The increase in complexity of engineered systems and naturally occurring systems, coupled with increasingly data-driven representations of these systems motivates the need for design of experiment frameworks for nonlinear system identification. In the case of a general nonlinear autonomous system (without inputs or control), designing an experiment for identification relies on the selection of persistently exciting flows and their corresponding initial conditions. This work investigates persistence of excitation conditions for discrete-time nonlinear systems that can be represented using Koopman operators. The Koopman operator presents a linear lifted representation of the evolution of a nonlinear system over a space of observable functions. We use this framework to derive spectral conditions for persistence of excitation, relating classical notions of persistence of excitation to the spectral properties of initial conditions, seen through the lens of Koopman observable functions . We illustrate these concepts on a repressilator circuit , a classical biological system from the field of synthetic biology, to motivate the proper selection of initial conditions. We show that when the rank properties of the flow's spectra are degenerate, the trained Koopman operator does not produce robust predictions on test data .
It is hard to identify nonlinear biological models strictly from data, with results that are often sensitive to experimental conditions. Automated experimental workflows and liquid handling enables unprecedented throughput, as well as the capacity to generate extremely large datasets. We seek to develop generalized identifiability conditions for informing the design of automated experiments to discover predictive nonlinear biological models. For linear systems, identifiability is characterized by persistence of excitation conditions. For nonlinear systems, no such persistence of excitation conditions exist. We use the input-Koopman operator method to model nonlinear systems and derive identifiability conditions for open-loop systems initialized from a single initial condition. We show that nonlinear identifiability is intrinsically tied to the rank of a given dataset's power spectral density, transformed through the lifted Koopman observable space . We illustrate these identifiability conditions with a simulated synthetic gene circuit model, the repressilator. We illustrate how rank degeneracy in datasets results in overfitted nonlinear models of the repressilator, resulting in poor predictive accuracy. Our findings provide novel experimental design criteria for discovery of globally predictive nonlinear models of biological phenomena .
R
The increase in complexity of engineered systems and naturally occurring systems, coupled with increasingly data-driven representations of these systems motivates the need for design of experiment frameworks for nonlinear system identification. In the case of a general nonlinear autonomous system (without inputs or control), designing an experiment for identification relies on the selection of persistently exciting flows and their corresponding initial conditions. This work investigates
It is hard to identify nonlinear biological models strictly from data, with results that are often sensitive to experimental conditions. Automated experimental workflows and liquid handling enables unprecedented throughput, as well as the capacity to generate extremely large datasets. We seek to develop generalized identifiability conditions for informing the design of automated experiments to discover predictive nonlinear biological models. For linear systems, identifiability is characterized by persistence of excitation conditions. For nonlinear systems, no such
R
for discrete-time nonlinear systems that can be represented using Koopman operators. The Koopman operator presents a linear lifted representation of the evolution of a nonlinear system over a space of observable functions. We use this framework to derive spectral conditions for persistence of excitation, relating classical notions of persistence of excitation to the spectral properties of initial conditions, seen through the lens of Koopman observable functions
exist. We use the input-Koopman operator method to model nonlinear systems and derive identifiability conditions for open-loop systems initialized from a single initial condition. We show that nonlinear identifiability is intrinsically tied to the rank of a given dataset's power spectral density, transformed through the lifted Koopman observable space
R
concepts on a repressilator circuit , a classical biological system from the field of synthetic biology, to motivate the proper selection of initial conditions. We show that when the rank properties of the flow's spectra are degenerate, the trained Koopman operator does not produce robust predictions on test data
identifiability conditions with a simulated synthetic gene circuit model, the repressilator. We illustrate how rank degeneracy in datasets results in overfitted nonlinear models of the repressilator, resulting in poor predictive accuracy. Our findings provide novel experimental design criteria for discovery of globally predictive nonlinear models of biological phenomena