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Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…

Biomolecules · Quantitative Biology 2025-03-25 Zhongyue Zhang , Runze Ma , Yanjie Huang , Shuangjia Zheng

Traditional linear subspace reduced order models (LS-ROMs) are able to accelerate physical simulations, in which the intrinsic solution space falls into a subspace with a small dimension, i.e., the solution space has a small Kolmogorov…

Numerical Analysis · Mathematics 2025-11-06 Youngkyu Kim , Youngsoo Choi , David Widemann , Tarek Zohdi

We introduce a method that combines neural operators, physics-informed machine learning, and standard numerical methods for solving PDEs. The proposed approach extends each of the aforementioned methods and unifies them within a single…

Computational Engineering, Finance, and Science · Computer Science 2025-12-02 Shahed Rezaei , Reza Najian Asl , Kianoosh Taghikhani , Ahmad Moeineddin , Michael Kaliske , Markus Apel

Delay embedding is a commonly employed technique in a wide range of data-driven model reduction methods for dynamical systems, including the Dynamic mode decomposition (DMD), the Hankel alternative view of the Koopman decomposition (HAVOK),…

Dynamical Systems · Mathematics 2023-01-12 Joar Axås , George Haller

Guided wave-based structural health monitoring (SHM) remains a powerful strategy for identifying early-stage defects and safeguarding vital aerospace structures. Yet, its practical use is often hindered by the enormous, high-dimensional…

Signal Processing · Electrical Eng. & Systems 2025-04-16 Yiming Fan , Dimitris G Giovanis , Fotis Kopsaftopoulos

The scaled boundary finite element method (SBFEM) has recently been employed as an efficient means to model three-dimensional structures, in particular when the geometry is provided as a voxel-based image. To this end, an octree…

Numerical Analysis · Mathematics 2023-10-31 Hauke Gravenkamp , Albert A. Saputra , Sascha Eisenträger

We consider the reduction of parametric families of linear dynamical systems having an affine parameter dependence that differ from one another by a low-rank variation in the state matrix. Usual approaches for parametric model reduction…

Numerical Analysis · Mathematics 2019-12-25 Christopher Beattie , Serkan Gugercin , Zoran Tomljanovic

Statistical shape modeling (SSM) has recently taken advantage of advances in deep learning to alleviate the need for a time-consuming and expert-driven workflow of anatomy segmentation, shape registration, and the optimization of…

Computer Vision and Pattern Recognition · Computer Science 2020-07-14 Jadie Adams , Riddhish Bhalodia , Shireen Elhabian

Statistical Shape Models (SSMs) excel at identifying population level anatomical variations, which is at the core of various clinical and biomedical applications, including morphology-based diagnostics and surgical planning. However, the…

Computer Vision and Pattern Recognition · Computer Science 2025-03-28 Asma Khan , Tushar Kataria , Janmesh Ukey , Shireen Y. Elhabian

Large scale dynamical systems (e.g. many nonlinear coupled differential equations) can often be summarized in terms of only a few state variables (a few equations), a trait that reduces complexity and facilitates exploration of behavioral…

Multiscale stochastic dynamical systems have been widely adopted to a variety of scientific and engineering problems due to their capability of depicting complex phenomena in many real world applications. This work is devoted to…

Machine Learning · Statistics 2024-01-02 Lingyu Feng , Ting Gao , Min Dai , Jinqiao Duan

Data driven models of dynamical systems help planners and controllers to provide more precise and accurate motions. Most model learning algorithms will try to minimize a loss function between the observed data and the model's predictions.…

Artificial Intelligence · Computer Science 2021-02-12 Clark Zhang , Santiago Paternain , Alejandro Ribeiro

The use of reduced-order models (ROMs) in physics-based modeling and simulation almost always involves the use of linear reduced basis (RB) methods such as the proper orthogonal decomposition (POD). For some nonlinear problems, linear RB…

Numerical Analysis · Mathematics 2022-04-19 Rakesh Halder , Krzysztof Fidkowski , Kevin Maki

Microstructural heterogeneity affects the macro-scale behavior of materials. Conversely, load distribution at the macro-scale changes the microstructural response. These up-scaling and down-scaling relations are often modeled using…

Materials Science · Physics 2023-06-13 Ashwini Gupta , Anindya Bhaduri , Lori Graham-Brady

Normalizing flows have shown great success as general-purpose density estimators. However, many real world applications require the use of domain-specific knowledge, which normalizing flows cannot readily incorporate. We propose…

Machine Learning · Statistics 2022-03-17 Gianluigi Silvestri , Emily Fertig , Dave Moore , Luca Ambrogioni

The discovery of constitutive laws for complex materials has historically faced a dichotomy between high-fidelity data-driven approaches, which demand prohibitive full-field experimental data, and traditional engineering fitting, which…

Computational Engineering, Finance, and Science · Computer Science 2026-03-23 Yue Wu , Tianhao Su , Mingchuan Zhao , Shunbo Hu , Deng Pan

Debiased machine learning estimators for smooth functionals in nonparametric models can exhibit substantial variability and instability, often leading practitioners to instead rely on parametric or semiparametric working models. Such…

Methodology · Statistics 2026-03-20 Lars van der Laan , Marco Carone , Alex Luedtke , Mark van der Laan

Simulating complex physical systems is crucial for understanding and predicting phenomena across diverse fields, such as fluid dynamics and heat transfer, as well as plasma physics and structural mechanics. Traditional approaches rely on…

Solving analytically intractable partial differential equations (PDEs) that involve at least one variable defined on an unbounded domain arises in numerous physical applications. Accurately solving unbounded domain PDEs requires efficient…

Machine Learning · Computer Science 2026-05-12 Mingtao Xia , Lucas Böttcher , Tom Chou

The computationally expensive estimation of engineering demand parameters (EDPs) via finite element (FE) models, while considering earthquake and parameter uncertainty limits the use of the Performance Based Earthquake Engineering…

Machine Learning · Statistics 2022-06-14 Siddharth S. Parida , Supratik Bose , Megan Butcher , Georgios Apostolakis , Prashant Shekhar