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Matthew S. Schmitt

Publications and source records attributed to Matthew S. Schmitt.

2 recordsLinked to original sources

Information theory for dimensionality reduction in dynamical systems

The dynamics of many-body systems can often be captured in terms of only a few relevant variables. Mathematical and numerical approaches exist to identify these variables by exploiting a separation of time scales between slow relevant and fast irrelevant variables, but such a separation of scales is not always obvious or even available. In this work, we introduce an information-theoretic framework for dimensionality reduction in dynamical systems that bypasses this limitation by instead identifying relevant variables based on how predictive they are of the system's future. To do so, we mathematically formalize the intuition that model reduction is about keeping "relevant" information while throwing away "irrelevant" information. We characterize the solution of the resulting optimization problem and prove that it reduces to standard approaches when a separation of time scales is indeed present in the dynamics. Importantly, we find that within this framework, the problems of identifying relevant variables and identifying their effective dynamics decouple and may be solved separately. This makes the method tractable in practice and enables us to derive dimensionally-reduced variables from data with neural networks. Combined with existing equation learning methods, the procedure introduced in this work reveals the dynamical rules governing the system's evolution in a data-driven manner. We illustrate these tools in diverse settings including simulated chaotic systems, uncurated satellite recordings of atmospheric fluid flows, and experimental videos of cyanobacteria colonies in which we discover an emergent synchronization order parameter.

cond-mat.stat-mech↗

Zyxin is all you need: machine learning adherent cell mechanics

Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

physics.bio-ph↗