arXiv subjects

Enoch Yeung

Publications and source records attributed to Enoch Yeung.

At least 19 recordsLinked to original sources

arXiv2025

Model Reduction of Multicellular Communication Systems via Singular Perturbation: Sender Receiver Systems

We investigate multicellular sender receiver systems embedded in hydrogel beads, where diffusible signals mediate interactions among heterogeneous cells. Such systems are modeled by PDE ODE couplings that combine three dimensional diffusion with nonlinear intracellular dynamics, making analysis and simulation challenging. We show that the diffusion dynamics converges exponentially to a quasi steady spatial profile and use singular perturbation theory to reduce the model to a finite dimensional multiagent network. A closed form communication matrix derived from the spherical Green's function captures the effective sender receiver coupling. Numerical results show the reduced model closely matches the full dynamics while enabling scalable simulation of large cell populations.

eess.SY↗

arXiv2025

Estimating Varying Parameters in Dynamical Systems: A Modular Framework Using Switch Detection, Optimization, and Sparse Regression

The estimation of static parameters in dynamical systems and control theory has been extensively studied, with significant progress made in estimating varying parameters in specific system types. Suppose, in the general case, we have data from a system with parameters that depend on an independent variable such as time or space. Further, suppose the system's model structure is known, but our aim is to identify functions describing parameter-varying elements as they change with respect to time or another variable. Focusing initially on the subclass of problems where parameters are discretely switching piecewise constant functions, we develop an algorithmic framework for detecting discrete parameter switches and fitting a piecewise constant model to data using optimization-based parameter estimation. Our modular framework allows for customization of switch detection, numerical integration, and optimization sub-steps to suit user requirements. Binary segmentation is used for switch detection, with Nelder-Mead and Powell methods employed for optimization. To address broader problems, we extend our framework using dictionary-based sparse regression with trigonometric and polynomial functions to obtain continuously varying parameter functions. Finally, we assess the framework's robustness to measurement noise. We demonstrate its capabilities across several examples, including time-varying promoter-gene expression, a genetic toggle switch, a parameter-switching manifold, the heat equation with a time-varying diffusion coefficient, and the advection-diffusion equation with a continuously varying parameter.

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arXiv2025

A novel model class for bowtie biological networks with universal classification properties

Cell sensory transcription networks are the intracellular computation structure that regulates and drives cellular activity. Activity in these networks determines the the cell's ability to adapt to changes in its environment. Resilient cells successfully identify (classify) and appropriately respond to environmental shifts. We present a model for identification and response to environmental changes in resilient bacteria. This model combines two known motifs in transcription networks: dense overlapping regulons (DORs) and single input modules (SIMs). DORs have the ability to perform cellular decision making and have a network structure similar to that of a shallow neural network, with a number of input transcription factors (TFs) mapping to a distinct set of genes. SIMs contain a master TF that simultaneously activates a number of target genes. Within most observed cell sensory transcription networks, the master transcription factor of SIMs are output genes of a DOR creating a fan-in-fan-out (bowtie) structure in the transcriptional network. We model this hybrid network motif (which we call the DOR2SIM motif) with a superposition of modular nonlinear functions to describe protein signaling in the network and basic mass action kinetics to describe the other chemical reactions in this process. We analyze this model's biological feasibility and capacity to perform classification, the first step in adaptation. We provide sufficient conditions for models of the DOR2SIM motif to classify constant (environmental) inputs. These conditions suggest that generally low monomer degradation rates as well as low expression of source node genes at equilibrium in the DOR component enable classification.

q-bio.MN↗

arXiv2025

Controlling Peak Sharpness in Multimodal Biomolecular Systems via the Chemical Fokker-Planck Equation

Intracellular biomolecular systems exhibit intrinsic stochasticity due to low molecular copy numbers, leading to multimodal probability distributions that play a crucial role in probabilistic differentiation and cellular decision-making. Controlling the dispersion of multimodal probability distributions in biomolecular systems is critical for regulating stochastic behavior, robustness, and adaptability. However, modifying system parameters to adjust dispersion often affects peak positions, potentially altering a desired phenotype or even fundamental behavior in a genetic pathway. In this paper, we establish a theoretical framework that enables independent control of dispersion while preserving peak positions and modality using the Chemical Fokker-Planck Equation (CFPE) and sharpness, a measure of probability concentration around individual peaks. By analyzing the steady-state solution of the CFPE, we derive explicit conditions under which peak sharpness can be tuned monotonically without changing peak positions or modality. We validate our approach through Monte Carlo simulations on a bimodal chemical system, demonstrating effective dispersion control while maintaining structural stability. This framework provides a systematic approach for designing biomolecular systems with tunable stochastic properties, contributing to advancements in synthetic biology and probabilistic cellular regulation.

