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This paper uses data-driven operator theoretic approaches to explore the global phase space of a dynamical system. We defined conditions for discovering new invariant subspaces in the state space of a dynamical system starting from an invariant subspace based on the spectral properties of the Koopman operator. When the system evolution is known locally in several invariant subspaces in the state space of a dynamical system, a phase space stitching result is derived that yields the global Koopman operator. Additionally, in the case of equivariant systems, a phase space stitching result is developed to identify the global Koopman operator using the symmetry properties between the invariant subspaces of the dynamical system and time-series data from any one of the invariant subspaces. Finally, these results are extended to topologically conjugate dynamical systems; in particular, the relation between the Koopman tuple of topologically conjugate systems is established. The proposed results are demonstrated on several second-order nonlinear dynamical systems including a bistable toggle switch. Our method elucidates a strategy for designing discovery experiments: experiment execution can be done in many steps, and models from different invariant subspaces can be combined to approximate the global Koopman operator., Comment: 32 pages, 19 figures. This paper is currently under review

Dictionary methods for system identification typically rely on one set of measurements to learn governing dynamics of a system. In this paper, we investigate how fusion of output measurements with state measurements affects the dictionary selection process in Koopman operator learning problems. While prior methods use dynamical conjugacy to show a direct link between Koopman eigenfunctions in two distinct data spaces (measurement channels), we explore the specific case where output measurements are nonlinear, non-invertible functions of the system state. This setup reflects the measurement constraints of many classes of physical systems, e.g., biological measurement data, where one type of measurement does not directly transform to another. We propose output constrained Koopman operators (OC-KOs) as a new framework to fuse two measurement sets. We show that OC-KOs are effective for sensor fusion by proving that when learning a Koopman operator, output measurement functions serve to constrain the space of potential Koopman observables and their eigenfunctions. Further, low-dimensional output measurements can be embedded to inform selection of Koopman dictionary functions for high-dimensional models. We propose two algorithms to identify OC-KO representations directly from data: a direct optimization method that uses state and output data simultaneously and a sequential optimization method. We prove a theorem to show that the solution spaces of the two optimization problems are equivalent. We illustrate these findings with a theoretical example and two numerical simulations., Comment: 20 pages, 7 figures

In this paper, we propose a novel algorithm for learning the Koopman operator of a dynamical system from a \textit{small} amount of training data. In many applications of data-driven modeling, e.g. biological network modeling, cybersecurity, modeling the Internet of Things, or smart grid monitoring, it is impossible to obtain regularly sampled time-series data with a sufficiently high sampling frequency. In such situations the existing Dynamic Mode Decomposition (DMD) or Extended Dynamic Mode Decomposition (EDMD) algorithms for Koopman operator computation often leads to a low fidelity approximate Koopman operator. To this end, this paper proposes an algorithm which can compute the Koopman operator efficiently when the training data-set is sparsely sampled across time. In particular, the proposed algorithm enriches the small training data-set by appending artificial data points, which are treated as noisy observations. The larger, albeit noisy data-set is then used to compute the Koopman operator, using techniques from Robust Optimization. The efficacy of the proposed algorithm is also demonstrated on three different dynamical systems, namely a linear network of oscillators, a nonlinear system and a dynamical system governed by a Partial Differential Equation (PDE)., Comment: arXiv admin note: substantial text overlap with arXiv:1901.03024

In this paper, we develop the Koopman operator theory for dynamical systems with symmetry. In particular, we investigate how the Koopman operator and eigenfunctions behave under the action of the symmetry group of the underlying dynamical system. Further, exploring the underlying symmetry, we propose an algorithm to construct a global Koopman operator from local Koopman operators. In particular, we show, by exploiting the symmetry, data from all the invariant sets are not required for constructing the global Koopman operator; that is, local knowledge of the system is enough to infer the global dynamics.

In this work, we propose to apply the recently developed Koopman operator techniques to explore the global phase space of a nonlinear system from time-series data. In particular, we address the problem of identifying various invariant subsets of a phase space from the spectral properties of the associated Koopman operator constructed from time-series data. Moreover, in the case when the system evolution is known locally in various invariant subspaces, then a phase space stitching result is proposed that can be applied to identify a global Koopman operator. A biological system, bistable toggle switch and a second-order nonlinear system example are considered to illustrate the proposed results. The construction of this global Koopman operator is very helpful in experimental works as multiple experiments can't be run at the same time starting from several initial conditions., Comment: This version is currently under review in ACC 2020

This paper describes the optimal selection of a control policy to program the steady state of controlled nonlinear systems with hyperbolic fixed points. This work is motivated by the field of synthetic biology, in which saddle points are common (along with limit cycles), and the aim is to program cells to perform both digital and analog computation, though developing genetic digital computation has been the main focus. We frame the analog computing challenge of generating a steady state input-output function inside living cells. To program the steady state, a data-driven approach is taken wherein an approximation of the Koopman operator, identified via deep dynamic mode decomposition, is used to describe the dynamics of the system linearly. The new representation of the dynamics are then used to solve an optimization problem for the input which maximizes a direction in state space. Some added structure on the Koopman operator learning process for controlled systems is given for dynamics that are separable in the state and input. Finally, the methods are demonstrated on simulation examples of an incoherent feedforward loop and a combinatorial promoter system, two common network architectures seen in the field of synthetic biology., Comment: 7 pages, 3 figures, accepted in 2020 American Control Conference

