arXiv subjects

Andreas Mang

Publications and source records attributed to Andreas Mang.

At least 19 recordsLinked to original sources

arXiv2026

Tensor-Based Reduced-Order Modeling for Optimization-Based Inverse Problems

We develop a tensor reduced-order modeling (TROM) framework for optimization-based inverse problems governed by parameter-dependent dynamical systems. The approach approximates the parameter-to-observation map directly in tensor-train (TT) format using TT-SVD or TT-Cross and integrates it into a regularized nonlinear least-squares formulation. Beyond accelerating forward evaluations, the low-rank tensor structure reformulates the inverse problem in reduced coordinates, assembles Gauss--Newton quantities without forming the full observation-space Jacobian, and minimizes the TROM objective over the discrete parameter grid. This tensor optimization provides either a stand-alone approximate solution or a data-informed initialization for a subsequent Gauss--Newton solve. We study an inverse heat-transfer problem in a heterogeneous medium, where the parameters describe the locations and radii of low-conductivity inclusions, and a FitzHugh--Nagumo parameter-estimation problem with a highly nonconvex landscape. Numerical experiments assess reduced-order model error, measurement noise, regularization, initialization, spatial discretization, and increasing parameter dimension. The results show that TROM reproduces full-order inversion at substantially reduced online cost. They also demonstrate that reduced-coordinate inversion, tensor-based optimization, and appropriate regularization improve robustness in higher-dimensional, noisy, and strongly nonconvex regimes. For the continuous TROM inverse problem, we develop an error-to-inversion analysis. Under local strong convexity of the regularized FOM objective and parametric smoothness of the FOM observation map, the error between the parameters recovered with the full-order model and TROM is bounded by controlled uniform errors in the surrogate map and its Jacobian, together with local FOM and curvature quantities.

math.NA↗

arXiv2026

Tensorial Reduced-Order Models for Parametric Coupled Reaction-Diffusion Systems: Application to Brain Tumor Growth Modeling

We construct efficient surrogate models for parametric forward operators arising in brain tumor growth simulations, governed by coupled semilinear parabolic reaction-diffusion systems on heterogeneous two- and three-dimensional domains. We consider two models of increasing complexity: a scalar single-species formulation and a six-state, nine-parameter multi-species go-or-grow model. The governing equations are discretized using a finite volume method and integrated in time via an operator-splitting strategy. We develop tensorial reduced-order model (TROM) surrogates based on the Higher-Order Singular Value Decomposition in Tucker format and the Tensor Train decomposition, each in intrusive and non-intrusive variants. The models are compared against a classical proper orthogonal decomposition (POD) ROM baseline. Numerical experiments with up to $m=9$ model parameters demonstrate speedups of $85\times$-$120\times$ relative to the full-order solver while maintaining excellent accuracy, establishing tensorial surrogates as a rigorous and efficient computational foundation for many-query workflows.

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arXiv2025

Fast $k$-means clustering in Riemannian manifolds via Fr\'{e}chet maps: Applications to large-dimensional SPD matrices

We introduce a novel, efficient framework for clustering data on high-dimensional, non-Euclidean manifolds that overcomes the computational challenges associated with standard intrinsic methods. The key innovation is the use of the $p$-Fr\'{e}chet map $F^p : \mathcal{M} \to \mathbb{R}^\ell$ -- defined on a generic metric space $\mathcal{M}$ -- which embeds the manifold data into a lower-dimensional Euclidean space $\mathbb{R}^\ell$ using a set of reference points $\{r_i\}_{i=1}^\ell$, $r_i \in \mathcal{M}$. Once embedded, we can efficiently and accurately apply standard Euclidean clustering techniques such as k-means. We rigorously analyze the mathematical properties of $F^p$ in the Euclidean space and the challenging manifold of $n \times n$ symmetric positive definite matrices $\mathit{SPD}(n)$. Extensive numerical experiments using synthetic and real $\mathit{SPD}(n)$ data demonstrate significant performance gains: our method reduces runtime by up to two orders of magnitude compared to intrinsic manifold-based approaches, all while maintaining high clustering accuracy, including scenarios where existing alternative methods struggle or fail.

