Data-Driven State Criticality and Observability with Koopman Operator Methods in Biological Networks

Abstract: I will present two major results to show the use of data- driven Koopman methods to identify critical states and observable subspaces to solve problems in synthetic biology. In the first, I present the use of dynamic mode decomposition (DMD) to model the transcriptome-wide response of a root-isolate bacterium to a novel chemical compound. By solving an observability maximization problem for the DMD model, we find a panel of biomarkers that can act as effective biosensors for the compound, even in field studies with the bacterium. This study establishes a new precedent for reasoning about state criticality and system observability, even without prior knowledge of a network model. Second, I present new theoretical results that show how Koopman methods can be used to evaluate criticality of states to optimize performance of a nonlinear system. Historically, this problem is solved using either direct sensitivity analysis on a known model or by generating local function distributions that span the nonlinear observable subspace of a system. In the absence of a known model, I present a new Koopman-based method for estimating the observable subspace of a nonlinear system purely from data. Our results provide a route for data-driven discovery of critical states that affect an output-based performance measure.

Bio: Enoch Yeung is an Assistant Professor in the Department of Mechanical Engineering at the University of California Santa Barbara. He is the director of the Biological Control Laboratory, which is an interdisciplinary laboratory that aims to bring together expertise in control theory, synthetic biology, and systems biology to develop new mechanisms for biological control and computing. Prior to his appointment at UCSB, Enoch was a Senior Research Scientist at the Pacific Northwest National Laboratory. He holds a PhD in Control and Dynamical Systems from the California Institute of Technology and is the recipient of the NSF CAREER award, the Army Young Investigator Program award, and a Keck Foundation award.

computational biologysystems biologybiotechnologycomputational engineering, finance, and sciencesystems and controlclassical analysis and ODEsdynamical systemsoptimization and controladaptation and self-organizing systems

Audience: researchers in the discipline

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Seminar on Biological Control Systems

Series comments: This seminar series focuses on the progress in the control of biological systems. The scope is broad and accommodates works addressing theoretical, computational, and experimental problems combining Systems and Synthetic Biology, Systems and Control Theory, Physics, Computer Science, and Applied Mathematics. Topics include, but are not limited to,

• Modeling, inference, simulation, analysis, filtering and control of reactions networks
• In-vivo and in-silico filtering, control and optimization of biological systems
• Understanding and engineering homeostatic behaviors in living organisms
• Understanding and exploiting noise for the analysis and the design of biological systems
• Fundamental limits in the control and filtering of (noisy) biological networks
• Networks as computing machines and network implementation of mathematical functions and dynamics
• Molecular tools for the implementation of in vivo or in silico control
• Realization and implementation of synthetic circuits
• Applications in biology, biotechnology, bioprocesses, environment, ecology, etc. as well as in bio-inspired design

We aim at providing a common forum for sharing knowledge and encouraging discussion and collaboration across subfields. In particular we aim at facilitating interactions between junior and established researchers in order to foster career development in academia and industry. These considerations are reflected in the choice of speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs (for now) once a month at 11am to noon EST (observe that this webpage shows the schedule in your current time zone). Each session consists of one 45-minute talk followed by questions. Attendees are welcome to stay longer for casual discussions and questions to the speakers which are not necessarily directly related to the talk.

For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

To register to the mailing list please follow this link.

We look forward hearing about new work and meeting many of you over zoom at the address: mit.zoom.us/j/94325327926?pwd=TTBMSXlhT2xJT1lzcEM3WTZmTFpBQT09

Please also feel free to join our Slack server, where we routinely share interesting papers, talks, and relevant career development opportunities.

The organizers.

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