Stochastic Dynamics in Computational Biology

The aim of this book is to provide a well-structured and coherent overview of existing mathematical modeling approaches for biochemical reaction systems, investigating relations between both the conventional models and several types of deterministic-stochastic hybrid model recombinations. Another main objective is to illustrate and compare diverse numerical simulation schemes and their computational effort. Unlike related works, this book presents a broad scope in its applications, from offering a detailed introduction to hybrid approaches for the case of multiple population scales to discussing the setting of time-scale separation resulting from widely varying firing rates of reaction channels. Additionally, it also addresses modeling approaches for non well-mixed reaction-diffusion dynamics, including deterministic and stochastic PDEs and spatiotemporal master equations. Finally, by translating and incorporating complex theory to a level accessible to non-mathematicians, this book effectively bridges the gap between mathematical research in computational biology and its practical use in biological, biochemical, and biomedical systems

Fredholm integral equations for function approximation and the training of neural networks

We present a novel and mathematically transparent approach to function approximation and the training of large, high-dimensional neural networks, based on the approximate least-squares solution of associated Fredholm integral equations of the first kind by Ritz-Galerkin discretization, Tikhonov regularization and tensor-train methods. Practical application to supervised learning problems of regression and classification type confirm that the resulting algorithms are competitive with state-of-the-art neural network-based methods

Quasi-Monte Carlo for partial differential equations with generalized Gaussian input uncertainty

There has been a surge of interest in uncertainty quantification for parametric partial differential equations (PDEs) with Gevrey regular inputs. The Gevrey class contains functions that are infinitely smooth with a growth condition on the higher-order partial derivatives, but which are nonetheless not analytic in general. Recent studies by Chernov and Le (Comput. Math. Appl., 2024, and SIAM J. Numer. Anal., 2024) as well as Harbrecht, Schmidlin, and Schwab (Math. Models Methods Appl. Sci., 2024) analyze the setting wherein the input random field is assumed to be uniformly bounded with respect to the uncertain parameters. In this paper, we relax this assumption and allow for parameter-dependent bounds. The parametric inputs are modeled as generalized Gaussian random variables, and we analyze the application of quasi-Monte Carlo (QMC) integration to assess the PDE response statistics using randomly shifted rank-1 lattice rules. In addition to the QMC error analysis, we also consider the dimension truncation and finite element errors in this setting

Uncertainty quantification for electrical impedance tomography using quasi-Monte Carlo methods

The theoretical development of quasi-Monte Carlo (QMC) methods for uncertainty quantification of partial differential equations (PDEs) is typically centered around simplified model problems such as elliptic PDEs subject to homogeneous zero Dirichlet boundary conditions. In this paper, we present a theoretical treatment of the application of randomly shifted rank-1 lattice rules to electrical impedance tomography (EIT). EIT is an imaging modality, where the goal is to reconstruct the interior conductivity of an object based on electrode measurements of current and voltage taken at the boundary of the object. This is an inverse problem, which we tackle using the Bayesian statistical inversion paradigm. As the reconstruction, we consider QMC integration to approximate the unknown conductivity given current and voltage measurements. We prove under moderate assumptions placed on the parameterization of the unknown conductivity that the QMC approximation of the reconstructed estimate has a dimension-independent, faster-than-Monte Carlo cubature convergence rate. Finally, we present numerical results for examples computed using simulated measurement data

Quasi-Monte Carlo for Bayesian design of experiment problems governed by parametric PDEs

This paper contributes to the study of optimal experimental design for Bayesian inverse problems governed by partial differential equations (PDEs). We derive estimates for the parametric regularity of multivariate double integration problems over high-dimensional parameter and data domains arising in Bayesian optimal design problems. We provide a detailed analysis for these double integration problems using two approaches: a full tensor product and a sparse tensor product combination of quasi-Monte Carlo (QMC) cubature rules over the parameter and data domains. Specifically, we show that the latter approach significantly improves the convergence rate, exhibiting performance comparable to that of QMC integration of a single high-dimensional integral. Furthermore, we numerically verify the predicted convergence rates for an elliptic PDE problem with an unknown diffusion coefficient in two spatial dimensions, offering empirical evidence supporting the theoretical results and highlighting practical applicability