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- ItemStatistical parametric maps for functional MRI experiments in R: The package fmri(Los Angeles : UCLA, 2011) Tabelow, K.; Polzehl, J.The purpose of the package fmri is the analysis of single subject functional magnetic resonance imaging (fMRI) data. It provides fMRI analysis from time series modeling by a linear model to signal detection and publication quality images. Specifically, it implements structural adaptive smoothing methods with signal detection for adaptive noise reduction which avoids blurring of activation areas. Within this paper we describe the complete pipeline for fMRI analysis using fmri. We describe data reading from various medical imaging formats and the linear modeling used to create the statistical parametric maps. We review the rationale behind the structural adaptive smoothing algorithms and explain their usage from the package fmri. We demonstrate the results of such analysis using two experimental datasets. Finally, we report on the usage of a graphical user interface for some of the package functions.
- ItemFirst-Order Methods for Convex Optimization(Amsterdam : Elsevier, 2021) Dvurechensky, Pavel; Shtern, Shimrit; Staudigl, MathiasFirst-order methods for solving convex optimization problems have been at the forefront of mathematical optimization in the last 20 years. The rapid development of this important class of algorithms is motivated by the success stories reported in various applications, including most importantly machine learning, signal processing, imaging and control theory. First-order methods have the potential to provide low accuracy solutions at low computational complexity which makes them an attractive set of tools in large-scale optimization problems. In this survey, we cover a number of key developments in gradient-based optimization methods. This includes non-Euclidean extensions of the classical proximal gradient method, and its accelerated versions. Additionally we survey recent developments within the class of projection-free methods, and proximal versions of primal-dual schemes. We give complete proofs for various key results, and highlight the unifying aspects of several optimization algorithms.
- ItemVariable Step Mollifiers and Applications(Berlin ; Heidelberg : Springer, 2020) Hintermüller, Michael; Papafitsoros, Kostas; Rautenberg, Carlos N.We consider a mollifying operator with variable step that, in contrast to the standard mollification, is able to preserve the boundary values of functions. We prove boundedness of the operator in all basic Lebesgue, Sobolev and BV spaces as well as corresponding approximation results. The results are then applied to extend recently developed theory concerning the density of convex intersections. © 2020, The Author(s).
- ItemOn the convergence order of the finite element error in the kinetic energy for high Reynolds number incompressible flows(Amsterdam [u.a.] : Elsevier Science, 2021) García-Archilla, Bosco; John, Volker; Novo, JuliaThe kinetic energy of a flow is proportional to the square of the norm of the velocity. Given a sufficient regular velocity field and a velocity finite element space with polynomials of degree , then the best approximation error in is of order . In this survey, the available finite element error analysis for the velocity error in is reviewed, where is a final time. Since in practice the case of small viscosity coefficients or dominant convection is of particular interest, which may result in turbulent flows, robust error estimates are considered, i.e., estimates where the constant in the error bound does not depend on inverse powers of the viscosity coefficient. Methods for which robust estimates can be derived enable stable flow simulations for small viscosity coefficients on comparatively coarse grids, which is often the situation encountered in practice. To introduce stabilization techniques for the convection-dominated regime and tools used in the error analysis, evolutionary linear convection–diffusion equations are studied at the beginning. The main part of this survey considers robust finite element methods for the incompressible Navier–Stokes equations of order , , and for the velocity error in . All these methods are discussed in detail. In particular, a sketch of the proof for the error bound is given that explains the estimate of important terms which determine finally the order of convergence. Among them, there are methods for inf–sup stable pairs of finite element spaces as well as for pressure-stabilized discretizations. Numerical studies support the analytic results for several of these methods. In addition, methods are surveyed that behave in a robust way but for which only a non-robust error analysis is available. The conclusion of this survey is that the problem of whether or not there is a robust method with optimal convergence order for the kinetic energy is still open.
- ItemDrift–diffusion simulation of S-shaped current–voltage relations for organic semiconductor devices(Dordrecht : Springer Science + Business Media B.V., 2020) Doan, Duy Hai; Fischer, Axel; Fuhrmann, Jürgen; Glitzky, Annegret; Liero, MatthiasWe present an electrothermal drift–diffusion model for organic semiconductor devices with Gauss–Fermi statistics and positive temperature feedback for the charge carrier mobilities. We apply temperature-dependent Ohmic contact boundary conditions for the electrostatic potential and discretize the system by a finite volume based generalized Scharfetter–Gummel scheme. Using path-following techniques, we demonstrate that the model exhibits S-shaped current–voltage curves with regions of negative differential resistance, which were only recently observed experimentally. © 2020, The Author(s).
- ItemHigh order discretization methods for spatial-dependent epidemic models(Amsterdam [u.a.] : Elsevier Science, 2022) Takács, Bálint; Hadjimichael, YiannisIn this paper, an epidemic model with spatial dependence is studied and results regarding its stability and numerical approximation are presented. We consider a generalization of the original Kermack and McKendrick model in which the size of the populations differs in space. The use of local spatial dependence yields a system of partial-differential equations with integral terms. The uniqueness and qualitative properties of the continuous model are analyzed. Furthermore, different spatial and temporal discretizations are employed, and step-size restrictions for the discrete model’s positivity, monotonicity preservation, and population conservation are investigated. We provide sufficient conditions under which high-order numerical schemes preserve the stability of the computational process and provide sufficiently accurate numerical approximations. Computational experiments verify the convergence and accuracy of the numerical methods.
