28,842 research outputs found
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
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