Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

This book was first published in 2006. Written by two of the foremost researchers in the field, this book studies the local times of Markov processes by employing isomorphism theorems that relate them to certain associated Gaussian processes. It builds to this material through self-contained but harmonized 'mini-courses' on the relevant ingredients, which assume only knowledge of measure-theoretic probability. The streamlined selection of topics creates an easy entrance for students and experts in related fields. The book starts by developing the fundamentals of Markov process theory and then of Gaussian process theory, including sample path properties. It then proceeds to more advanced results, bringing the reader to the heart of contemporary research. It presents the remarkable isomorphism theorems of Dynkin and Eisenbaum and then shows how they can be applied to obtain new properties of Markov processes by using well-established techniques in Gaussian process theory. This original, readable book will appeal to both researchers and advanced graduate students.

Kiyosi Ito's greatest contribution to probability theory may be his introduction of stochastic differential equations to explain the Kolmogorov-Feller theory of Markov processes. Starting with the geometric ideas that guided him, this book gives an account of Ito's program.

The modern theory of Markov processes was initiated by A. N. Kolmogorov. However, Kolmogorov's approach was too analytic to reveal the probabilistic foundations on which it rests. In particular, it hides the central role played by the simplest Markov processes: those with independent, identically distributed increments. To remedy this defect, Ito interpreted Kolmogorov's famous forward equation as an equation that describes the integral curve of a vector field on the space of probability measures. Thus, in order to show how Ito's thinking leads to his theory of stochastic integral equations, Stroock begins with an account of integral curves on the space of probability measures and then arrives at stochastic integral equations when he moves to a pathspace setting. In the first half of the book, everything is done in the context of general independent increment processes and without explicit use of Ito's stochastic integral calculus. In the second half, the author provides a systematic development of Ito's theory of stochastic integration: first for Brownian motion and then for continuous martingales. The final chapter presents Stratonovich's variation on Ito's theme and ends with an application to the characterization of the paths on which a diffusion is supported.

The book should be accessible to readers who have mastered the essentials of modern probability theory and should provide such readers with a reasonably thorough introduction to continuous-time, stochastic processes."

Twenty-five articles have been selected from the first 14 volumes of the "SA(c)minaire de ProbabilitA(c)s," all out of print, for their historical and/or mathematical interest. Among the many articles devoted to Martingale theory in the early volumes of the SA(c)minaire, we have chosen to reprint those that are particularly significant from a historical point of view, as well as those that can still be useful today. They are reprinted here verbatim, with a short retrospective comment, for the benefit of researchers in the theory of stochastic processes, in mathematical finance, or in history of mathematics.

The second volume concentrates on stochastic integrals, stochastic differential equations, excursion theory and the general theory of processes. These subjects are made accessible in the many concrete examples that illustrate techniques of calculation, and in the treatment of all topics from the ground up, starting from simple cases. Many of the examples and proofs are new; some important calculational techniques appear for the first time in this book.

This important work addresses problems in financial mathematics of pricing and hedging derivative securities in an environment of uncertain and changing market volatility. These problems are important to investors from large trading institutions to pension funds. The authors present mathematical and statistical tools that exploit the volatile nature of the market. The mathematics is introduced through examples and illustrated with simulations and the modeling approach that is described is validated and tested on market data. The material is suitable for a one-semester course for graduate students with some exposure to methods of stochastic modeling and arbitrage pricing theory in finance. The volume is easily accessible to derivatives practitioners in the financial engineering industry.

Now available in paperback, this celebrated book remains a key systematic guide to a large part of the modern theory of Probability. The authors not only present the subject of Brownian motion as a dry part of mathematical analysis, but convey its real meaning and fascination. The opening, heuristic chapter does just this, and it is followed by a comprehensive and self-contained account of the foundations of theory of stochastic processes. Chapter 3 is a lively presentation of the theory of Markov processes. Together with its companion volume, this book equips graduate students for research into a subject of great intrinsic interest and wide applications.

All the papers in the volume are original research papers, discussing fundamental properties of stochastic processes. The topics under study (martingales, filtrations, path properties, etc.) represent an important part of the current research performed in 1996-97 by various groups of probabilists in France and abroad.

