Overview
Title: Data-driven modeling of complex biological systems
Abstract:
Finding simple data-driven and interpretable models of complex biological systems requires engaging with experimental and real-world data, which often come with a range of challenges. Typical biological data sets often feature sources of extrinsic and intrinsic noise, infrequent temporal sampling of the dynamics, and, usually, not all relevant states of the system can be experimentally measured. Additionally, for many biological systems, the true dimensionality is unknown. In this talk, I walk through a series of recent modeling projects using experimental and real-world data, each featuring a different data-related challenge. In particular, I will discuss using wolves as an ecological control strategy to limit the spread of Chronic Wasting Disease in deer populations, an inference problem in which we fit 13,824 separate gene regulatory network models to an RNA-seq data set in an attempt to learn what can honestly be said about the underlying regulatory mechanism, and using model selection for partially observed systems to infer a physiological model of the thermoregulatory system for Arctic hibernators. Finally, I will describe recent ongoing work using a super high-dimensional spatio-temporal data set from the City of Chicago, in which we attempt to understand the city as a cellular organism and infer its “organelles” directly from data.
Cody Fitzgerald is a James S. McDonnell Foundation Postdoctoral Fellow at Northwestern University. He is interested in understanding how different organisms use environmental cues to make developmental and seasonal decisions. This work involves various techniques from applied mathematics and data science and close collaborations with experimental biologists.
The NSF-Simons National Institute for Theory and Mathematics in Biology Seminar Series aims to bring together a mix of mathematicians and biologists to foster discussion and collaboration between the two fields. The seminar series will take place on Fridays from 10am – 11am at the NITMB in the John Hancock Center in downtown Chicago. There will be both an in-person and virtual component.