Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

PA Saa, LK Nielsen - Biotechnology advances, 2017 - Elsevier
Kinetic models are critical to predict the dynamic behaviour of metabolic networks.
Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting …

A survey of feedback particle filter and related controlled interacting particle systems (CIPS)

A Taghvaei, PG Mehta - Annual Reviews in Control, 2023 - Elsevier
In this survey, we describe controlled interacting particle systems (CIPS) to approximate the
solution of the optimal filtering and the optimal control problems. Part I of the survey is …

Can local particle filters beat the curse of dimensionality?

P Rebeschini, R Van Handel - 2015 - projecteuclid.org
The discovery of particle filtering methods has enabled the use of nonlinear filtering in a
wide array of applications. Unfortunately, the approximation error of particle filters typically …

On the stability of sequential Monte Carlo methods in high dimensions

A Beskos, D Crisan, A Jasra - 2014 - projecteuclid.org
We investigate the stability of a Sequential Monte Carlo (SMC) method applied to the
problem of sampling from a target distribution on R^d for large d. It is well known Bengtsson …

Better together? Statistical learning in models made of modules

PE Jacob, LM Murray, CC Holmes… - arXiv preprint arXiv …, 2017 - arxiv.org
In modern applications, statisticians are faced with integrating heterogeneous data
modalities relevant for an inference, prediction, or decision problem. In such circumstances …

A stable particle filter for a class of high-dimensional state-space models

A Beskos, D Crisan, A Jasra, K Kamatani… - Advances in Applied …, 2017 - cambridge.org
We consider the numerical approximation of the filtering problem in high dimensions, that is,
when the hidden state lies in ℝd with large d. For low-dimensional problems, one of the most …

Sequential Monte Carlo methods for high-dimensional inverse problems: A case study for the Navier--Stokes equations

N Kantas, A Beskos, A Jasra - SIAM/ASA Journal on Uncertainty Quantification, 2014 - SIAM
We consider the inverse problem of estimating the initial condition of a partial differential
equation, which is observed only through noisy measurements at discrete time intervals. In …

[HTML][HTML] Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

PA Saa, LK Nielsen - Scientific reports, 2016 - nature.com
Kinetic models are essential to quantitatively understand and predict the behaviour of
metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism …

An optimal transport formulation of Bayes' law for nonlinear filtering algorithms

A Taghvaei, B Hosseini - 2022 IEEE 61st Conference on …, 2022 - ieeexplore.ieee.org
This paper presents a variational representation of the Bayes' law using optimal
transportation theory. The variational representation is in terms of the optimal transportation …

A particle filter for stochastic advection by Lie transport: a case study for the damped and forced incompressible two-dimensional Euler equation

C Cotter, D Crisan, DD Holm, W Pan… - SIAM/ASA Journal on …, 2020 - SIAM
In this work, we combine a stochastic model reduction with a particle filter augmented with
tempering and jittering, and apply the combined algorithm to a damped and forced …