arXiv subjects

Enoch Yeung

Publications and source records attributed to Enoch Yeung.

34 records · Page 2Linked to original sources

arXiv2020

Data Driven Online Learning of Power System Dynamics

With the advancement of sensing and communication in power networks, high-frequency real-time data from a power network can be used as a resource to develop better monitoring capabilities. In this work, a systematic approach based on data-driven operator theoretic methods involving Koopman operator is proposed for the online identification of power system dynamics. In particular, a new algorithm is provided, which unlike any previously existing algorithms, updates the Koopman operator iteratively as new data points are acquired. The proposed algorithm has three advantages: a) allows for real-time monitoring of the power system dynamics b) linear power system dynamics (this linear system is usually in a higher dimensional feature space and is not same as linearization of the underlying nonlinear dynamics) and c) computationally fast and less intensive when compared to the popular Extended Dynamic Mode Decomposition (EDMD) algorithm. The efficiency of the proposed algorithm is illustrated on an IEEE 9 bus system using synthetic data from the nonlinear model and on IEEE 39 bus system using synthetic data from the linearized model.

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arXiv2019

Data-Driven Operator Theoretic Methods for Global Phase Space Learning

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.

math.DS↗

arXiv2019

Information Transfer in Dynamical Systems and Optimal Placement of Actuators and Sensors for Control of Non-equilibrium Dynamics

In this paper we develop the concept of information transfer between the Borel-measurable sets for a dynamical system described by a measurable space and a non-singular transformation. The concept is based on how Shannon entropy is transferred between the measurable sets, as the dynamical system evolves. We show that the proposed definition of information transfer satisfies the usual notions of information transfer and causality, namely, zero transfer and transfer asymmetry. Furthermore, we show how the information transfer measure can be used to classify ergodicity and mixing. We also develop the computational methods for information transfer computation and apply the framework for optimal placements of actuators and sensors for control of non-equilibrium dynamics.

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arXiv2019

Online Learning of Dynamical Systems: An Operator Theoretic Approach

In this paper, we provide an algorithm for online computation of Koopman operator in real-time using streaming data. In recent years, there has been an increased interest in data-driven analysis of dynamical systems, with operator theoretic techniques being the most popular. Existing algorithms, like Dynamic Mode Decomposition (DMD) and Extended Dynamic Mode Decomposition (EDMD), use the entire data set for computation of the Koopman operator. However, many real life applications like power system analysis, biological systems, building systems etc. requires the real-time computation and updating of the Koopman operator, as new data streams in. In this paper, we propose an iterative algorithm for online computation of Koopman operator such that at each time step the Koopman operator is updated incrementally. In particular, we propose a Recursive Extended Dynamic Decomposition (rEDMD) algorithm for computation of Koopman operator from streaming data. Further, we test the algorithm in three different dynamical systems, namely, a linear system, a nonlinear system and a system governed by a Partial Differential Equation (PDE) and illustrate the computational efficiency of the iterative algorithm over the existing DMD and EDMD algorithms.

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arXiv2019

Optimal reporter placement in sparsely measured genetic networks using the Koopman operator

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.

q-bio.MN↗

arXiv2019

Koopman Operators for Generalized Persistence of Excitation Conditions for Nonlinear Systems

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.

math.DS↗

arXiv2019

A data-driven method for quantifying the impact of a genetic circuit on its host

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.

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arXiv2019

Enforcing constraints for interpolation and extrapolation in Generative Adversarial Networks

We suggest ways to enforce given constraints in the output of a Generative Adversarial Network (GAN) generator both for interpolation and extrapolation (prediction). For the case of dynamical systems, given a time series, we wish to train GAN generators that can be used to predict trajectories starting from a given initial condition. In this setting, the constraints can be in algebraic and/or differential form. Even though we are predominantly interested in the case of extrapolation, we will see that the tasks of interpolation and extrapolation are related. However, they need to be treated differently. For the case of interpolation, the incorporation of constraints is built into the training of the GAN. The incorporation of the constraints respects the primary game-theoretic setup of a GAN so it can be combined with existing algorithms. However, it can exacerbate the problem of instability during training that is well-known for GANs. We suggest adding small noise to the constraints as a simple remedy that has performed well in our numerical experiments. The case of extrapolation (prediction) is more involved. During training, the GAN generator learns to interpolate a noisy version of the data and we enforce the constraints. This approach has connections with model reduction that we can utilize to improve the efficiency and accuracy of the training. Depending on the form of the constraints, we may enforce them also during prediction through a projection step. We provide examples of linear and nonlinear systems of differential equations to illustrate the various constructions.

