16 papers · ranked by Valyu relevance
Gabriele Lillacci, Mustafa Khammash, Anand R. Asthagiri
A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course…
Yingyi Zhang, Chang Liu, Yu-Pin Lin, Marta Otero
Parametric thinking has found wide acceptance in both the building industry and environmental sciences. In the context of environmental urban morphology however, parametric thinking has been neglected. This paper critically assesses environmental optimization with a focus on parametric urbanism. The analysis addresses…
Akatsuki Kimura, Antonio Celani, Hiromichi Nagao, Timothy Stasevich + 1 more
'Kazuyuki Nakamura'] Construction of quantitative models is a primary goal of quantitative biology, which aims to understand cellular and organismal phenomena in a quantitative manner. In this article, we introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental…
Andreas Raue, Marcel Schilling, Julie Bachmann, Andrew Matteson + 9 more
'Max Schelke' 'Daniel Kaschek' 'Sabine Hug' 'Clemens Kreutz' 'Brian D. Harms' 'Fabian J. Theis' 'Ursula Klingmüller' 'Jens Timmer' 'Enrique Hernandez-Lemus'] Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A…
Katerina Tashkova, Peter Korošec, Jurij Šilc, Ljupčo Todorovski + 1 more
'Sašo Džeroski'] Background We address the task of parameter estimation in models of the dynamics of biological systems based on ordinary differential equations (ODEs) from measured data, where the models are typically non-linear and have many parameters, the measurements are imperfect due to noise, and the studied…
Omid Ghasemi, Merry L Lindsey, Tianyi Yang, Nguyen Nguyen + 2 more
'Yufei Huang' 'Yu-Fang Jin'] Background The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, mathematical frameworks such as ordinary differential equations have been…
Nikolaos Evangelou, Noah J Wichrowski, George A Kevrekidis, Felix Dietrich + 4 more
We present a data-driven approach to characterizing nonidentifiability of a model’s parameters and illustrate it through dynamic as well as steady kinetic models. By employing Diffusion Maps and their extensions, we discover the minimal combinations of parameters required to characterize the output behavior of a…
Nathaniel J. Linden, Boris Kramer, Padmini Rangamani, Jeffrey J. Saucerman
'Jeffrey J. Saucerman'] Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent advances in experimental measurements, including sensor…
Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue + 12 more
'Bernhard Steiert' 'Jens Timmer' 'Clemens Kreutz' '' 'Simon Wilkinson' 'Brandon A. Allgood' 'Brian M. Bot' 'Bruce R. Hoff' 'Michael R. Kellen' 'Markus W. Covert' 'Gustavo A. Stolovitzky' 'Pablo Meyer' 'Herbert Sauro'] Whole-cell models that explicitly represent all cellular components at the molecular level have the…
Harald Penasso, Sigrid Thaller
This study investigated the effect of isometrically induced fatigue on Hill-type muscle model parameters and related task-dependent effects. Parameter identification methods were used to extract fatigue-related parameter trends from isometric and ballistic dynamic maximum voluntary knee extensions. Nine subjects, who…
Qianqian Tong, Zhiyong Yuan, Mianlun Zheng, Xiangyun Liao + 2 more
'Weixu Zhu' 'Guian Zhang'] The elastic parameters of soft tissues are important for medical diagnosis and virtual surgery simulation. In this study, we propose a novel nonlinear parameter estimation method for soft tissues. Firstly, an in-house data acquisition platform was used to obtain external forces and their…
Jonathan Shimwell, John Billingsley, Rémi Delaporte-Mathurin, Declan Morbey + 3 more
'Declan Morbey' 'Matthew Bluteau' 'Patrick Shriwise' 'Andrew Davis'] During the conceptual design process of fusion reactors it is useful to rapidly prototype different design concepts and assess their suitability against a range of high level requirements. Rapid prototyping allows the 'fail early' mantra of other…
Ankush Aggarwal
Several nonlinear and anisotropic constitutive models have been proposed to describe the biomechanical properties of soft tissues, and reliably estimating the unknown parameters in these models using experimental data is an important step towards developing predictive capabilities. However, the effect of parameter…
Hong Qin
Parameter identification is an important branch of automatic control. Due to its special function, it has been widely used in various fields, especially the modeling of complex systems or systems whose parameters are not easy to determine. With the development of control technology, the scale of the control object is…
Mirela Domijan, David A. Rand
We provide analytical tools to facilitate a rigorous assessment of the quality and value of the fit of a complex model to data. We use this to provide approaches to model fitting, parameter estimation, the design of optimization functions and experimental optimization. This is in the context where multiple constraints…
Mirela Domijan, Paul E. Brown, Boris V. Shulgin, David A. Rand
Background Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest…