Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2610.36746

ODAT-SE: A modular and parallel framework for simulation-based inverse problems

Tatsumi Aoyama·Kazuyoshi Yoshimi·Yuichi Motoyama·Akito Nakano·Hengyu Li·Yusuke Konishi·Takeo Hoshi
View original source ↗Read source document ↗Export metadata ↓

Abstract

Open Data Analysis Tool for Science and Engineering (ODAT-SE) is an open-source Python framework for inverse problems that are solved by repeated forward simulations. It succeeds 2DMAT, which was developed for surface-structure analysis with quantum-beam diffraction and has since been applied to other fields. In version 3, the search algorithms were separated from the application-specific solvers, which became independent packages, and the software was renamed; this paper describes the current version 4.0. The framework connects optimization and sampling algorithms to solvers through a common interface for parameter mapping, constraints, and objective evaluation, so that an existing simulation code can be used with any of the algorithms. Relative to the previously published 2DMAT, it provides two-level MPI parallelism, which distributes candidate evaluations over processes and each evaluation over a parallel solver, checkpoint and continuation facilities, random search, global optimizers from SciPy, tensor-train optimization, and a Bayesian workflow that estimates partition-function ratios, model evidence, effective noise levels, and marginal posterior distributions. We validate the Bayesian workflow against closed-form results for a linear regression, benchmark tensor-train optimization on continuous, binary, and mixed-integer problems, and verify the two-level parallelization by the same optimum for all process decompositions. Taking up the positron-diffraction example of the 2DMAT paper, the workflow identifies the correlated structural solutions and an effective noise scale close to the imposed perturbation, while exposing incomplete convergence of symmetry-related mode weights. Solver packages, templates, and a gallery of examples support the use of the framework as a general platform for inverse-problem analysis.

Explore related subjects

math.NAcond-mat.mtrl-scics.NA

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tatsumi Aoyama, Kazuyoshi Yoshimi, Yuichi Motoyama, Akito Nakano, Hengyu Li, Yusuke Konishi, Takeo Hoshi. 2026-10-27. ODAT-SE: A modular and parallel framework for simulation-based inverse problems. https://arxiv.org/abs/2610.36746

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Extracting Dual Analytic Geometries of Linear Transformations to Achieve Efficient Computation

We generalize the Calderon-Zygmund methodology for operator analysis and the Rokhlin-Greengard fast multipole algorithms, in which the domain and range of an operator are jointly organized. Our methods analyze unstructured kernels by uncovering the joint hidden geometries of their domain and range. The main tool is the Questionnaire algorithm, an iterative procedure that constructs adaptive bi-hierarchical partition trees that reveal latent multiscale organization and local low-rank structure in the kernel. When the geometry is unknown, the iteration starts from any initial affinity, even a random one, and, with a stochastic flip perturbation and a spectral space-filling curve that fixes the left-right order of every tree, reorganizes the matrix into an image of the operator's "phase space": the joint space of its sources and sensors, in duality, as positions and frequencies are for the Fourier transform. This ordering gives the phase space an analytic structure on which any classical transform can be carried out; the resulting compression is direct evidence of that structure. Guided by these geometries, we obtain efficient factorizations and fast matrix-vector products in two ways: (1) the Butterfly algorithm, which exploits the learned bi-hierarchical localized low-rank structure; and (2) the adaptive eGHWT, which selects best tilings in space and sequency from all levels of generalized Haar-Walsh wavelet packets. We call the resulting algorithms the Questionnaire Factorization and Fast Transform (QFFT). Unlike classical approaches requiring prior knowledge of the geometry, QFFT is fully data-driven and applies to matrices from irregular or unknown distributions. We demonstrate it on heterogeneous oscillatory operators and on orthogonal eigenvector expansions with high multiplicity and random sampling, reducing storage from O(N^2) to O(N log N) and enabling fast, scalable computation.

math.NA↗
arXiv2026

Decoupled energy-stable Runge-Kutta schemes of arbitrary order for the anisotropic phase-field dendritic crystal growth model

This paper introduces a novel and general framework for constructing arbitrary-order, energy-stable, and decoupled schemes for the anisotropic phase-field dendritic crystal growth model. The proposed framework combines a time-dependent auxiliary variable, an algebraically stable Runge-Kutta method, and a matrix diagonalization technique. This unique combination yields a scheme that is proven to be unconditionally energy-dissipative while requiring only the solution of independent, constant-coefficient elliptic equations at each time step, which can be solved in parallel. The auxiliary variable is recovered from a uniquely solvable $q\times q$ algebraic system. We provide a rigorous proof of $q$th-order convergence in time for a $q$-stage Runge-Kutta method within a fixed Fourier-Galerkin space. Numerical experiments in 2D and 3D not only confirm the theoretical convergence and energy stability but also demonstrate the efficiency of the decoupled approach and provide a detailed investigation of key parameters' effects on dendritic morphology.

math.NA↗
arXiv2026

Automated Numerical Stability Analysis of Deep Learning Operators

Finite-precision arithmetic unavoidably introduces numerical approximation errors. Numerical computations may use insufficient precision or an improper formulation, which leads to numerical instability. In this paper, we introduce a unified software tool for stochastic numerical validation of deep-learning operators. The tool follows CESTAC on supported exposed operations and uses an operator-level data-perturbation approximation for GEMM-like kernels. Our developed software not only enables numerical validation with a single computation pass but also detects the sources of numerical instability and provides numerical stability monitoring during deep learning training and inference. We verified its effectiveness on the detection of polluted operators with injected numerical instabilities across various tasks. We believe that our developed method and tools provide valuable insights into developing numerically stable computing kernels, which are particularly critical for numerically stable and efficient deep learning training and inference.

math.NA↗