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NITMB Seminar Series Recordings

Veronica Ciocanel

Recorded on 11/08/2024

Title: Parameter identifiability for PDE models of fluorescence microscopy experiments

Abstract: The dynamics of intracellular proteins is key to many cellular functions. One of the most versatile experimental techniques for probing protein dynamics in living cells is FRAP (fluorescence recovery after photobleaching). This experiment generates time-series data that average out spatial information about diffusion, transport, and binding dynamics of proteins. Partial differential equations (PDE) models provide the appropriate framework to model the fluorescence dynamics and to infer parameters such as diffusion coefficients or reaction rates. However, it is not known whether these parameters can be identified based on the spatially-averaged data available from FRAP experiments. We recently investigated limitations of known methods in assessing parameter identifiability for PDE models and proposed methods for learning parameter combinations based on re-parametrization and profile likelihoods analysis. In this work, our motivation stems from studying dynamic RNA binding proteins in biomolecular condensates that play key roles in the development of frog oocytes.

Jorge Nocedal

Recorded on 10/25/2024

Title: How is it Possible to Train Deep Neural Networks?

Abstract: In 1961, Minsky, one of the founders of AI, perceived a fundamental flaw within the burgeoning field of artificial neural networks. He doubted that such a nonlinear system could be effectively trained using gradient methods, because unless the “structure of the search space is special, the optimization may do more harm than good.” Fast forward to today, and we observe deep neural networks — far more complex than those envisioned at the field's inception — being successfully trained with methods akin to gradient descent. It has, indeed, become evident that the objective function displays a highly benign structure that we are only starting to comprehend. In this lecture, I aim to summarize our current understanding of this enigmatic optimization process. I will discuss several themes, including intrinsic dimensionality, the optimization landscape, and implicit regularization, all within the context of deep networks and large language models. Speaker Bio: Jorge Nocedal is the Walter P. Murphy Professor of Industrial Engineering and Management Sciences and (by courtesy) Engineering Sciences and Applied Mathematics at Northwestern University. Nocedal is also the Director of the Center for Optimization and Statistical Learning. Nocedal's main area of research is optimization, with applications in machine learning, engineering design, and the physical sciences. Research activities range from the design of new algorithms, to their software implementation and mathematical analysis. Areas of emphasis include large scale problems (with millions of variables), optimization under uncertainty, and parallel computing.

Thomas P Wytock

Recorded on 10/11/2024

Title: Cell reprogramming and bacterial memory predicted by mathematical modeling and transfer learning

Abstract: Determining how molecular changes propagate to affect the whole cell is a fundamental goal in systems biology. The challenge inherent to this pursuit is the number and diversity of molecular entities that give rise to cell behavior. In this talk, I will show how nonlinear dynamics and machine learning uncover unexpected behaviors in recent studies concerning irreversibility in bacterial regulatory networks [1] and cell reprogramming [2]. In the first study, Boolean networks reveal that the same DNA sequence can counterintuitively encode multiple behaviors through information stored in the state of the gene regulatory network. In the second study, a machine learning model provides an effective representation of the regulatory interactions between genes and cell phenotypes. We use this model to identify gene perturbations that can reprogram cells to different phenotypes. Both contributions demonstrate how the abundance of biological data provides opportunities for mathematical modeling to derive unexpected insights. Speaker Bio: Thomas P. Wytock is a postdoctoral researcher in the Motter Group at Northwestern University, where he focuses on the modeling of genetic networks.

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