Download or read book Markov chain Monte Carlo methods for parameter identification in systems biology models written by Theresa Niederberger and published by . This book was released on 2012 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Application of Markov Chain Monte Carlo Techniques in Non linear Parameter Estimation for Chemical Engineering Models written by Manoj Mathew and published by . This book was released on 2013 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling of chemical engineering systems often necessitates using non-linear models. These models can range in complexity, from a simple analytical equation to a system of differential equations. Regardless of what type of model is being utilized, determining parameter estimates is essential in everyday chemical engineering practice. One promising approach to non-linear regression is a technique called Markov Chain Monte Carlo (MCMC).This method produces reliable parameter estimates and generates joint confidence regions (JCRs) with correct shape and correct probability content. Despite these advantages, its application in chemical engineering literature has been limited. Therefore, in this project, MCMC methods were applied to a variety of chemical engineering models. The objectives of this research is to (1) illustrate how to implement MCMC methods in complex non-linear models (2) show the advantages of using MCMC techniques over classical regression approaches and (3) provide practical guidelines on how to reduce the computational time. MCMC methods were first applied to the biological oxygen demand (BOD) problem. In this case study, an implementation procedure was outlined using specific examples from the BOD problem. The results from the study illustrated the importance of estimating the pure error variance as a parameter rather than fixing its value based on the mean square error. In addition, a comparison was carried out between the MCMC results and the results obtained from using classical regression approaches. The findings show that although similar point estimates are obtained, JCRs generated from approximation methods cannot model the parameter uncertainty adequately. Markov Chain Monte Carlo techniques were then applied in estimating reactivity ratios in the Mayo-Lewis model, Meyer-Lowry model, the direct numerical integration model and the triad fraction multiresponse model. The implementation steps for each of these models were discussed in detail and the results from this research were once again compared to previously used approximation methods. Once again, the conclusion drawn from this work showed that MCMC methods must be employed in order to obtain JCRs with the correct shape and correct probability content. MCMC methods were also applied in estimating kinetic parameter used in the solid oxide fuel cell study. More specifically, the kinetics of the water-gas shift reaction, which is used in generating hydrogen for the fuel cell, was studied. The results from this case study showed how the MCMC output can be analyzed in order to diagnose parameter observability and correlation. A significant portion of the model needed to be reduced due to these issues of observability and correlation. Point estimates and JCRs were then generated using the reduced model and diagnostic checks were carried out in order to ensure the model was able to capture the data adequately. A few select parameters in the Waterloo Polymer Simulator were estimated using the MCMC algorithm. Previous studies have shown that accurate parameter estimates and JCRs could not be obtained using classical regression approaches. However, when MCMC techniques were applied to the same problem, reliable parameter estimates and correct shape and correct probability content confidence regions were observed. This case study offers a strong argument as to why classical regression approaches should be replaced by MCMC techniques. Finally, a very brief overview of the computational times for each non-linear model used in this research was provided. In addition, a serial farming approach was proposed and a significant decrease in computational time was observed when this procedure was implemented.

Download or read book Implementation of Markov Chain Monte Carlo Techniques in Parameter Estimation for Engineering Models written by Jessada Jitjareonchai and published by . This book was released on 2006 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Advanced Markov Chain Monte Carlo Methods written by Faming Liang and published by John Wiley & Sons. This book was released on 2011-07-05 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: Markov Chain Monte Carlo (MCMC) methods are now an indispensable tool in scientific computing. This book discusses recent developments of MCMC methods with an emphasis on those making use of past sample information during simulations. The application examples are drawn from diverse fields such as bioinformatics, machine learning, social science, combinatorial optimization, and computational physics. Key Features: Expanded coverage of the stochastic approximation Monte Carlo and dynamic weighting algorithms that are essentially immune to local trap problems. A detailed discussion of the Monte Carlo Metropolis-Hastings algorithm that can be used for sampling from distributions with intractable normalizing constants. Up-to-date accounts of recent developments of the Gibbs sampler. Comprehensive overviews of the population-based MCMC algorithms and the MCMC algorithms with adaptive proposals. This book can be used as a textbook or a reference book for a one-semester graduate course in statistics, computational biology, engineering, and computer sciences. Applied or theoretical researchers will also find this book beneficial.

Download or read book Advances in Systems Biology written by Igor I. Goryanin and published by Springer Science & Business Media. This book was released on 2011-12-08 with total page 679 pages. Available in PDF, EPUB and Kindle. Book excerpt: The International Society for Systems Biology (ISSB) is a society aimed at advancing world-wide systems biology research by providing a forum for scientific discussions and various academic services. The ISSB helps coordinate researchers to form alliances for meeting the unique needs of multidisciplinary and international systems biology research. The annual International Conference on Systems Biology (ICSB) serves as the main meeting for the society and is one of the largest academic and commercial gatherings under the broad heading of ‘Systems Biology’.