Genetic circuits are designed to implement certain logic in living cells, keeping burden on the host cell minimal. However, manipulating the genome often will have a significant impact for various reasons (usage of the cell machinery to express new genes, toxicity of genes, interactions with native genes, etc.). In this work we utilize Koopman operator theory to construct data-driven models of transcriptomic-level dynamics from noisy and temporally sparse RNAseq measurements. We show how Koopman models can be used to quantify impact on genetic circuits. We consider an experimental example, using high-throughput RNAseq measurements collected from wild-type E. coli, single gate components transformed in E. coli, and a NAND circuit composed from individual gates in E. coli, to explore how Koopman subspace functions encode increasing circuit interference on E. coli chassis dynamics. The algorithm provides a novel method for quantifying the impact of synthetic biological circuits on host-chassis dynamics., Comment: 4 pages Accepted in 2019 IEEE Biomedical Circuits and Systems Conference

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., Comment: 6 pages. 2 figures, accepted for 58th IEEE Conference on Decision and Control - Nice, France - December 11th-13th 2019

Optimal sensor placement is an important yet unsolved problem in control theory. In biological organisms, genetic activity is often highly nonlinear, making it difficult to design libraries of promoters to act as reporters of the cell state. We make use of the Koopman observability gramian to develop an algorithm for optimal sensor (or reporter) placement for discrete time nonlinear dynamical systems to ease the difficulty of design of the promoter library. This ease is enabled due to the fact that the Koopman operator represents the evolution of a nonlinear system linearly by lifting the states to an infinite-dimensional space of observables. The Koopman framework ideally demands high temporal resolution, but data in biology are often sampled sparsely in time. Therefore we compute what we call the temporally fine-grained Koopman operator from the temporally coarse-grained Koopman operator, the latter of which is identified from the sparse data. The optimal placement of sensors then corresponds to maximizing the observability of the fine-grained system. We demonstrate the algorithm on a simulation example of a circadian oscillator., Comment: 6 pages, 3 figures, to appear in 2019 IEEE Conference on Decision and Control (CDC)

In this paper we propose a novel approach to compute the Koopman operator from sparse time series data. In recent years there has been considerable interests in operator theoretic methods for data-driven analysis of dynamical systems. Existing techniques for the approximation of the Koopman operator require sufficiently large data sets, but in many applications, the data set may not be large enough to approximate the operators to acceptable limits. In this paper, using ideas from robust optimization, we propose an algorithm to compute the Koopman operator from sparse data. We enrich the sparse data set with artificial data points, generated by adding bounded artificial noise and and formulate the noisy robust learning problem as a robust optimization problem and show that the optimal solution is the Koopman operator with smallest error. We illustrate the efficiency of our proposed approach in three different dynamical systems, namely, a linear system, a nonlinear system and a dynamical system governed by a partial differential equation.

In analysis and control of large-scale nonlinear dynamical systems, a distributed approach is often an attractive option due to its computational tractability and usually low communication requirements. Success of the distributed control design relies on the separability of the network into weakly interacting subsystems such that minimal information exchange between subsystems is sufficient to achieve satisfactory control performance. While distributed analysis and control design for dynamical network have been well studied, decomposition of nonlinear networks into weakly interacting subsystems has not received as much attention. In this article we propose a vector Lyapunov functions based approach to quantify the energy-flow in a dynamical network via a model of a comparison system. Introducing a notion of power and energy flow in a dynamical network, we use sum-of-squares programming tools to partition polynomial networks into weakly interacting subsystems. Examples are provided to illustrate the proposed method of decomposition., Comment: to be presented at ECC 2018

In this paper we propose a new Koopman operator approach to the decomposition of nonlinear dynamical systems using Koopman Gramians. We introduce the notion of an input-Koopman operator, and show how input-Koopman operators can be used to cast a nonlinear system into the classical state-space form, and identify conditions under which input and state observable functions are well separated. We then extend an existing method of dynamic mode decomposition for learning Koopman operators from data known as deep dynamic mode decomposition to systems with controls or disturbances. We illustrate the accuracy of the method in learning an input-state separable Koopman operator for an example system, even when the underlying system exhibits mixed state-input terms. We next introduce a nonlinear decomposition algorithm, based on Koopman Gramians, that maximizes internal subsystem observability and disturbance rejection from unwanted noise from other subsystems. We derive a relaxation based on Koopman Gramians and multi-way partitioning for the resulting NP-hard decomposition problem. We lastly illustrate the proposed algorithm with the swing dynamics for an IEEE 39-bus system., Comment: 8 pages, submitted to IEEE 2018 ACC

The Koopman operator has recently garnered much attention for its value in dynamical systems analysis and data-driven model discovery. However, its application has been hindered by the computational complexity of extended dynamic mode decomposition; this requires a combinatorially large basis set to adequately describe many nonlinear systems of interest, e.g. cyber-physical infrastructure systems, biological networks, social systems, and fluid dynamics. Often the dictionaries generated for these problems are manually curated, requiring domain-specific knowledge and painstaking tuning. In this paper we introduce a deep learning framework for learning Koopman operators of nonlinear dynamical systems. We show that this novel method automatically selects efficient deep dictionaries, outperforming state-of-the-art methods. We benchmark this method on partially observed nonlinear systems, including the glycolytic oscillator and show it is able to predict quantitatively 100 steps into the future, using only a single timepoint, and qualitative oscillatory behavior 400 steps into the future., Comment: 16 pages, 5 figures