79,080 research outputs found
Enabling High-Dimensional Hierarchical Uncertainty Quantification by ANOVA and Tensor-Train Decomposition
Hierarchical uncertainty quantification can reduce the computational cost of
stochastic circuit simulation by employing spectral methods at different
levels. This paper presents an efficient framework to simulate hierarchically
some challenging stochastic circuits/systems that include high-dimensional
subsystems. Due to the high parameter dimensionality, it is challenging to both
extract surrogate models at the low level of the design hierarchy and to handle
them in the high-level simulation. In this paper, we develop an efficient
ANOVA-based stochastic circuit/MEMS simulator to extract efficiently the
surrogate models at the low level. In order to avoid the curse of
dimensionality, we employ tensor-train decomposition at the high level to
construct the basis functions and Gauss quadrature points. As a demonstration,
we verify our algorithm on a stochastic oscillator with four MEMS capacitors
and 184 random parameters. This challenging example is simulated efficiently by
our simulator at the cost of only 10 minutes in MATLAB on a regular personal
computer.Comment: 14 pages (IEEE double column), 11 figure, accepted by IEEE Trans CAD
of Integrated Circuits and System
Data-driven modelling of biological multi-scale processes
Biological processes involve a variety of spatial and temporal scales. A
holistic understanding of many biological processes therefore requires
multi-scale models which capture the relevant properties on all these scales.
In this manuscript we review mathematical modelling approaches used to describe
the individual spatial scales and how they are integrated into holistic models.
We discuss the relation between spatial and temporal scales and the implication
of that on multi-scale modelling. Based upon this overview over
state-of-the-art modelling approaches, we formulate key challenges in
mathematical and computational modelling of biological multi-scale and
multi-physics processes. In particular, we considered the availability of
analysis tools for multi-scale models and model-based multi-scale data
integration. We provide a compact review of methods for model-based data
integration and model-based hypothesis testing. Furthermore, novel approaches
and recent trends are discussed, including computation time reduction using
reduced order and surrogate models, which contribute to the solution of
inference problems. We conclude the manuscript by providing a few ideas for the
development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and
Multiscale Dynamics (American Scientific Publishers
DOLFIN: Automated Finite Element Computing
We describe here a library aimed at automating the solution of partial differential equations using the finite element method. By employing novel techniques for automated code generation, the library combines a high level of expressiveness with efficient computation. Finite element variational forms may be expressed in near mathematical notation, from which low-level code is automatically generated, compiled and seamlessly integrated with efficient implementations of
computational meshes and high-performance linear algebra. Easy-to-use object-oriented interfaces to the library are provided in the form of a C++ library and a Python module. This paper discusses the mathematical abstractions and methods used in the design of the library and its implementation. A number of examples are presented to demonstrate the use of the library in application code
Spatially Distributed Stochastic Systems: equation-free and equation-assisted preconditioned computation
Spatially distributed problems are often approximately modelled in terms of
partial differential equations (PDEs) for appropriate coarse-grained quantities
(e.g. concentrations). The derivation of accurate such PDEs starting from finer
scale, atomistic models, and using suitable averaging, is often a challenging
task; approximate PDEs are typically obtained through mathematical closure
procedures (e.g. mean-field approximations). In this paper, we show how such
approximate macroscopic PDEs can be exploited in constructing preconditioners
to accelerate stochastic simulations for spatially distributed particle-based
process models. We illustrate how such preconditioning can improve the
convergence of equation-free coarse-grained methods based on coarse
timesteppers. Our model problem is a stochastic reaction-diffusion model
capable of exhibiting Turing instabilities.Comment: 8 pages, 6 figures, submitted to Journal of Chemical Physic
Bayesian Deep Net GLM and GLMM
Deep feedforward neural networks (DFNNs) are a powerful tool for functional
approximation. We describe flexible versions of generalized linear and
generalized linear mixed models incorporating basis functions formed by a DFNN.
The consideration of neural networks with random effects is not widely used in
the literature, perhaps because of the computational challenges of
incorporating subject specific parameters into already complex models.
Efficient computational methods for high-dimensional Bayesian inference are
developed using Gaussian variational approximation, with a parsimonious but
flexible factor parametrization of the covariance matrix. We implement natural
gradient methods for the optimization, exploiting the factor structure of the
variational covariance matrix in computation of the natural gradient. Our
flexible DFNN models and Bayesian inference approach lead to a regression and
classification method that has a high prediction accuracy, and is able to
quantify the prediction uncertainty in a principled and convenient way. We also
describe how to perform variable selection in our deep learning method. The
proposed methods are illustrated in a wide range of simulated and real-data
examples, and the results compare favourably to a state of the art flexible
regression and classification method in the statistical literature, the
Bayesian additive regression trees (BART) method. User-friendly software
packages in Matlab, R and Python implementing the proposed methods are
available at https://github.com/VBayesLabComment: 35 pages, 7 figure, 10 table
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