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Inference of gene regulatory networks (GRNs) based on experimental data is a challenging task in bioinformatics. In this paper, we present a bi-objective minimization model (BoMM) for inference of GRNs, where one objective is the fitting…

Computational Engineering, Finance, and Science · Computer Science 2015-12-17 Yu Chen , Xiufen Zou

Spatiotemporally chaotic systems, such as the solutions of some nonlinear partial differential equations, are dynamical systems that evolve toward a lower dimensional manifold. This manifold has an intricate geometry with heterogeneous…

Computational Physics · Physics 2025-06-17 Antonio Colanera , Luca Magri

Seismic imaging from sparsely acquired data faces challenges such as low image quality, discontinuities, and migration swing artifacts. Existing convolutional neural network (CNN)-based methods struggle with complex feature distributions…

Geophysics · Physics 2024-08-01 Xingchen Shi , Shijun Cheng , Weijian Mao , Wei Ouyang

We propose a new reduced order modeling strategy for tackling parametrized Partial Differential Equations (PDEs) with linear constraints, in particular Darcy flow systems in which the constraint is given by mass conservation. Our approach…

Numerical Analysis · Mathematics 2023-11-27 Wietse M. Boon , Nicola R. Franco , Alessio Fumagalli , Paolo Zunino

Hamiltonian Operator Inference has been introduced in [Sharma, H., Wang, Z., Kramer, B., Physica D: Nonlinear Phenomena, 431, p.133122, 2022] to learn structure-preserving reduced-order models (ROMs) for Hamiltonian systems. This approach…

Numerical Analysis · Mathematics 2024-05-10 Yuwei Geng , Jasdeep Singh , Lili Ju , Boris Kramer , Zhu Wang

We develop an unsupervised machine learning algorithm for the automated discovery and identification of traveling waves in spatio-temporal systems governed by partial differential equations (PDEs). Our method uses sparse regression and…

Computational Physics · Physics 2020-05-20 Ariana Mendible , Steven L. Brunton , Aleksandr Y. Aravkin , Wes Lowrie , J. Nathan Kutz

The present work proposes a framework for nonlinear model order reduction based on a Graph Convolutional Autoencoder (GCA-ROM). In the reduced order modeling (ROM) context, one is interested in obtaining real-time and many-query evaluations…

Numerical Analysis · Mathematics 2023-11-08 Federico Pichi , Beatriz Moya , Jan S. Hesthaven

Recent advances in quantum hardware motivate the development of algorithmic frameworks that integrate quantum sampling with classical inference. This work introduces a segmentation-based regression method tailored to quantum neural networks…

Quantum Physics · Physics 2025-07-02 James C. Hateley

We propose a new stochastic optimization framework for empirical risk minimization problems such as those that arise in machine learning. The traditional approaches, such as (mini-batch) stochastic gradient descent (SGD), utilize an…

Machine Learning · Statistics 2020-02-04 Kenji Kawaguchi , Haihao Lu

Multiscale dynamical systems characterized by interacting fast and slow processes are ubiquitous across scientific domains, from climate dynamics to fluid mechanics. Accurate modeling of such systems requires capturing both the long-term…

Chaotic Dynamics · Physics 2025-11-07 Giulio Del Felice , Ludovico Theo Giorgini

Suitable reduced order models (ROMs) are computationally efficient tools in characterizing key dynamical and statistical features of nature. In this paper, a systematic multiscale stochastic ROM framework is developed for complex systems…

Computational Physics · Physics 2022-03-23 Changhong Mou , Nan Chen , Traian Iliescu

Highly accurate simulations of complex phenomena governed by partial differential equations (PDEs) typically require intrusive methods and entail expensive computational costs, which might become prohibitive when approximating steady-state…

Machine Learning · Computer Science 2023-05-17 Paolo Conti , Giorgio Gobat , Stefania Fresca , Andrea Manzoni , Attilio Frangi

Graph Neural Networks have achieved impressive results across diverse network modeling tasks, but accurately estimating uncertainty on graphs remains difficult, especially under distributional shifts. Unlike traditional uncertainty…

Machine Learning · Computer Science 2025-10-15 Fred Xu , Thomas Markovich

Accurate and inexpensive Reduced Order Models (ROMs) for forecasting turbulent flows can facilitate rapid design iterations and thus prove critical for predictive control in engineering problems. Galerkin projection based Reduced Order…

Fluid Dynamics · Physics 2023-01-27 Surya Chakrabarti , Arvind T. Mohan , Datta V. Gaitonde , Daniel Livescu

Reduced-order models (ROMs) are essential for rapid simulation of complex biomechanical systems and for bridging the gap between high fidelity models and clinical application. However, ROMs for tissue growth and remodeling (G&R) remain…

Computational Engineering, Finance, and Science · Computer Science 2026-04-16 Joel Laudo , Adrian Buganza Tepole

We propose a novel diffusion-based image generation method called the observation-guided diffusion probabilistic model (OGDM), which effectively addresses the tradeoff between quality control and fast sampling. Our approach reestablishes…

Machine Learning · Computer Science 2024-04-02 Junoh Kang , Jinyoung Choi , Sungik Choi , Bohyung Han

A multi-fidelity framework is established and demonstrated for prediction of combustion instabilities in rocket engines. The major idea is to adapt appropriate fidelity modeling approaches for different components in a rocket engine to…

Fluid Dynamics · Physics 2019-05-31 Jiayang Xu , Cheng Huang , Karthik Duraisamy

Reduced order modeling methods are often used as a mean to reduce simulation costs in industrial applications. Despite their computational advantages, reduced order models (ROMs) often fail to accurately reproduce complex dynamics…

In this work, a new hybrid predictive Reduced Order Model (ROM) is proposed to solve reacting flow problems. This algorithm is based on a dimensionality reduction using Proper Orthogonal Decomposition (POD) combined with deep learning…

Machine Learning · Computer Science 2023-01-25 Adrián Corrochano , Rodolfo S. M. Freitas , Alessandro Parente , Soledad Le Clainche

We present a framework for solving a broad class of ill-posed inverse problems governed by partial differential equations (PDEs), where the target coefficients of the forward operator are recovered through an iterative regularization scheme…