturbations, which has many applications in drug discovery and functional genomics research. The main strategy for obtaining cellular morphology readouts relies on microscopy imaging and computing methods. In this talk, we describe our research efforts for building a foundation model of cellular morphology using large scale self-supervised learning. One of the major challenges of microscopy imaging in biological sciences is the wide diversity of imaging protocols, including microscope settings, and specifically the number of channels that an image can have. We investigate channel-adaptive strategies that dynamically process images with any number of channels, which can extend the benefits of pre-trained models to small experiments with an unknown imaging configuration. Our results show that channel-adaptive models match the performance of specialized fixed-channel models, with lower computational cost.

Bio: Juan C. Caicedo is a Morgridge Investigator and Assistant Professor in the Biostatistics and Medical Informatics Department at the University of Wisconsin-Madison. Juan investigates the use of machine learning for bioimage analysis to power the next generation of biological discoveries. He was a Schmidt Fellow and principal investigator at the Broad Institute of MIT and Harvard, where he also was a postdoctoral researcher. Before focusing on biological image analysis, Juan’s research spanned various computer vision problems, including image enhancement, image search, and object detection. As a graduate student, he conducted research projects at Google and Microsoft Research, and later was a research associate at Queen Mary University of London, and a postdoctoral researcher at the University of Illinois in Urbana-Champaign.