Controllability of networks: influence of structure and memory

openIn this work we borrow some ideas from the the theory of lifted Markov chains, which can accelerate convergence of random walks algorithms thanks to the introduced memory effects, and apply them to the control of networks of dynamical systems arranged on a line and on a grid. We lift the dynamics by enlarging each node state and discuss how to compare the effect of a control input on the lifted network and on the original one. We compute some metrics for energy-related controllability, showing that the lifted network has better controllability properties than the non-lifted one. This proves an advantage induced by the extra internal dynamics that allows for memory effects. The potential of lifts is then explored via numerical simulations for some paradigmatic examples

Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits

We present a Python-based software package to automatically obtain phenomenological models of input-controlled synthetic biological circuits that guide the design using chemical reaction-level descriptive models. From the parts and mechanism description of a synthetic biological circuit, it is easy to obtain a chemical reaction model of the circuit under the assumptions of mass-action kinetics using various existing tools. However, using these models to guide design decisions during an experiment is difficult due to a large number of reaction rate parameters and species in the model. Hence, phenomenological models are often developed that describe the effective relationships among the circuit inputs, outputs, and only the key states and parameters. In this paper, we present an algorithm to obtain these phenomenological models in an automated manner using a Python package for circuits with inputs that control the desired outputs. This model reduction approach combines the common assumptions of time-scale separation, conservation laws, and species' abundance to obtain the reduced models that can be used for design of synthetic biological circuits. We consider an example of a simple gene expression circuit and another example of a layered genetic feedback control circuit to demonstrate the use of the model reduction procedure

On Submodularity and Controllability in Complex Dynamical Networks

Controllability and observability have long been recognized as fundamental structural properties of dynamical systems, but have recently seen renewed interest in the context of large, complex networks of dynamical systems. A basic problem is sensor and actuator placement: choose a subset from a finite set of possible placements to optimize some real-valued controllability and observability metrics of the network. Surprisingly little is known about the structure of such combinatorial optimization problems. In this paper, we show that several important classes of metrics based on the controllability and observability Gramians have a strong structural property that allows for either efficient global optimization or an approximation guarantee by using a simple greedy heuristic for their maximization. In particular, the mapping from possible placements to several scalar functions of the associated Gramian is either a modular or submodular set function. The results are illustrated on randomly generated systems and on a problem of power electronic actuator placement in a model of the European power grid.Comment: Original arXiv version of IEEE Transactions on Control of Network Systems paper (Volume 3, Issue 1), with a addendum (located in the ancillary documents) that explains an error in a proof of the original paper and provides a counterexample to the corresponding resul

The Parameter Houlihan: a solution to high-throughput identifiability indeterminacy for brutally ill-posed problems

One way to interject knowledge into clinically impactful forecasting is to use data assimilation, a nonlinear regression that projects data onto a mechanistic physiologic model, instead of a set of functions, such as neural networks. Such regressions have an advantage of being useful with particularly sparse, non-stationary clinical data. However, physiological models are often nonlinear and can have many parameters, leading to potential problems with parameter identifiability, or the ability to find a unique set of parameters that minimize forecasting error. The identifiability problems can be minimized or eliminated by reducing the number of parameters estimated, but reducing the number of estimated parameters also reduces the flexibility of the model and hence increases forecasting error. We propose a method, the parameter Houlihan, that combines traditional machine learning techniques with data assimilation, to select the right set of model parameters to minimize forecasting error while reducing identifiability problems. The method worked well: the data assimilation-based glucose forecasts and estimates for our cohort using the Houlihan-selected parameter sets generally also minimize forecasting errors compared to other parameter selection methods such as by-hand parameter selection. Nevertheless, the forecast with the lowest forecast error does not always accurately represent physiology, but further advancements of the algorithm provide a path for improving physiologic fidelity as well. Our hope is that this methodology represents a first step toward combining machine learning with data assimilation and provides a lower-threshold entry point for using data assimilation with clinical data by helping select the right parameters to estimate

A Comparative Study of Reservoir Computing for Temporal Signal Processing

Reservoir computing (RC) is a novel approach to time series prediction using recurrent neural networks. In RC, an input signal perturbs the intrinsic dynamics of a medium called a reservoir. A readout layer is then trained to reconstruct a target output from the reservoir's state. The multitude of RC architectures and evaluation metrics poses a challenge to both practitioners and theorists who study the task-solving performance and computational power of RC. In addition, in contrast to traditional computation models, the reservoir is a dynamical system in which computation and memory are inseparable, and therefore hard to analyze. Here, we compare echo state networks (ESN), a popular RC architecture, with tapped-delay lines (DL) and nonlinear autoregressive exogenous (NARX) networks, which we use to model systems with limited computation and limited memory respectively. We compare the performance of the three systems while computing three common benchmark time series: H{\'e}non Map, NARMA10, and NARMA20. We find that the role of the reservoir in the reservoir computing paradigm goes beyond providing a memory of the past inputs. The DL and the NARX network have higher memorization capability, but fall short of the generalization power of the ESN

Submodularity of Energy Related Controllability Metrics

The quantification of controllability and observability has recently received new interest in the context of large, complex networks of dynamical systems. A fundamental but computationally difficult problem is the placement or selection of actuators and sensors that optimize real-valued controllability and observability metrics of the network. We show that several classes of energy related metrics associated with the controllability Gramian in linear dynamical systems have a strong structural property, called submodularity. This property allows for an approximation guarantee by using a simple greedy heuristic for their maximization. The results are illustrated for randomly generated systems and for placement of power electronic actuators in a model of the European power grid.Comment: 7 pages, 2 figures; submitted to the 2014 IEEE Conference on Decision and Contro

Controllability Metrics, Limitations and Algorithms for Complex Networks

This paper studies the problem of controlling complex networks, that is, the joint problem of selecting a set of control nodes and of designing a control input to steer a network to a target state. For this problem (i) we propose a metric to quantify the difficulty of the control problem as a function of the required control energy, (ii) we derive bounds based on the system dynamics (network topology and weights) to characterize the tradeoff between the control energy and the number of control nodes, and (iii) we propose an open-loop control strategy with performance guarantees. In our strategy we select control nodes by relying on network partitioning, and we design the control input by leveraging optimal and distributed control techniques. Our findings show several control limitations and properties. For instance, for Schur stable and symmetric networks: (i) if the number of control nodes is constant, then the control energy increases exponentially with the number of network nodes, (ii) if the number of control nodes is a fixed fraction of the network nodes, then certain networks can be controlled with constant energy independently of the network dimension, and (iii) clustered networks may be easier to control because, for sufficiently many control nodes, the control energy depends only on the controllability properties of the clusters and on their coupling strength. We validate our results with examples from power networks, social networks, and epidemics spreading