Nearly one hundred years ago Jacques Hadamard used infinite sequences of symbols to analyze the distribution of geodesics on certain surfaces. That was the beginning of symbolic dynamics. In the 1930's and 40's Arnold Hedlund and Marston Morse again used infinite sequences to investigate geodesics on surfaces of negative curvature. They coined the term symbolic dynamics and began to study sequence spaces with the shift transformation as dynamical systems. In the 1940's Claude Shannon used sequence spaces to describe infor mation channels. Since that time symbolic dynamics has been used in ergodic theory, topological dynamics, hyperbolic dynamics, information theory and complex dynamics. Symbolic dynamical systems with a finite memory are stud ied in this book. They are the topological Markov shifts. Each can be defined by transition rules and the rules can be summarized by a transition matrix. The study naturally divides into two parts. The first part is about topological Markov shifts where the alphabet is finite. The second part is concerned with topological Markov shifts whose alphabet is count ably infinite. The techniques used in the two cases are quite different. When the alphabet is finite most of the methods are combinatorial or algebraic. When the alphabet is infinite the methods are much more analytic. This book grew from notes for a graduate course taught at Wesleyan Uni versity in the fall of 1994 and is intended as a graduate text and as a reference book for mathematicians working in related fields."

This two-volume set provides a comprehensive and self-contained approach to the dynamics, ergodic theory, and geometry of elliptic functions mapping the complex plane onto the Riemann sphere. Volume I discusses many fundamental results from ergodic theory and geometric measure theory in detail, including finite and infinite abstract ergodic theory, Young's towers, measure-theoretic Kolmogorov-Sinai entropy, thermodynamics formalism, geometric function theory, various conformal measures, conformal graph directed Markov systems and iterated functions systems, classical theory of elliptic functions. In Volume II, all these techniques, along with an introduction to topological dynamics of transcendental meromorphic functions, are applied to describe the beautiful and rich dynamics and fractal geometry of elliptic functions. Much of this material is appearing for the first time in book or even paper form. Both researchers and graduate students will appreciate the detailed explanations of essential concepts and full proofs provided in what is sure to be an indispensable reference.

Stochastic Modeling for Medical Image Analysis provides a brief introduction to medical imaging, stochastic modeling, and model-guided image analysis. Today, image-guided computer-assisted diagnostics (CAD) faces two basic challenging problems. The first is the computationally feasible and accurate modeling of images from different modalities to obtain clinically useful information. The second is the accurate and fast inferring of meaningful and clinically valid CAD decisions and/or predictions on the basis of model-guided image analysis. To help address this, this book details original stochastic appearance and shape models with computationally feasible and efficient learning techniques for improving the performance of object detection, segmentation, alignment, and analysis in a number of important CAD applications. The book demonstrates accurate descriptions of visual appearances and shapes of the goal objects and their background to help solve a number of important and challenging CAD problems. The models focus on the first-order marginals of pixel/voxel-wise signals and second- or higher-order Markov-Gibbs random fields of these signals and/or labels of regions supporting the goal objects in the lattice. This valuable resource presents the latest state of the art in stochastic modeling for medical image analysis while incorporating fully tested experimental results throughout.

Optimal filtering applied to stationary and non-stationary signals provides the most efficient means of dealing with problems arising from the extraction of noise signals. Moreover, it is a fundamental feature in a range of applications, such as in navigation in aerospace and aeronautics, filter processing in the telecommunications industry, etc. This book provides a comprehensive overview of this area, discussing random and Gaussian vectors, outlining the results necessary for the creation of Wiener and adaptive filters used for stationary signals, as well as examining Kalman filters which are used in relation to non-stationary signals. Exercises with solutions feature in each chapter to demonstrate the practical application of these ideas using Matlab.

The different papers contained in this volume are all research papers. The main directions of research which are being developed are: quantum probability, semimartingales and stochastic calculus.

