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Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…

Molecular Networks · Quantitative Biology 2017-12-06 Abhishek Dey , Shaunak Sen

In system identification, estimating parameters of a model using limited observations results in poor identifiability. To cope with this issue, we propose a new method to simultaneously select and estimate sensitive parameters as key model…

The use of machine learning algorithms to predict behaviors of complex systems is booming. However, the key to an effective use of machine learning tools in multi-physics problems, including combustion, is to couple them to physical and…

Design-space dimensionality reduction is essential to mitigate the cost of high-fidelity simulation-based optimization, especially when dealing with high-dimensional geometric parameterizations. Traditional linear techniques, such as…

Optimization and Control · Mathematics 2025-07-23 Andrea Serani , Giorgio Palma , Jeroen Wackers , Domenico Quagliarella , Stefano Gaggero , Matteo Diez

This paper presents a novel non-linear model reduction method: Probabilistic Manifold Decomposition (PMD), which provides a powerful framework for constructing non-intrusive reduced-order models (ROMs) by embedding a high-dimensional system…

Numerical Analysis · Mathematics 2026-01-09 Jiaming Guo , Dunhui Xiao

Multivariable parametric models are essential for optimizing the performance of high-tech systems. The main objective of this paper is to develop an identification strategy that provides accurate parametric models for complex multivariable…

Systems and Control · Electrical Eng. & Systems 2025-03-05 M. van der Hulst , R. A. González , K. Classens , P. Tacx , N. Dirkx , J. van de Wijdeven , T. Oomen

Focusing on a specific crowd dynamics situation, including real life experiments and measurements, our paper targets a twofold aim: (1) we present a Bayesian probabilistic method to estimate the value and the uncertainty (in the form of a…

Data Analysis, Statistics and Probability · Physics 2018-04-12 Alessandro Corbetta , Adrian Muntean , Federico Toschi , Kiamars Vafayi

Topic models are statistical methods that extract underlying topics from document collections. When performing topic modeling, a user usually desires topics that are coherent, diverse between each other, and that constitute good document…

Computation and Language · Computer Science 2022-02-16 Silvia Terragni , Ismail Harrando , Pasquale Lisena , Raphael Troncy , Elisabetta Fersini

A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…

Biological Physics · Physics 2011-08-08 Juan R. Perilla , Thomas B. Woolf

Parameter-dependent models arise in many contexts such as uncertainty quantification, sensitivity analysis, inverse problems or optimization. Parametric or uncertainty analyses usually require the evaluation of an output of a model for many…

Numerical Analysis · Mathematics 2018-10-22 Anthony Nouy

In this work, we propose a method for determining a non-uniform sampling scheme for multi-dimensional signals by solving a convex optimization problem reminiscent of the sensor selection problem. The resulting sampling scheme minimizes the…

Methodology · Statistics 2017-07-12 Johan Swärd , Filip Elvander , Andreas Jakobsson

To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…

Molecular Networks · Quantitative Biology 2014-04-23 Yi Ming Zou

In this paper, we present a novel general framework grounded in the factor graph theory to solve kinematic and dynamic problems for multi-body systems. Although the motion of multi-body systems is considered to be a well-studied problem and…

Robotics · Computer Science 2021-07-27 José-Luis Blanco-Claraco , Antonio Leanza , Giulio Reina

The model selection procedure is usually a single-criterion decision making in which we select the model that maximizes a specific metric in a specific set, such as the Validation set performance. We claim this is very naive and can perform…

Machine Learning · Computer Science 2022-07-15 Felipe Costa Farias , Teresa Bernarda Ludermir , Carmelo José Albanez Bastos-Filho

Model-Based Diagnosis deals with the identification of the real cause of a system's malfunction based on a formal system model and observations of the system behavior. When a malfunction is detected, there is usually not enough information…

Artificial Intelligence · Computer Science 2017-11-16 Patrick Rodler , Wolfgang Schmid , Konstantin Schekotihin

Model-based clustering is a popular approach for clustering multivariate data which has seen applications in numerous fields. Nowadays, high-dimensional data are more and more common and the model-based clustering approach has adapted to…

Methodology · Statistics 2018-09-25 Michael Fop , Thomas Brendan Murphy

Highly overparametrized neural networks can display curiously strong generalization performance - a phenomenon that has recently garnered a wealth of theoretical and empirical research in order to better understand it. In contrast to most…

Machine Learning · Computer Science 2020-09-29 Jorg Bornschein , Francesco Visin , Simon Osindero

We provide a brief overview of both Bayes and classical model selection. We argue tentatively that model selection has at least two major goals, that of finding the correct model or predicting well, and that in general both these goals may…

Statistics Theory · Mathematics 2015-10-05 Ritabrata Dutta , Malgortaza Bogdan , Jayanta K. Ghosh

The optimization of large-scale multibody systems is a numerically challenging task, in particular when considering multiple conflicting criteria at the same time. In this situation, we need to approximate the Pareto set of optimal…

Optimization and Control · Mathematics 2024-12-20 Augustina C. Amakor , Manuel B. Berkemeier , Meike Wohlleben , Walter Sextro , Sebastian Peitz

Development of several alternative mathematical models for the biological system in question and discrimination between such models using experimental data is the best way to robust conclusions. Models which challenge existing theories are…

Quantitative Methods · Quantitative Biology 2016-02-01 Vitaly V. Ganusov
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