- ItemA function space framework for structural total variation regularization with applications in inverse problems(Bristol [u.a.] : Inst., 2018) Hintermüller, Michael; Holler, Martin; Papafitsoros, KostasIn this work, we introduce a function space setting for a wide class of structural/weighted total variation (TV) regularization methods motivated by their applications in inverse problems. In particular, we consider a regularizer that is the appropriate lower semi-continuous envelope (relaxation) of a suitable TV type functional initially defined for sufficiently smooth functions. We study examples where this relaxation can be expressed explicitly, and we also provide refinements for weighted TV for a wide range of weights. Since an integral characterization of the relaxation in function space is, in general, not always available, we show that, for a rather general linear inverse problems setting, instead of the classical Tikhonov regularization problem, one can equivalently solve a saddle-point problem where no a priori knowledge of an explicit formulation of the structural TV functional is needed. In particular, motivated by concrete applications, we deduce corresponding results for linear inverse problems with norm and Poisson log-likelihood data discrepancy terms. Finally, we provide proof-of-concept numerical examples where we solve the saddle-point problem for weighted TV denoising as well as for MR guided PET image reconstruction.
- ItemNumerical upscaling of parametric microstructures in a possibilistic uncertainty framework with tensor trains(Heidelberg : Springer, 2022) Eigel, Martin; Gruhlke, Robert; Moser, Dieter; Grasedyck, LarsA fuzzy arithmetic framework for the efficient possibilistic propagation of shape uncertainties based on a novel fuzzy edge detection method is introduced. The shape uncertainties stem from a blurred image that encodes the distribution of two phases in a composite material. The proposed framework employs computational homogenisation to upscale the shape uncertainty to a effective material with fuzzy material properties. For this, many samples of a linear elasticity problem have to be computed, which is significantly sped up by a highly accurate low-rank tensor surrogate. To ensure the continuity of the underlying mapping from shape parametrisation to the upscaled material behaviour, a diffeomorphism is constructed by generating an appropriate family of meshes via transformation of a reference mesh. The shape uncertainty is then propagated to measure the distance of the upscaled material to the isotropic and orthotropic material class. Finally, the fuzzy effective material is used to compute bounds for the average displacement of a non-homogenized material with uncertain star-shaped inclusion shapes.
- ItemLow-rank tensor reconstruction of concentrated densities with application to Bayesian inversion(Dordrecht [u.a.] : Springer Science + Business Media B.V, 2022) Eigel, Martin; Gruhlke, Robert; Marschall, ManuelThis paper presents a novel method for the accurate functional approximation of possibly highly concentrated probability densities. It is based on the combination of several modern techniques such as transport maps and low-rank approximations via a nonintrusive tensor train reconstruction. The central idea is to carry out computations for statistical quantities of interest such as moments based on a convenient representation of a reference density for which accurate numerical methods can be employed. Since the transport from target to reference can usually not be determined exactly, one has to cope with a perturbed reference density due to a numerically approximated transport map. By the introduction of a layered approximation and appropriate coordinate transformations, the problem is split into a set of independent approximations in seperately chosen orthonormal basis functions, combining the notions h- and p-refinement (i.e. “mesh size” and polynomial degree). An efficient low-rank representation of the perturbed reference density is achieved via the Variational Monte Carlo method. This nonintrusive regression technique reconstructs the map in the tensor train format. An a priori convergence analysis with respect to the error terms introduced by the different (deterministic and statistical) approximations in the Hellinger distance and the Kullback–Leibler divergence is derived. Important applications are presented and in particular the context of Bayesian inverse problems is illuminated which is a main motivation for the developed approach. Several numerical examples illustrate the efficacy with densities of different complexity and degrees of perturbation of the transport to the reference density. The (superior) convergence is demonstrated in comparison to Monte Carlo and Markov Chain Monte Carlo methods.
- ItemReconstruction of Quasi-Local Numerical Effective Models from Low-Resolution Measurements(New York, NY [u.a.] : Springer Science + Business Media B.V., 2020) Caiazzo, A.; Maier, R.; Peterseim, D.We consider the inverse problem of reconstructing an effective model for a prototypical diffusion process in strongly heterogeneous media based on coarse measurements. The approach is motivated by quasi-local numerical effective forward models that are provably reliable beyond periodicity assumptions and scale separation. The goal of this work is to show that an identification of the matrix representation related to these effective models is possible. On the one hand, this provides a reasonable surrogate in cases where a direct reconstruction is unfeasible due to a mismatch between the coarse data scale and the microscopic quantities to be reconstructed. On the other hand, the approach allows us to investigate the requirement for a certain non-locality in the context of numerical homogenization. Algorithmic aspects of the inversion procedure and its performance are illustrated in a series of numerical experiments. © 2020, The Author(s).