Structure identification and parameter estimation of biological s-systems

Liu, Lizhi; Wu, Fang‐Xiang; Han, Ling; Zhang, W. J.

doi:10.1109/bibm.2010.5706586

Cited by 3 publications

(2 citation statements)

References 13 publications

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“…Alves and colleagues used a combination of bioinformatics and structural biology, along with genomic, proteomic, and metabolic time series data, to reconstruct pathways and generate novel hypotheses [39]. Liu and colleagues devised a structure identi�cation method that combines parameter estimation with a pruning strategy that adds a regularization term to the objective function and prunes the solution according to a user-speci�ed threshold value [356]. Džeroski and Todorovski proposed machine-learning methods [212].…”

Section: �� T�or� ��Co�str�ctio� A�� St�� Ti�catio�mentioning

confidence: 99%

Biochemical Systems Theory: A Review

Voit

2013

ISRN Biomathematics

149

154

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Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools that facilitate the analysis of dynamic biological systems. is paper depicts major developments in BST up to the current state of the art in 2012. It discusses its rationale, describes the typical strategies and methods of designing, diagnosing, analyzing, and utilizing BST models, and reviews areas of application. e paper is intended as a guide for investigators entering the fascinating �eld of biological systems analysis and as a resource for practitioners and experts. PreambleBiochemical systems theory (BST) is a mathematical and computational framework for analyzing and simulating systems. It was originally developed for biochemical pathways but by now has become much more widely applied to systems throughout biology and beyond. BST is called "canonical, " which means that model construction, diagnosis, and analysis follow stringent rules, which will be discussed throughout this paper. e key ingredient of BST is the power-law representation of all processes in a system.BST has been the focus of a number of books [1-6], including some in Chinese and Japanese [7][8][9]. e most detailed modern text dedicated speci�cally to BST is [3]. Moreover, since its inception, numerous reviews have portrayed the evolving state of the art in BST. Most of these reviews summarized methodological advances for the analysis of biochemical pathway systems . Others compared BST models with alternative modeling frameworks [32,[51][52][53][54][55][56][57][58][59][60][61][62][63]; some of these comparisons will be discussed later. Yet other reviews focused on specialty areas, such as customized methods for optimizing BST models (e.g., [64][65][66][67]) or estimating their parameters (e.g., [68][69][70][71][72]), strategies for discovering design and operating principles in natural system (e.g., [73][74][75][76][77][78]), and even the use of BST models in statistics [79][80][81]. A historical account of the �rst twenty years of BST was presented in [82].Supporting the methodological developments in the �eld, several soware packages were developed for different aspects of BST analysis. e earliest was ESSYNS [83][84][85], which supported all standard steady-state analyses and also contained a numerical solver that, at the time, was many times faster than any off-the-shelf soware [86,87]; see also [88]. Utilizing advances in computing and an extension of the solver from ESSYNS, Ferreira created the very user-friendly package PLAS, which is openly available and still very widely used [89] (see also [3]). Yamada and colleagues developed soware to translate E-cell models into BST models in PLAS format [90]. Okamoto's group created the soware BestKit, which permits the graphical design and translation of models, along with their analysis [91][92][93]. Vera and colleagues developed the soware tool PLMaddon for analyzing BST models within SBML [94]; see also [95]. It expands the Matlab SBToolbox with speci�c functionalities for power-law repr...

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Section: �� T�or� ��Co�str�ctio� A�� St�� Ti�catio�mentioning

confidence: 99%

Biochemical Systems Theory: A Review

Voit

2013

ISRN Biomathematics

149

154

View full text Add to dashboard Cite

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“…The identification of Systems is of extreme importance for any study involving physical systems, [1], and even biological ones such as [2] and [3], which say that identification begins with simple human attitudes and [24], which says that it is the detection of behavioral patterns of physical systems. Thus, identifying is a natural practice of the complex system of the human body and began to be transcribed in a mathematical way to represent physical systems.…”

Section: Introductionmentioning

confidence: 99%

Artificial Neural Networks Models Based on ARX and State Space Forms and Adaptive Control PID/LQR of Systems Based on Peltier Cells

Sá

Neto

2021

Int J Innov Educ Res

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To improve the performance of a thermal plant based on Peltier cell actuators, an online parametric estimation via artificial neural networks and adaptive controller is presented. The control actions are based on adaptive digital controller and an adaptive quadratic linear regulator approaches. The Artificial neural networks topology is based on ARX and NARX models, and its training algorithms, such as accelerated backpropagation and recursive least square. The Control strategies are design-oriented to adaptive digital PID controller and quadratic linear regulator framework. The proposal is evaluated on temperature control of an object that is inside of a chamber.

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Alternating weighted least squares parameter estimation for biological S-systems

Liu

Zhang

2012

2012 IEEE 6th International Conference on Systems Biology (ISB)

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Structure identification and parameter estimation of biological s-systems

Cited by 3 publications

References 13 publications

Biochemical Systems Theory: A Review

Biochemical Systems Theory: A Review

Artificial Neural Networks Models Based on ARX and State Space Forms and Adaptive Control PID/LQR of Systems Based on Peltier Cells

Alternating weighted least squares parameter estimation for biological S-systems

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