cs.LG↗

arXiv2025

Neural Networks for Bayesian Inverse Problems Governed by a Nonlinear ODE

We investigate the use of neural networks (NNs) for the estimation of hidden model parameters and uncertainty quantification from noisy observational data for inverse parameter estimation problems. We formulate the parameter estimation as a Bayesian inverse problem. We consider a parametrized system of nonlinear ordinary differential equations (ODEs), which is the FitzHugh--Nagumo model. The considered problem exhibits significant mathematical and computational challenges for classical parameter estimation methods, including strong nonlinearities, nonconvexity, and sharp gradients. We explore how NNs overcome these challenges by approximating reconstruction maps for parameter estimation from observational data. The considered data are time series of the spiking membrane potential of a biological neuron. We infer parameters controlling the dynamics of the model, noise parameters of autocorrelated additive noise, and noise modeled via stochastic differential equations, as well as the covariance matrix of the posterior distribution to expose parameter uncertainties--all with just one forward evaluation of an appropriate NN. We report results for different NN architectures and study the influence of noise on prediction accuracy. We also report timing results for training NNs on dedicated hardware. Our results demonstrate that NNs are a versatile tool to estimate parameters of the dynamical system, stochastic processes, as well as uncertainties, as they propagate through the governing ODE.

math.NA↗

arXiv2025

VPREG: An Optimal Control Formulation for Diffeomorphic Image Registration Based on the Variational Principle Grid Generation Method

This paper introduces VPreg, a novel diffeomorphic image registration method. This work provides several improvements to our past work on mesh generation and diffeomorphic image registration. VPreg aims to achieve excellent registration accuracy while controlling the quality of the registration transformations. It ensures a positive Jacobian determinant of the spatial transformation and provides an accurate approximation of the inverse of the registration, a crucial property for many neuroimaging workflows. Unlike conventional methods, VPreg generates this inverse transformation within the group of diffeomorphisms rather than operating on the image space. The core of VPreg is a grid generation approach, referred to as \emph{Variational Principle} (VP), which constructs non-folding grids with prescribed Jacobian determinant and curl. These VP-generated grids guarantee diffeomorphic spatial transformations essential for computational anatomy and morphometry, and provide a more accurate inverse than existing methods. To assess the potential of the proposed approach, we conduct a performance analysis for 150 registrations of brain scans from the OASIS-1 dataset. Performance evaluation based on Dice scores for 35 regions of interest, along with an empirical analysis of the properties of the computed spatial transformations, demonstrates that VPreg outperforms state-of-the-art methods in terms of Dice scores, regularity properties of the computed transformation, and accuracy and consistency of the provided inverse map. We compare our results to ANTs-SyN, Freesurfer-Easyreg, and FSL-Fnirt.

cs.CV↗

arXiv2025

A Unified Framework for Lifted Training and Inversion Approaches

The training of deep neural networks predominantly relies on a combination of gradient-based optimisation and back-propagation for the computation of the gradient. While incredibly successful, this approach faces challenges such as vanishing or exploding gradients, difficulties with non-smooth activations, and an inherently sequential structure that limits parallelisation. Lifted training methods offer an alternative by reformulating the nested optimisation problem into a higher-dimensional, constrained optimisation problem where the constraints are no longer enforced directly but penalised with penalty terms. This chapter introduces a unified framework that encapsulates various lifted training strategies, including the Method of Auxiliary Coordinates, Fenchel Lifted Networks, and Lifted Bregman Training, and demonstrates how diverse architectures, such as Multi-Layer Perceptrons, Residual Neural Networks, and Proximal Neural Networks fit within this structure. By leveraging tools from convex optimisation, particularly Bregman distances, the framework facilitates distributed optimisation, accommodates non-differentiable proximal activations, and can improve the conditioning of the training landscape. We discuss the implementation of these methods using block-coordinate descent strategies, including deterministic implementations enhanced by accelerated and adaptive optimisation techniques, as well as implicit stochastic gradient methods. Furthermore, we explore the application of this framework to inverse problems, detailing methodologies for both the training of specialised networks (e.g., unrolled architectures) and the stable inversion of pre-trained networks. Numerical results on standard imaging tasks validate the effectiveness and stability of the lifted Bregman approach compared to conventional training, particularly for architectures employing proximal activations.

cs.LG↗

arXiv2025

A generalized alternating NGMRES method for PDE-constrained optimization problems governed by transport equations

In this work, we propose a generalized alternating nonlinear generalized minimal residual method (GA-NGMRES) to accelerate first-order optimization schemes for PDE-constrained optimization problems governed by transport equations. We apply GA-NGMRES to a preconditioned first-order optimization scheme by interpreting the update rule as a fixed-point (FP) iteration. Our approach introduces a novel periodic mixing strategy that integrates NGMRES updates with FP steps. This new scheme improves efficiency in terms of both iteration count and runtime compared to the state-of-the-art. We include a comparison to first-order preconditioned gradient descent and preconditioned, inexact Gauss--Newton--Krylov methods. Since the proposed optimization scheme only relies on first-order derivative information, its implementation is straightforward. We evaluate performance as a function of hyperparameters, the mesh size, and the regularization parameter. We consider advection, incompressible flows, and mass-preserving transport (i.e., optimal transport-type problems) as PDE models. Stipulating adequate smoothness requirements based on variational regularization of the control variable ensures that the computed transport maps are diffeomorphic. Numerical experiments on real-world and synthetic problems highlight the robustness and effectiveness of the proposed method. Our approach yields runtimes that are up to 5x faster than state-of-the-art Newton--Krylov methods, without sacrificing accuracy. Additionally, our GA-NGMRES algorithm outperforms the well-known Anderson acceleration for the models and numerical approach considered in this work.

math.OC↗

arXiv2024

CLAIRE: Scalable GPU-Accelerated Algorithms for Diffeomorphic Image Registration in 3D

We present our work on scalable, GPU-accelerated algorithms for diffeomorphic image registration. The associated software package is termed CLAIRE. Image registration is a non-linear inverse problem. It is about computing a spatial mapping from one image of the same object or scene to another. In diffeomorphic image registration, the set of admissible spatial transformations is restricted to maps that are smooth, one-to-one, and have a smooth inverse. We formulate diffeomorphic image registration as a variational problem governed by transport equations. We use an inexact, globalized (Gauss--)Newton--Krylov method for numerical optimization. We consider semi-Lagrangian methods for numerical time integration. Our solver features mixed-precision, hardware-accelerated computational kernels for optimal computational throughput. We use the message-passing interface for distributed-memory parallelism and deploy our code on modern high-performance computing architectures. Our solver allows us to solve clinically relevant problems in under four seconds on a single GPU. It can also be applied to large-scale 3D imaging applications with data that is discretized on meshes with billions of voxels. We demonstrate that our numerical framework yields high-fidelity results in only a few seconds, even if we search for an optimal regularization parameter.

math.OC↗

arXiv2023

Rare Events Analysis and Computation for Stochastic Evolution of Bacterial Populations

In this paper, we develop a computational approach for computing most likely trajectories describing rare events that correspond to the emergence of non-dominant genotypes. This work is based on the large deviations approach for discrete Markov chains describing the genetic evolution of large bacterial populations. We demonstrate that a gradient descent algorithm developed in this paper results in the fast and accurate computation of most-likely trajectories for a large number of bacterial genotypes. We supplement our analysis with extensive numerical simulations demonstrating the computational advantage of the designed gradient descent algorithm over other, more simplified, approaches.

