Identifiability and Regression Analysis of Biological Systems Models
| Author | : Paola Lecca |
| Publisher | : Springer Nature |
| Total Pages | : 130 |
| Release | : |
| Genre | : |
| ISBN | : 3031747488 |
Identifiability And Regression Analysis Of Biological Systems Models
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Identifiability and Regression Analysis of Biological Systems Models
| Author | : Paola Lecca |
| Publisher | : |
| Total Pages | : 90 |
| Release | : 2020 |
| Genre | : Biochemistry |
| ISBN | : 9783030412562 |
This richly illustrated book presents the objectives of, and the latest techniques for, the identifiability analysis and standard and robust regression analysis of complex dynamical models. The book first provides a definition of complexity in dynamic systems by introducing readers to the concepts of system size, density of interactions, stiff dynamics, and hybrid nature of determination. In turn, it presents the mathematical foundations of and algorithmic procedures for model structural and practical identifiability analysis, multilinear and non-linear regression analysis, and best predictor selection. Although the main fields of application discussed in the book are biochemistry and systems biology, the methodologies described can also be employed in other disciplines such as physics and the environmental sciences. Readers will learn how to deal with problems such as determining the identifiability conditions, searching for an identifiable model, and conducting their own regression analysis and diagnostics without supervision. Featuring a wealth of real-world examples, exercises, and codes in R, the book addresses the needs of doctoral students and researchers in bioinformatics, bioengineering, systems biology, biophysics, biochemistry, the environmental sciences and experimental physics. Readers should be familiar with the fundamentals of probability and statistics (as provided in first-year university courses) and a basic grasp of R.
2019-20 MATRIX Annals
| Author | : Jan de Gier |
| Publisher | : Springer Nature |
| Total Pages | : 798 |
| Release | : 2021-02-10 |
| Genre | : Mathematics |
| ISBN | : 3030624978 |
MATRIX is Australia’s international and residential mathematical research institute. It facilitates new collaborations and mathematical advances through intensive residential research programs, each 1-4 weeks in duration. This book is a scientific record of the ten programs held at MATRIX in 2019 and the two programs held in January 2020: · Topology of Manifolds: Interactions Between High and Low Dimensions · Australian-German Workshop on Differential Geometry in the Large · Aperiodic Order meets Number Theory · Ergodic Theory, Diophantine Approximation and Related Topics · Influencing Public Health Policy with Data-informed Mathematical Models of Infectious Diseases · International Workshop on Spatial Statistics · Mathematics of Physiological Rhythms · Conservation Laws, Interfaces and Mixing · Structural Graph Theory Downunder · Tropical Geometry and Mirror Symmetry · Early Career Researchers Workshop on Geometric Analysis and PDEs · Harmonic Analysis and Dispersive PDEs: Problems and Progress The articles are grouped into peer-reviewed contributions and other contributions. The peer-reviewed articles present original results or reviews on a topic related to the MATRIX program; the remaining contributions are predominantly lecture notes or short articles based on talks or activities at MATRIX.
Modelling Methodology for Physiology and Medicine
| Author | : Ewart Carson |
| Publisher | : Elsevier |
| Total Pages | : 437 |
| Release | : 2000-12-31 |
| Genre | : Mathematics |
| ISBN | : 0080511902 |
Modelling Methodology for Physiology and Medicine offers a unique approach and an unprecedented range of coverage of the state-of-the-art, advanced modelling methodology that is widely applicable to physiology and medicine. The book opens with a clear and integrated treatment of advanced methodology for developing mathematical models of physiology and medical systems. Readers are then shown how to apply this methodology beneficially to real-world problems in physiology and medicine, such as circulation and respiration. - Builds upon and enhances the readers existing knowledge of modelling methodology and practice - Editors are internationally renowned leaders in their respective fields
Identification of Dynamic Systems
| Author | : Rolf Isermann |
| Publisher | : Springer |
| Total Pages | : 705 |
| Release | : 2011-04-08 |
| Genre | : Technology & Engineering |
| ISBN | : 9783540871552 |
Precise dynamic models of processes are required for many applications, ranging from control engineering to the natural sciences and economics. Frequently, such precise models cannot be derived using theoretical considerations alone. Therefore, they must be determined experimentally. This book treats the determination of dynamic models based on measurements taken at the process, which is known as system identification or process identification. Both offline and online methods are presented, i.e. methods that post-process the measured data as well as methods that provide models during the measurement. The book is theory-oriented and application-oriented and most methods covered have been used successfully in practical applications for many different processes. Illustrative examples in this book with real measured data range from hydraulic and electric actuators up to combustion engines. Real experimental data is also provided on the Springer webpage, allowing readers to gather their first experience with the methods presented in this book. Among others, the book covers the following subjects: determination of the non-parametric frequency response, (fast) Fourier transform, correlation analysis, parameter estimation with a focus on the method of Least Squares and modifications, identification of time-variant processes, identification in closed-loop, identification of continuous time processes, and subspace methods. Some methods for nonlinear system identification are also considered, such as the Extended Kalman filter and neural networks. The different methods are compared by using a real three-mass oscillator process, a model of a drive train. For many identification methods, hints for the practical implementation and application are provided. The book is intended to meet the needs of students and practicing engineers working in research and development, design and manufacturing.