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arXiv2024

An SVD-like Decomposition of Bounded-Input Bounded-Output Functions

The Singular Value Decomposition (SVD) of linear functions facilitates the calculation of their 2-induced norm and row and null spaces, hallmarks of linear control theory. In this work, we present a function representation that, similar to SVD, provides an upper bound on the 2-induced norm of bounded-input bounded-output functions, as well as facilitates the computation of generalizations of the notions of row and null spaces. Borrowing from the notion of "lifting" in Koopman operator theory, we construct a finite-dimensional lifting of inputs that relaxes the unitary property of the right-most matrix in traditional SVD, $V^*$, to be an injective, norm-preserving mapping to a slightly higher-dimensional space.

math.OC↗

arXiv2022

Learning Invariant Subspaces of Koopman Operators--Part 1: A Methodology for Demonstrating a Dictionary's Approximate Subspace Invariance

Koopman operators model nonlinear dynamics as a linear dynamic system acting on a nonlinear function as the state. This nonstandard state is often called a Koopman observable and is usually approximated numerically by a superposition of functions drawn from a dictionary. In a widely used algorithm, Extended Dynamic Mode Decomposition, the dictionary functions are drawn from a fixed class of functions. Recently, deep learning combined with EDMD has been used to learn novel dictionary functions in an algorithm called deep dynamic mode decomposition (deepDMD). The learned representation both (1) accurately models and (2) scales well with the dimension of the original nonlinear system. In this paper we analyze the learned dictionaries from deepDMD and explore the theoretical basis for their strong performance. We explore State-Inclusive Logistic Lifting (SILL) dictionary functions to approximate Koopman observables. Error analysis of these dictionary functions show they satisfy a property of subspace approximation, which we define as uniform finite approximate closure. Our results provide a hypothesis to explain the success of deep neural networks in learning numerical approximations to Koopman operators. Part 2 of this paper will extend this explanation by demonstrating the subspace invariant of heterogeneous dictionaries and presenting a head-to-head numerical comparison of deepDMD and low-parameter heterogeneous dictionary learning.

eess.SY↗

arXiv2022

Learning Invariant Subspaces of Koopman Operators--Part 2: Heterogeneous Dictionary Mixing to Approximate Subspace Invariance

This work builds on the models and concepts presented in part 1 to learn approximate dictionary representations of Koopman operators from data. Part I of this paper presented a methodology for arguing the subspace invariance of a Koopman dictionary. This methodology was demonstrated on the state-inclusive logistic lifting (SILL) basis. This is an affine basis augmented with conjunctive logistic functions. The SILL dictionary's nonlinear functions are homogeneous, a norm in data-driven dictionary learning of Koopman operators. In this paper, we discover that structured mixing of heterogeneous dictionary functions drawn from different classes of nonlinear functions achieve the same accuracy and dimensional scaling as the deep-learning-based deepDMD algorithm. We specifically show this by building a heterogeneous dictionary comprised of SILL functions and conjunctive radial basis functions (RBFs). This mixed dictionary achieves the same accuracy and dimensional scaling as deepDMD with an order of magnitude reduction in parameters, while maintaining geometric interpretability. These results strengthen the viability of dictionary-based Koopman models to solving high-dimensional nonlinear learning problems.

eess.SY↗

arXiv2022

Data-Driven Observability Decomposition with Koopman Operators for Optimization of Output Functions of Nonlinear Systems

When complex systems with nonlinear dynamics achieve an output performance objective, only a fraction of the state dynamics significantly impacts that output. Those minimal state dynamics can be identified using the differential geometric approach to the observability of nonlinear systems, but the theory is limited to only analytical systems. In this paper, we extend the notion of nonlinear observable decomposition to the more general class of data-informed systems. We employ Koopman operator theory, which encapsulates nonlinear dynamics in linear models, allowing us to bridge the gap between linear and nonlinear observability notions. We propose a new algorithm to learn Koopman operator representations that capture the system dynamics while ensuring that the output performance measure is in the span of its observables. We show that a transformation of this linear, output-inclusive Koopman model renders a new minimum Koopman representation. This representation embodies only the observable portion of the nonlinear observable decomposition of the original system. A prime application of this theory is to identify genes in biological systems that correspond to specific phenotypes, the performance measure. We simulate two biological gene networks and demonstrate that the observability of Koopman operators can successfully identify genes that drive each phenotype. We anticipate our novel system identification tool will effectively discover reduced gene networks that drive complex behaviors in biological systems.

math.OC↗

arXiv2022

Heterogeneous mixtures of dictionary functions to approximate subspace invariance in Koopman operators

Koopman operators model nonlinear dynamics as a linear dynamic system acting on a nonlinear function as the state. This nonstandard state is often called a Koopman observable and is usually approximated numerically by a superposition of functions drawn from a \textit{dictionary}. A widely used algorithm, is \textit{Extended Dynamic Mode Decomposition}, where the dictionary functions are drawn from a fixed, homogeneous class of functions. Recently, deep learning combined with EDMD has been used to learn novel dictionary functions in an algorithm called deep dynamic mode decomposition (deepDMD). The learned representation both (1) accurately models and (2) scales well with the dimension of the original nonlinear system. In this paper we analyze the learned dictionaries from deepDMD and explore the theoretical basis for their strong performance. We discover a novel class of dictionary functions to approximate Koopman observables. Error analysis of these dictionary functions show they satisfy a property of subspace approximation, which we define as uniform finite approximate closure. We discover that structured mixing of heterogeneous dictionary functions drawn from different classes of nonlinear functions achieve the same accuracy and dimensional scaling as deepDMD. This mixed dictionary does so with an order of magnitude reduction in parameters, while maintaining geometric interpretability. Our results provide a hypothesis to explain the success of deep neural networks in learning numerical approximations to Koopman operators.