A fascinating and instructive guide to Markov chains for experienced users and newcomers alike This unique guide to Markov chains approaches the subject along the four convergent lines of mathematics, implementation, simulation, and experimentation. It introduces readers to the art of stochastic modeling, shows how to design computer implementations, and provides extensive worked examples with case studies. Markov Chains: From Theory to Implementation and Experimentation begins with a general introduction to the history of probability theory in which the author uses quantifiable examples to illustrate how probability theory arrived at the concept of discrete-time and the Markov model from experiments involving independent variables. An introduction to simple stochastic matrices and transition probabilities is followed by a simulation of a two-state Markov chain. The notion of steady state is explored in connection with the long-run distribution behavior of the Markov chain. Predictions based on Markov chains with more than two states are examined, followed by a discussion of the notion of absorbing Markov chains. Also covered in detail are topics relating to the average time spent in a state, various chain configurations, and n-state Markov chain simulations used for verifying experiments involving various diagram configurations. Fascinating historical notes shed light on the key ideas that led to the development of the Markov model and its variants Various configurations of Markov Chains and their limitations are explored at length Numerous examples from basic to complex are presented in a comparative manner using a variety of color graphics All algorithms presented can be analyzed in either Visual Basic, Java Script, or PHP Designed to be useful to professional statisticians as well as readers without extensive knowledge of probability theory Covering both the theory underlying the Markov model and an array of Markov chain implementations, within a common conceptual framework, Markov Chains: From Theory to Implementation and Experimentation is a stimulating introduction to and a valuable reference for those wishing to deepen their understanding of this extremely valuable statistical tool. Paul A. Gagniuc, PhD, is Associate Professor at Polytechnic University of Bucharest, Romania. He obtained his MS and his PhD in genetics at the University of Bucharest. Dr. Ganiuc s work has been published in numerous high profile scientific journals, ranging from the Public Library of Science to BioMed Central and Nature journals. He is the recipient of several awards for exceptional scientific results and a highly active figure in the review process for different scientific areas.

Probability theory has become a convenient language and a useful tool in many areas of modern analysis. The main purpose of this book is to explore part of this connection concerning the relations between Brownian motion on a manifold and analytical aspects of differential geometry. A dominant theme of the book is the probabilistic interpretation of the curvature of a manifold.The book begins with a brief review of stochastic differential equations on Euclidean space. After presenting the basics of stochastic analysis on manifolds, the author introduces Brownian motion on a Riemannian manifold and studies the effect of curvature on its behavior. He then applies Brownian motion to geometric problems and vice versa, using many well-known examples, e.g., short-time behavior of the heat kernel on a manifold and probabilistic proofs of the Gauss-Bonnet-Chem theorem and the Atiyah-Singer index theorem for Dirac operators. The book concludes with an introduction to stochastic analysis on the path space over a Riemannian manifold.

This volume presents topics in probability theory covered during a first-year graduate course given at the Courant Institute of Mathematical Sciences, USA. The necessary background material in measure theory is developed, including the standard topics, such as extension theorem, construction of measures, integration, product spaces, Radon-Nikodym theorem, and conditional expectation In the first part of the book, characteristic functions are introduced, followed by the study of weak convergence of probability distributions. Then both the weak and strong limit theorems for sums of independent random variables are proved, including the weak and strong laws of large numbers, central limit theorems, laws of the iterated logarithm, and the Kolmogorov three series theorem. The first part concludes with infinitely divisible distributions and limit theorems for sums of uniformly infinitesimal independent random variables. The second part of the book mainly deals with dependent random variables, particularly martingales and Markov chains. Topics include standard results regarding discrete parameter martingales and Doob's inequalities.

This book provides an overview of global sensitivity analysis methods and algorithms, including their theoretical basis and mathematical properties. The authors use a practical point of view and real case studies as well as numerous examples, and applications of the different approaches are illustrated throughout using R code to explain their usage and usefulness in practice. Basics and Trends in Sensitivity Analysis: Theory and Practice in R covers a lot of material, including theoretical aspects of Sobol' indices as well as sampling-based formulas, spectral methods, and metamodel-based approaches for estimation purposes; screening techniques devoted to identifying influential and noninfluential inputs; variance-based measures when model inputs are statistically dependent (and several other approaches that go beyond variance-based sensitivity measures); and a case study in R related to a COVID-19 epidemic model where the full workflow of sensitivity analysis combining several techniques is presented. This book is intended for engineers, researchers, and undergraduate students who use complex numerical models and have an interest in sensitivity analysis techniques and is appropriate for anyone with a solid mathematical background in basic statistical and probability theories who develops and uses numerical models in all scientific and engineering domains.