Stochastic Methods for Parameter Estimation and Design of Experiments in Systems Biology PDF Download
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Author: Andrei Kramer
Publisher: Logos Verlag Berlin GmbH
ISBN: 3832541950
Category : Computers
Languages : en
Pages : 164
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Book Description
Markov Chain Monte Carlo (MCMC) methods are sampling based techniques, which use random numbers to approximate deterministic but unknown values. They can be used to obtain expected values, estimate parameters or to simply inspect the properties of a non-standard, high dimensional probability distribution. Bayesian analysis of model parameters provides the mathematical foundation for parameter estimation using such probabilistic sampling. The strengths of these stochastic methods are their robustness and relative simplicity even for nonlinear problems with dozens of parameters as well as a built-in uncertainty analysis. Because Bayesian model analysis necessarily involves the notion of prior knowledge, the estimation of unidentifiable parameters can be regularised (by priors) in a straight forward way. This work draws the focus on typical cases in systems biology: relative data, nonlinear ordinary differential equation models and few data points. It also investigates the consequences of parameter estimation from steady state data; consequences such as performance benefits. In biology the data is almost exclusively relative, the raw measurements (e.g. western blot intensities) are normalised by control experiments or a reference value within a series and require the model to do the same when comparing its output to the data. Several sampling algorithms are compared in terms of effective sampling speed and necessary adaptations to relative and steady state data are explained.
Author: Andrei Kramer
Publisher: Logos Verlag Berlin GmbH
ISBN: 3832541950
Category : Computers
Languages : en
Pages : 164
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Book Description
Markov Chain Monte Carlo (MCMC) methods are sampling based techniques, which use random numbers to approximate deterministic but unknown values. They can be used to obtain expected values, estimate parameters or to simply inspect the properties of a non-standard, high dimensional probability distribution. Bayesian analysis of model parameters provides the mathematical foundation for parameter estimation using such probabilistic sampling. The strengths of these stochastic methods are their robustness and relative simplicity even for nonlinear problems with dozens of parameters as well as a built-in uncertainty analysis. Because Bayesian model analysis necessarily involves the notion of prior knowledge, the estimation of unidentifiable parameters can be regularised (by priors) in a straight forward way. This work draws the focus on typical cases in systems biology: relative data, nonlinear ordinary differential equation models and few data points. It also investigates the consequences of parameter estimation from steady state data; consequences such as performance benefits. In biology the data is almost exclusively relative, the raw measurements (e.g. western blot intensities) are normalised by control experiments or a reference value within a series and require the model to do the same when comparing its output to the data. Several sampling algorithms are compared in terms of effective sampling speed and necessary adaptations to relative and steady state data are explained.
Author: Peter Benner
Publisher: Springer
ISBN: 3319084372
Category : Mathematics
Languages : en
Pages : 401
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Book Description
This edited volume provides insights into and tools for the modeling, analysis, optimization, and control of large-scale networks in the life sciences and in engineering. Large-scale systems are often the result of networked interactions between a large number of subsystems, and their analysis and control are becoming increasingly important. The chapters of this book present the basic concepts and theoretical foundations of network theory and discuss its applications in different scientific areas such as biochemical reactions, chemical production processes, systems biology, electrical circuits, and mobile agents. The aim is to identify common concepts, to understand the underlying mathematical ideas, and to inspire discussions across the borders of the various disciplines. The book originates from the interdisciplinary summer school “Large Scale Networks in Engineering and Life Sciences” hosted by the International Max Planck Research School Magdeburg, September 26-30, 2011, and will therefore be of interest to mathematicians, engineers, physicists, biologists, chemists, and anyone involved in the network sciences. In particular, due to their introductory nature the chapters can serve individually or as a whole as the basis of graduate courses and seminars, future summer schools, or as reference material for practitioners in the network sciences.
Author: Masumi Ishikawa
Publisher: Springer Science & Business Media
ISBN: 3540691545
Category : Computers
Languages : en
Pages : 1165
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Book Description
The two volume set LNCS 4984 and LNCS 4985 constitutes the thoroughly refereed post-conference proceedings of the 14th International Conference on Neural Information Processing, ICONIP 2007, held in Kitakyushu, Japan, in November 2007, jointly with BRAINIT 2007, the 4th International Conference on Brain-Inspired Information Technology. The 228 revised full papers presented were carefully reviewed and selected from numerous ordinary paper submissions and 15 special organized sessions. The 116 papers of the first volume are organized in topical sections on computational neuroscience, learning and memory, neural network models, supervised/unsupervised/reinforcement learning, statistical learning algorithms, optimization algorithms, novel algorithms, as well as motor control and vision. The second volume contains 112 contributions related to statistical and pattern recognition algorithms, neuromorphic hardware and implementations, robotics, data mining and knowledge discovery, real world applications, cognitive and hybrid intelligent systems, bioinformatics, neuroinformatics, brain-conputer interfaces, and novel approaches.