Download or read book Markov Chain Monte Carlo Methods in Biological Mechanistic Models written by Irena Kuzmanovska and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Network Bioscience 2nd Edition written by Marco Pellegrini and published by Frontiers Media SA. This book was released on 2020-03-27 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Network science has accelerated a deep and successful trend in research that influences a range of disciplines like mathematics, graph theory, physics, statistics, data science and computer science (just to name a few) and adapts the relevant techniques and insights to address relevant but disparate social, biological, technological questions. We are now in an era of 'big biological data' supported by cost-effective high-throughput genomic, transcriptomic, proteomic, metabolomic data collection techniques that allow one to take snapshots of the cells' molecular profiles in a systematic fashion. Moreover recently, also phenotypic data, data on diseases, symptoms, patients, etc. are being collected at nation-wide level thus giving us another source of highly related (causal) 'big data'. This wealth of data is usually modeled as networks (aka binary relations, graphs or webs) of interactions, (including protein-protein, metabolic, signaling and transcription-regulatory interactions). The network model is a key view point leading to the uncovering of mesoscale phenomena, thus providing an essential bridge between the observable phenotypes and 'omics' underlying mechanisms. Moreover, network analysis is a powerful 'hypothesis generation' tool guiding the scientific cycle of 'data gathering', 'data interpretation, 'hypothesis generation' and 'hypothesis testing'. A major challenge in contemporary research is the synthesis of deep insights coming from network science with the wealth of data (often noisy, contradictory, incomplete and difficult to replicate) so to answer meaningful biological questions, in a quantifiable way using static and dynamic properties of biological networks.

Download or read book Model Based Parameter Estimation written by Hans Georg Bock and published by Springer Science & Business Media. This book was released on 2013-02-26 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: This judicious selection of articles combines mathematical and numerical methods to apply parameter estimation and optimum experimental design in a range of contexts. These include fields as diverse as biology, medicine, chemistry, environmental physics, image processing and computer vision. The material chosen was presented at a multidisciplinary workshop on parameter estimation held in 2009 in Heidelberg. The contributions show how indispensable efficient methods of applied mathematics and computer-based modeling can be to enhancing the quality of interdisciplinary research. The use of scientific computing to model, simulate, and optimize complex processes has become a standard methodology in many scientific fields, as well as in industry. Demonstrating that the use of state-of-the-art optimization techniques in a number of research areas has much potential for improvement, this book provides advanced numerical methods and the very latest results for the applications under consideration.

Download or read book Markov Chain Monte Carlo written by W. S. Kendall and published by World Scientific. This book was released on 2005 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Markov Chain Monte Carlo (MCMC) originated in statistical physics, but has spilled over into various application areas, leading to a corresponding variety of techniques and methods. That variety stimulates new ideas and developments from many different places, and there is much to be gained from cross-fertilization. This book presents five expository essays by leaders in the field, drawing from perspectives in physics, statistics and genetics, and showing how different aspects of MCMC come to the fore in different contexts. The essays derive from tutorial lectures at an interdisciplinary program at the Institute for Mathematical Sciences, Singapore, which exploited the exciting ways in which MCMC spreads across different disciplines.

Download or read book MCMC from Scratch written by Masanori Hanada and published by Springer Nature. This book was released on 2022-10-20 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook explains the fundamentals of Markov Chain Monte Carlo (MCMC) without assuming advanced knowledge of mathematics and programming. MCMC is a powerful technique that can be used to integrate complicated functions or to handle complicated probability distributions. MCMC is frequently used in diverse fields where statistical methods are important – e.g. Bayesian statistics, quantum physics, machine learning, computer science, computational biology, and mathematical economics. This book aims to equip readers with a sound understanding of MCMC and enable them to write simulation codes by themselves. The content consists of six chapters. Following Chap. 2, which introduces readers to the Monte Carlo algorithm and highlights the advantages of MCMC, Chap. 3 presents the general aspects of MCMC. Chap. 4 illustrates the essence of MCMC through the simple example of the Metropolis algorithm. In turn, Chap. 5 explains the HMC algorithm, Gibbs sampling algorithm and Metropolis-Hastings algorithm, discussing their pros, cons and pitfalls. Lastly, Chap. 6 presents several applications of MCMC. Including a wealth of examples and exercises with solutions, as well as sample codes and further math topics in the Appendix, this book offers a valuable asset for students and beginners in various fields.

