Computational Cell Biology Faculty Candidate Research Seminar – Dr. Yuchi Qiu

Speaker: Dr. Yuchi Qiu – Postdoc, University of California, Department of Mathematics

This seminar will be presented in a hybrid format. The speaker will be delivering their talk in person at the MSL Lecture Theatre (room 102). Audience members are welcome to attend either in person or via the zoom link. Those connecting via zoom will be able to ask questions during the Q&A portion using the chat function.

Zoom link: https://ubc.zoom.us/meeting/register/u50tdOqqrTIpHNUyC3gCxGnQFmk4UyWvIc1N

Talk title: Multiscale modeling and topological data analysis in artificial intelligence-driven biology

Abstract: Artificial intelligence (AI), powerful in analyzing complex biological data, has challenges in interpretability for underlying mechanisms. This talk addresses these by integrating AI with multiscale modeling and topological data analysis (TDA). We’ll discuss a data-driven model that utilizes high-dimensional partial differential equations (PDEs) for reconstructing cellular dynamics and gene regulatory networks from time-course single-cell transcriptomics data. The model is formulated within an unbalanced dynamic optimal transport framework, and we have developed a deep learning-based solver for it. Through interdisciplinary collaborations, we have also developed multiscale models for embryonic pattern formation in zebrafish hindbrain and Drosophila wing discs, as well as mouse skin wound healing. These models employ moving- boundary PDEs, stochastic simulations, and subcellular element methods. Additionally, we’ll discuss TDA-enhanced AI models for protein design that integrate a persistent spectral Laplacian, protein language models, and a hierarchical clustering-based decision-making method. Finally, the talk will conclude with future perspectives on investigating cell-cell communications in spatial transcriptomics by integrating approaches in AI, multiscale modeling and TDA.