Author: Christoph Herwig
Publisher: Springer Nature
ISBN: 3030716562
Category : Technology & Engineering
Languages : en
Pages : 254
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Book Description
This is the second of two volumes that together provide an overview of the latest advances in the generation and application of digital twins in bioprocess design and optimization. Both processes have undergone significant changes over the past few decades, moving from data-driven approaches into the 21st-century digitalization of the bioprocess industry. Moreover, the high demand for biotechnological products calls for efficient methods during research and development, as well as during tech transfer and routine manufacturing. In this regard, one promising tool is the use of digital twins, which offer a virtual representation of the bioprocess. They reflect the mechanistics of the biological system and the interactions between process parameters, key performance indicators and product quality attributes in the form of a mathematical process model. Furthermore, digital twins allow us to use computer-aided methods to gain an improved process understanding, to test and plan novel bioprocesses, and to efficiently monitor them. This book focuses on the application of digital twins in various contexts, e.g. computer-aided experimental design, seed train prediction, and lifeline analysis. Covering fundamentals as well as applications, the two volumes offers the ideal introduction to the topic for researchers in academy and industry alike.
Author:
Publisher: John Wiley & Sons
ISBN: 3527631348
Category : Technology & Engineering
Languages : en
Pages : 628
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Book Description
Inspired by the leading authority in the field, the Centre for Process Systems Engineering at Imperial College London, this book includes theoretical developments, algorithms, methodologies and tools in process systems engineering and applications from the chemical, energy, molecular, biomedical and other areas. It spans a whole range of length scales seen in manufacturing industries, from molecular and nanoscale phenomena to enterprise-wide optimization and control. As such, this will appeal to a broad readership, since the topic applies not only to all technical processes but also due to the interdisciplinary expertise required to solve the challenge. The ultimate reference work for years to come.
Author: Ashutosh Gupta
Publisher: Springer
ISBN: 3642407080
Category : Computers
Languages : en
Pages : 299
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Book Description
This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.
Author: Olaf Wolkenhauer
Publisher: Portland Press, London
ISBN:
Category : Science
Languages : en
Pages : 276
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Book Description
Contains topics including modelling the dynamics of signalling pathways, modelling metabolic networks using power-laws and S-systems, modelling reaction kinetics in cells, the regulatory design of cellular processes, metabolomics and fluxomics, modelling cellular signalling systems, and systems analysis of MAPK signal transduction.
Author: Toon Calders
Publisher: Springer
ISBN: 3662448513
Category : Computers
Languages : en
Pages : 746
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Book Description
This three-volume set LNAI 8724, 8725 and 8726 constitutes the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases: ECML PKDD 2014, held in Nancy, France, in September 2014. The 115 revised research papers presented together with 13 demo track papers, 10 nectar track papers, 8 PhD track papers, and 9 invited talks were carefully reviewed and selected from 550 submissions. The papers cover the latest high-quality interdisciplinary research results in all areas related to machine learning and knowledge discovery in databases.
Author: Oded Maler
Publisher: Springer
ISBN: 3319276565
Category : Computers
Languages : en
Pages : 185
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Book Description
This book constitutes the thoroughly refereed post-workshop proceedings of the Second International Workshop on Hybrid Systems Biology, HSB 2013, held as part of the ECAL 2013 event, in Taormina, Italy, in September 2013; and the Third International Workshop on Hybrid Systems Biology, HSB 2014, held as part of CAV 2014, in Vienna, Austria, in July 2014. This volume presents 8 full papers together with 2 invited tutorials/surveys from 21 submissions. The HSB 2013 workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. The scope of the HSB 2014 workshop is the general area of dynamical models in biology with an emphasis on hybrid approaches, which are not restricted to a narrow class of mathematical models, and which take advantage of techniques developed separately in different sub-fields. “br> /div
Author: Liesbet Geris
Publisher: Springer
ISBN: 3319212966
Category : Technology & Engineering
Languages : en
Pages : 471
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Book Description
Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process. This book wants to address four main issues related to the building and validation of computational models of biomedical processes: 1. Modeling establishment under uncertainty 2. Model selection and parameter fitting 3. Sensitivity analysis and model adaptation 4. Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples. This book is intended for graduate students and researchers active in the field of computational modeling of biomedical processes who seek to acquaint themselves with the different ways in which to study the parameter space of their model as well as its overall behavior.