q-bio.PE↗

arXiv2023

An Operator-Splitting Approach for Variational Optimal Control Formulations for Diffeomorphic Shape Matching

We present formulations and numerical algorithms for solving diffeomorphic shape matching problems. We formulate shape matching as a variational problem governed by a dynamical system that models the flow of diffeomorphism $f_t \in \operatorname{diff}(\mathbb{R}^3)$. We overview our contributions in this area, and present an improved, matrix-free implementation of an operator splitting strategy for diffeomorphic shape matching. We showcase results for diffeomorphic shape matching of real clinical cardiac data in $\mathbb{R}^3$ to assess the performance of our methodology.

math.OC↗

arXiv2022

Automatic classification of deformable shapes

Let $\mathcal{D}$ be a dataset of smooth 3D-surfaces, partitioned into disjoint classes $\mathit{CL}_j$, $j= 1, \ldots, k$. We show how optimized diffeomorphic registration applied to large numbers of pairs $S,S' \in \mathcal{D}$ can provide descriptive feature vectors to implement automatic classification on $\mathcal{D}$, and generate classifiers invariant by rigid motions in $\mathbb{R}^3$. To enhance accuracy of automatic classification, we enrich the smallest classes $\mathit{CL}_j$ by diffeomorphic interpolation of smooth surfaces between pairs $S,S' \in \mathit{CL}_j$. We also implement small random perturbations of surfaces $S\in \mathit{CL}_j$ by random flows of smooth diffeomorphisms $F_t:\mathbb{R}^3 \to \mathbb{R}^3$. Finally, we test our automatic classification methods on a cardiology data base of discretized mitral valve surfaces.

cs.CV↗

arXiv2022

CLAIRE -- Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications

We study the performance of CLAIRE -- a diffeomorphic multi-node, multi-GPU image-registration algorithm, and software -- in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower-resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality -- but not always. For example, downsampling a synthetic image from $1024^3$ to $256^3$ decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low-contrast high-resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in a reasonable time. The highest resolution considered is CLARITY images of size $2816\times3016\times1162$. To the best of our knowledge, this is the first study on image registration quality at such resolutions.

cs.CV↗

arXiv2021

Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies

Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate the proposed automatic cell tracking algorithm using (i) recordings of simulated cell colonies that closely mimic the growth dynamics of E. coli in microfluidic traps and (ii) real data. On a batch of 1100 simulated image frames, cell registration accuracies per frame ranged from 94.5% to 100%, with a high average. Our initial tests using experimental image sequences (i.e., real data) of E. coli colonies also yield convincing results, with a registration accuracy ranging from 90% to 100%.

cs.CV↗

arXiv2020

Diffeomorphic Shape Matching by Operator Splitting in 3D Cardiology Imaging

We develop an operator splitting approach to solve diffeomorphic matching problems for sequences of surfaces in three-dimensional space. The goal is to smoothly match, at a very fast rate, finite sequences of observed 3D-snapshots extracted from movies recording the smooth dynamic deformations of "soft" surfaces. We have implemented our algorithms in a proprietary software installed at The Methodist Hospital (Cardiology) to monitor mitral valve strain through computer analysis of noninvasive patients' echocardiographies.

math.OC↗

arXiv2020

Multi-Node Multi-GPU Diffeomorphic Image Registration for Large-Scale Imaging Problems

We present a Gauss-Newton-Krylov solver for large deformation diffeomorphic image registration. We extend the publicly available CLAIRE library to multi-node multi-graphics processing unit (GPUs) systems and introduce novel algorithmic modifications that significantly improve performance. Our contributions comprise ($i$) a new preconditioner for the reduced-space Gauss-Newton Hessian system, ($ii$) a highly-optimized multi-node multi-GPU implementation exploiting device direct communication for the main computational kernels (interpolation, high-order finite difference operators and Fast-Fourier-Transform), and ($iii$) a comparison with state-of-the-art CPU and GPU implementations. We solve a $256^3$-resolution image registration problem in five seconds on a single NVIDIA Tesla V100, with a performance speedup of 70% compared to the state-of-the-art. In our largest run, we register $2048^3$ resolution images (25 B unknowns; approximately 152$\times$ larger than the largest problem solved in state-of-the-art GPU implementations) on 64 nodes with 256 GPUs on TACC's Longhorn system.