Download or read book Handbook of Markov Chain Monte Carlo written by Steve Brooks and published by CRC Press. This book was released on 2011-05-10 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since their popularization in the 1990s, Markov chain Monte Carlo (MCMC) methods have revolutionized statistical computing and have had an especially profound impact on the practice of Bayesian statistics. Furthermore, MCMC methods have enabled the development and use of intricate models in an astonishing array of disciplines as diverse as fisherie

Download or read book Lectures on Monte Carlo Methods written by Neal Noah Madras and published by Springer Science & Business. This book was released on 2002 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monte Carlo methods form an experimental branch of mathematics that employs simulations driven by random number generators. These methods are often used when others fail, since they are much less sensitive to the ``curse of dimensionality'', which plagues deterministic methods in problems with a large number of variables. Monte Carlo methods are used in many fields: mathematics, statistics, physics, chemistry, finance, computer science, and biology, for instance. This book is an introduction to Monte Carlo methods for anyone who would like to use these methods to study various kinds of mathematical models that arise in diverse areas of application. The book is based on lectures in a graduate course given by the author. It examines theoretical properties of Monte Carlo methods as well as practical issues concerning their computer implementation and statistical analysis. The only formal prerequisite is an undergraduate course in probability. The book is intended to be accessible to students from a wide range of scientific backgrounds. Rather than being a detailed treatise, it covers the key topics of Monte Carlo methods to the depth necessary for a researcher to design, implement, and analyze a full Monte Carlo study of a mathematical or scientific problem. The ideas are illustrated with diverse running examples. There are exercises sprinkled throughout the text. The topics covered include computer generation of random variables, techniques and examples for variance reduction of Monte Carlo estimates, Markov chain Monte Carlo, and statistical analysis of Monte Carlo output.

Download or read book Monte Carlo Strategies in Scientific Computing written by Jun S. Liu and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a self-contained and up-to-date treatment of the Monte Carlo method and develops a common framework under which various Monte Carlo techniques can be "standardized" and compared. Given the interdisciplinary nature of the topics and a moderate prerequisite for the reader, this book should be of interest to a broad audience of quantitative researchers such as computational biologists, computer scientists, econometricians, engineers, probabilists, and statisticians. It can also be used as a textbook for a graduate-level course on Monte Carlo methods.

Download or read book Markov Chain Monte Carlo Simulations and Their Statistical Analysis written by Bernd A Berg and published by World Scientific Publishing Company. This book was released on 2004-10-01 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book teaches modern Markov chain Monte Carlo (MC) simulation techniques step by step. The material should be accessible to advanced undergraduate students and is suitable for a course. It ranges from elementary statistics concepts (the theory behind MC simulations), through conventional Metropolis and heat bath algorithms, autocorrelations and the analysis of the performance of MC algorithms, to advanced topics including the multicanonical approach, cluster algorithms and parallel computing. Therefore, it is also of interest to researchers in the field. The book relates the theory directly to Web-based computer code. This allows readers to get quickly started with their own simulations and to verify many numerical examples easily. The present code is in Fortran 77, for which compilers are freely available. The principles taught are important for users of other programming languages, like C or C++.

Download or read book A First Course in Systems Biology written by Eberhard Voit and published by Garland Science. This book was released on 2017-09-05 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.

Download or read book Monte Carlo Statistical Methods written by Christian Robert and published by Springer Science & Business Media. This book was released on 2013-03-14 with total page 670 pages. Available in PDF, EPUB and Kindle. Book excerpt: We have sold 4300 copies worldwide of the first edition (1999). This new edition contains five completely new chapters covering new developments.

Download or read book Model Calibration and Parameter Estimation written by Ne-Zheng Sun and published by Springer. This book was released on 2015-07-01 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: This three-part book provides a comprehensive and systematic introduction to these challenging topics such as model calibration, parameter estimation, reliability assessment, and data collection design. Part 1 covers the classical inverse problem for parameter estimation in both deterministic and statistical frameworks, Part 2 is dedicated to system identification, hyperparameter estimation, and model dimension reduction, and Part 3 considers how to collect data and construct reliable models for prediction and decision-making. For the first time, topics such as multiscale inversion, stochastic field parameterization, level set method, machine learning, global sensitivity analysis, data assimilation, model uncertainty quantification, robust design, and goal-oriented modeling, are systematically described and summarized in a single book from the perspective of model inversion, and elucidated with numerical examples from environmental and water resources modeling. Readers of this book will not only learn basic concepts and methods for simple parameter estimation, but also get familiar with advanced methods for modeling complex systems. Algorithms for mathematical tools used in this book, such as numerical optimization, automatic differentiation, adaptive parameterization, hierarchical Bayesian, metamodeling, Markov chain Monte Carlo, are covered in details. This book can be used as a reference for graduate and upper level undergraduate students majoring in environmental engineering, hydrology, and geosciences. It also serves as an essential reference book for professionals such as petroleum engineers, mining engineers, chemists, mechanical engineers, biologists, biology and medical engineering, applied mathematicians, and others who perform mathematical modeling.