cs.LG↗

arXiv2019

On Computation of Koopman Operator from Sparse Data

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.

math.DS↗

arXiv2019

A Constructive Approach for One-Shot Training of Neural Networks Using Hypercube-Based Topological Coverings

In this paper we presented a novel constructive approach for training deep neural networks using geometric approaches. We show that a topological covering can be used to define a class of distributed linear matrix inequalities, which in turn directly specify the shape and depth of a neural network architecture. The key insight is a fundamental relationship between linear matrix inequalities and their ability to bound the shape of data, and the rectified linear unit (ReLU) activation function employed in modern neural networks. We show that unit cover geometry and cover porosity are two design variables in cover-constructive learning that play a critical role in defining the complexity of the model and generalizability of the resulting neural network classifier. In the context of cover-constructive learning, these findings underscore the age old trade-off between model complexity and overfitting (as quantified by the number of elements in the data cover) and generalizability on test data. Finally, we benchmark on algorithm on the Iris, MNIST, and Wine dataset and show that the constructive algorithm is able to train a deep neural network classifier in one shot, achieving equal or superior levels of training and test classification accuracy with reduced training time.

cs.LG↗

arXiv2018

Decomposition of Nonlinear Dynamical Networks via Comparison Systems

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.

math.DS↗

arXiv2017

A Class of Logistic Functions for Approximating State-Inclusive Koopman Operators

An outstanding challenge in nonlinear systems theory is identification or learning of a given nonlinear system's Koopman operator directly from data or models. Advances in extended dynamic mode decomposition approaches and machine learning methods have enabled data-driven discovery of Koopman operators, for both continuous and discrete-time systems. Since Koopman operators are often infinite-dimensional, they are approximated in practice using finite-dimensional systems. The fidelity and convergence of a given finite-dimensional Koopman approximation is a subject of ongoing research. In this paper we introduce a class of Koopman observable functions that confer an approximate closure property on their corresponding finite-dimensional approximations of the Koopman operator. We derive error bounds for the fidelity of this class of observable functions, as well as identify two key learning parameters which can be used to tune performance. We illustrate our approach on two classical nonlinear system models: the Van Der Pol oscillator and the bistable toggle switch.

cs.LG↗

arXiv2017

Learning Deep Neural Network Representations for Koopman Operators of Nonlinear Dynamical Systems

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.

cs.LG↗

arXiv2017

Solving differential equations with unknown constitutive relations as recurrent neural networks

We solve a system of ordinary differential equations with an unknown functional form of a sink (reaction rate) term. We assume that the measurements (time series) of state variables are partially available, and we use recurrent neural network to "learn" the reaction rate from this data. This is achieved by including a discretized ordinary differential equations as part of a recurrent neural network training problem. We extend TensorFlow's recurrent neural network architecture to create a simple but scalable and effective solver for the unknown functions, and apply it to a fedbatch bioreactor simulation problem. Use of techniques from recent deep learning literature enables training of functions with behavior manifesting over thousands of time steps. Our networks are structurally similar to recurrent neural networks, but differences in design and function require modifications to the conventional wisdom about training such networks.

cs.LG↗

arXiv2017

Decomposition of Nonlinear Dynamical Systems Using Koopman Gramians

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.

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arXiv2017

A Koopman Operator Approach for Computing and Balancing Gramians for Discrete Time Nonlinear Systems

In this paper, we consider the problem of quantifying controllability and observability of a nonlinear discrete time dynamical system. We introduce the Koopman operator as a canonical representation of the system and apply a lifting technique to compute gramians in the space of full-state observables. We illustrate the properties of these gramians and identify several relationships with canonical results on local controllability and observability. Once defined, we show that these gramians can be balanced through a change of coordinates on the observables space, which in turn allows for direct application of balanced truncation. Throughout the paper, we highlight the aspects of our approach with an example nonlinear system.

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