eess.SY↗

arXiv2021

On the Stability, Economic Efficiency and Incentive Compatibility of Electricity Market Dynamics

This paper focuses on the operation of an electricity market that accounts for participants that bid at a sub-minute timescale. To that end, we model the market-clearing process as a dynamical system, called market dynamics, which is temporally coupled with the grid frequency dynamics and is thus required to guarantee system-wide stability while meeting the system operational constraints. We characterize participants as price-takers who rationally update their bids to maximize their utility in response to real-time schedules of prices and dispatch. For two common bidding mechanisms, based on quantity and price, we identify a notion of alignment between participants' behavior and planners' goals that leads to a saddle-based design of the market that guarantees convergence to a point meeting all operational constraints. We further explore cases where this alignment property does not hold and observe that misaligned participants' bidding can destabilize the closed-loop system. We thus design a regularized version of the market dynamics that recovers all the desirable stability and steady-state performance guarantees. Numerical tests validate our results on the IEEE 39-bus system.

math.OC↗

arXiv2021

The Effect of Sensor Fusion on Data-Driven Learning of Koopman Operators

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.

math.OC↗

arXiv2021

Data-Driven Operator Theoretic Methods for Phase Space Learning and Analysis

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.

math.DS↗

arXiv2021

On Few Shot Learning of Dynamical Systems: A Koopman Operator Theoretic Approach

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).

math.DS↗

arXiv2020

Computationally Efficient Learning of Large Scale Dynamical Systems: A Koopman Theoretic Approach

In recent years there has been a considerable drive towards data-driven analysis, discovery and control of dynamical systems. To this end, operator theoretic methods, namely, Koopman operator methods have gained a lot of interest. In general, the Koopman operator is obtained as a solution to a least-squares problem, and as such, the Koopman operator can be expressed as a closed-form solution that involves the computation of Moore-Penrose inverse of a matrix. For high dimensional systems and also if the size of the obtained data-set is large, the computation of the Moore-Penrose inverse becomes computationally challenging. In this paper, we provide an algorithm for computing the Koopman operator for high dimensional systems in a time-efficient manner. We further demonstrate the efficacy of the proposed approach on two different systems, namely a network of coupled oscillators (with state-space dimension up to 2500) and IEEE 68 bus system (with state-space dimension 204 and up to 24,000 time-points).

eess.SY↗

arXiv2020

Prediction of fitness in bacteria with causal jump dynamic mode decomposition

In this paper, we consider the problem of learning a predictive model for population cell growth dynamics as a function of the media conditions. We first introduce a generic data-driven framework for training operator-theoretic models to predict cell growth rate. We then introduce the experimental design and data generated in this study, namely growth curves of Pseudomonas putida as a function of casein and glucose concentrations. We use a data driven approach for model identification, specifically the nonlinear autoregressive (NAR) model to represent the dynamics. We show theoretically that Hankel DMD can be used to obtain a solution of the NAR model. We show that it identifies a constrained NAR model and to obtain a more general solution, we define a causal state space system using 1-step,2-step,...,τ-step predictors of the NAR model and identify a Koopman operator for this model using extended dynamic mode decomposition. The hybrid scheme we call causal-jump dynamic mode decomposition, which we illustrate on a growth profile or fitness prediction challenge as a function of different input growth conditions. We show that our model is able to recapitulate training growth curve data with 96.6% accuracy and predict test growth curve data with 91% accuracy.

math.OC↗

arXiv2020

Steady state programming of controlled nonlinear systems via deep dynamic mode decomposition

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.

math.DS↗

arXiv2020

Towards Scalable Koopman Operator Learning: Convergence Rates and A Distributed Learning Algorithm

We propose an alternating optimization algorithm to the nonconvex Koopman operator learning problem for nonlinear dynamic systems. We show that the proposed algorithm will converge to a critical point with rate $O(1/T)$ and $O(\frac{1}{\log T})$ for the constant and diminishing learning rates, respectively, under some mild conditions. To cope with the high dimensional nonlinear dynamical systems, we present the first-ever distributed Koopman operator learning algorithm. We show that the distributed Koopman operator learning has the same convergence properties as the centralized Koopman operator learning, in the absence of optimal tracker, so long as the basis functions satisfy a set of state-based decomposition conditions. Numerical experiments are provided to complement our theoretical results.

eess.SP↗

arXiv2020

Koopman Operator Methods for Global Phase Space Exploration of Equivariant Dynamical Systems

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.

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