Understanding Regression Analysis
| Author | : Peter H. Westfall |
| Publisher | : CRC Press |
| Total Pages | : 453 |
| Release | : 2020-06-25 |
| Genre | : Business & Economics |
| ISBN | : 100006963X |
Understanding Regression Analysis unifies diverse regression applications including the classical model, ANOVA models, generalized models including Poisson, Negative binomial, logistic, and survival, neural networks, and decision trees under a common umbrella -- namely, the conditional distribution model. It explains why the conditional distribution model is the correct model, and it also explains (proves) why the assumptions of the classical regression model are wrong. Unlike other regression books, this one from the outset takes a realistic approach that all models are just approximations. Hence, the emphasis is to model Nature’s processes realistically, rather than to assume (incorrectly) that Nature works in particular, constrained ways. Key features of the book include: Numerous worked examples using the R software Key points and self-study questions displayed "just-in-time" within chapters Simple mathematical explanations ("baby proofs") of key concepts Clear explanations and applications of statistical significance (p-values), incorporating the American Statistical Association guidelines Use of "data-generating process" terminology rather than "population" Random-X framework is assumed throughout (the fixed-X case is presented as a special case of the random-X case) Clear explanations of probabilistic modelling, including likelihood-based methods Use of simulations throughout to explain concepts and to perform data analyses This book has a strong orientation towards science in general, as well as chapter-review and self-study questions, so it can be used as a textbook for research-oriented students in the social, biological and medical, and physical and engineering sciences. As well, its mathematical emphasis makes it ideal for a text in mathematics and statistics courses. With its numerous worked examples, it is also ideally suited to be a reference book for all scientists.
Statistical Methods in Biology
| Author | : S.J. Welham |
| Publisher | : CRC Press |
| Total Pages | : 592 |
| Release | : 2014-08-22 |
| Genre | : Mathematics |
| ISBN | : 1439898057 |
Written in simple language with relevant examples, this illustrative introductory book presents best practices in experimental design and simple data analysis. Taking a practical and intuitive approach, it only uses mathematical formulae to formalize the methods where necessary and appropriate. The text features extended discussions of examples that include real data sets arising from research. The authors analyze data in detail to illustrate the use of basic formulae for simple examples while using the GenStat statistical package for more complex examples. Each chapter offers instructions on how to obtain the example analyses in GenStat and R.
Systems Biology
| Author | : Aleš Prokop |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 569 |
| Release | : 2013-08-28 |
| Genre | : Medical |
| ISBN | : 9400768036 |
Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.
Quantitative Biology
| Author | : Brian Munsky |
| Publisher | : MIT Press |
| Total Pages | : 729 |
| Release | : 2018-08-21 |
| Genre | : Science |
| ISBN | : 0262038080 |
An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
Dynamic Systems Biology Modeling and Simulation
| Author | : Joseph DiStefano III |
| Publisher | : Academic Press |
| Total Pages | : 886 |
| Release | : 2015-01-10 |
| Genre | : Science |
| ISBN | : 0124104932 |
Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author's own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. - Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics - The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of "math modeling with life sciences - Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization - Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models - A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course - Importantly, the slides are editable, so they can be readily adapted to a lecturer's personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content - The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: [email protected]