cs.DC↗

arXiv2020

Fast GPU 3D Diffeomorphic Image Registration

3D image registration is one of the most fundamental and computationally expensive operations in medical image analysis. Here, we present a mixed-precision, Gauss--Newton--Krylov solver for diffeomorphic registration of two images. Our work extends the publicly available CLAIRE library to GPU architectures. Despite the importance of image registration, only a few implementations of large deformation diffeomorphic registration packages support GPUs. Our contributions are new algorithms to significantly reduce the run time of the two main computational kernels in CLAIRE: calculation of derivatives and scattered-data interpolation. We deploy (i) highly-optimized, mixed-precision GPU-kernels for the evaluation of scattered-data interpolation, (ii) replace Fast-Fourier-Transform (FFT)-based first-order derivatives with optimized 8th-order finite differences, and (iii) compare with state-of-the-art CPU and GPU implementations. As a highlight, we demonstrate that we can register $256^3$ clinical images in less than 6 seconds on a single NVIDIA Tesla V100. This amounts to over 20$\times$ speed-up over the current version of CLAIRE and over 30$\times$ speed-up over existing GPU implementations.

cs.DC↗

arXiv2020

Integrated Biophysical Modeling and Image Analysis: Application to Neuro-Oncology

Central nervous system (CNS) tumors come with the vastly heterogeneous histologic, molecular and radiographic landscape, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics have shown promise in better characterizing the molecular, spatial, and temporal heterogeneity of tumors. Integrative analysis of CNS tumors, including clinically-acquired multi-parametric magnetic resonance imaging (mpMRI) and the inverse problem of calibrating biophysical models to mpMRI data, assists in identifying macroscopic quantifiable tumor patterns of invasion and proliferation, potentially leading to improved (i) detection/segmentation of tumor sub-regions, and (ii) computer-aided diagnostic/prognostic/predictive modeling. This paper presents a summary of (i) biophysical growth modeling and simulation, (ii) inverse problems for model calibration, (iii) their integration with imaging workflows, and (iv) their application on clinically-relevant studies. We anticipate that such quantitative integrative analysis may even be beneficial in a future revision of the World Health Organization (WHO) classification for CNS tumors, ultimately improving patient survival prospects.

q-bio.QM↗

arXiv2019

CLAIRE: A distributed-memory solver for constrained large deformation diffeomorphic image registration

With this work, we release CLAIRE, a distributed-memory implementation of an effective solver for constrained large deformation diffeomorphic image registration problems in three dimensions. We consider an optimal control formulation. We invert for a stationary velocity field that parameterizes the deformation map. Our solver is based on a globalized, preconditioned, inexact reduced space Gauss--Newton--Krylov scheme. We exploit state-of-the-art techniques in scientific computing to develop an effective solver that scales to thousands of distributed memory nodes on high-end clusters. We present the formulation, discuss algorithmic features, describe the software package, and introduce an improved preconditioner for the reduced space Hessian to speed up the convergence of our solver. We test registration performance on synthetic and real data. We demonstrate registration accuracy on several neuroimaging datasets. We compare the performance of our scheme against different flavors of the Demons algorithm for diffeomorphic image registration. We study convergence of our preconditioner and our overall algorithm. We report scalability results on state-of-the-art supercomputing platforms. We demonstrate that we can solve registration problems for clinically relevant data sizes in two to four minutes on a standard compute node with 20 cores, attaining excellent data fidelity. With the present work we achieve a speedup of (on average) 5$\times$ with a peak performance of up to 17$\times$ compared to our former work.

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