5,671 research outputs found
Global parameter identification of stochastic reaction networks from single trajectories
We consider the problem of inferring the unknown parameters of a stochastic
biochemical network model from a single measured time-course of the
concentration of some of the involved species. Such measurements are available,
e.g., from live-cell fluorescence microscopy in image-based systems biology. In
addition, fluctuation time-courses from, e.g., fluorescence correlation
spectroscopy provide additional information about the system dynamics that can
be used to more robustly infer parameters than when considering only mean
concentrations. Estimating model parameters from a single experimental
trajectory enables single-cell measurements and quantification of cell--cell
variability. We propose a novel combination of an adaptive Monte Carlo sampler,
called Gaussian Adaptation, and efficient exact stochastic simulation
algorithms that allows parameter identification from single stochastic
trajectories. We benchmark the proposed method on a linear and a non-linear
reaction network at steady state and during transient phases. In addition, we
demonstrate that the present method also provides an ellipsoidal volume
estimate of the viable part of parameter space and is able to estimate the
physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems
Biology
Tensor Computation: A New Framework for High-Dimensional Problems in EDA
Many critical EDA problems suffer from the curse of dimensionality, i.e. the
very fast-scaling computational burden produced by large number of parameters
and/or unknown variables. This phenomenon may be caused by multiple spatial or
temporal factors (e.g. 3-D field solvers discretizations and multi-rate circuit
simulation), nonlinearity of devices and circuits, large number of design or
optimization parameters (e.g. full-chip routing/placement and circuit sizing),
or extensive process variations (e.g. variability/reliability analysis and
design for manufacturability). The computational challenges generated by such
high dimensional problems are generally hard to handle efficiently with
traditional EDA core algorithms that are based on matrix and vector
computation. This paper presents "tensor computation" as an alternative general
framework for the development of efficient EDA algorithms and tools. A tensor
is a high-dimensional generalization of a matrix and a vector, and is a natural
choice for both storing and solving efficiently high-dimensional EDA problems.
This paper gives a basic tutorial on tensors, demonstrates some recent examples
of EDA applications (e.g., nonlinear circuit modeling and high-dimensional
uncertainty quantification), and suggests further open EDA problems where the
use of tensor computation could be of advantage.Comment: 14 figures. Accepted by IEEE Trans. CAD of Integrated Circuits and
System
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