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Nonlinear Analysis of Biological Models and Stochastic Analysis of Machine Learning Methods

Nonlinear Analysis of Biological Models and Stochastic Analysis of Machine Learning Methods PDF Author: Jing An
Publisher:
ISBN:
Category :
Languages : en
Pages :

Book Description
This dissertation consists of two independent parts: nonlinear analysis of biological models (Part I), and stochastic analysis of machine learning methods (Part II). In the first part, we investigate two nonlinear partial differential equations arising in biology. The first model we consider is the Euler alignment system, which is a hydrodynamics limit of the Cucker-Smale model describing the collective dynamics of a flock of $N$ individuals (birds, fish, etc.) that tend to align their velocities locally. We prove that, as long as the weakly singular interaction kernel is not integrable, the solutions of the Euler alignment system stay globally regular. This result extends the previous regularity results to the critical case. The second model we consider is the Burgers-FKPP equation, which is a reaction-diffusion equation equipped with an advection term of the Burgers type. The Burgers-FKPP equation appears in many applications from chemical physics to population genetics, but the large time behavior of its solutions is rarely studied. An interesting feature of Burgers-FKPP is that when the coefficient of the Burgers nonlinearity increases, the propagating solutions have a phase transition from pulled fronts to pushed fronts. In this work, we show the convergence of a solution to a single traveling wave in the Burgers-FKPP equation, as well as some side discoveries including front asymptotics in higher orders. In the second part, we study the several machine learning models from the stochastic analysis viewpoint. Taking the continuous-time limit and using approximate stochastic differential equations (SDE) to analyze stochastic gradients algorithms has become popular in recent years, since it provides many new insights and compact proofs using developed toolkits. We exhibit the power of stochastic analysis in machine learning from two independent projects. In the first project, we consider the asynchronous stochastic gradient descent (ASGD) algorithm that updates iterates with a delay read, which plays an important role in large scale parallel computing. We derive corresponding SDEs to characterize the dynamics of the ASGD algorithm. Based on that, we can further explore algorithmic properties by considering the temperature factors in Langevin type equations, as well as identifying optimal hyper-parameters by using optimal control theory. In the second project, we consider data, model, and stochastic optimization algorithms as an integrated system. On the one side, we focus on comparing resampling and reweighting for correcting sampling biases. On the other side, we propose a combined resampling and reweighting strategy to handle the data feature disparities. Both problems arise as the models are non-convex, and by SDE approaches we explain how stochastic gradient algorithms select the minimum in different regions.

Nonlinear Analysis of Biological Models and Stochastic Analysis of Machine Learning Methods

Nonlinear Analysis of Biological Models and Stochastic Analysis of Machine Learning Methods PDF Author: Jing An
Publisher:
ISBN:
Category :
Languages : en
Pages :

Book Description
This dissertation consists of two independent parts: nonlinear analysis of biological models (Part I), and stochastic analysis of machine learning methods (Part II). In the first part, we investigate two nonlinear partial differential equations arising in biology. The first model we consider is the Euler alignment system, which is a hydrodynamics limit of the Cucker-Smale model describing the collective dynamics of a flock of $N$ individuals (birds, fish, etc.) that tend to align their velocities locally. We prove that, as long as the weakly singular interaction kernel is not integrable, the solutions of the Euler alignment system stay globally regular. This result extends the previous regularity results to the critical case. The second model we consider is the Burgers-FKPP equation, which is a reaction-diffusion equation equipped with an advection term of the Burgers type. The Burgers-FKPP equation appears in many applications from chemical physics to population genetics, but the large time behavior of its solutions is rarely studied. An interesting feature of Burgers-FKPP is that when the coefficient of the Burgers nonlinearity increases, the propagating solutions have a phase transition from pulled fronts to pushed fronts. In this work, we show the convergence of a solution to a single traveling wave in the Burgers-FKPP equation, as well as some side discoveries including front asymptotics in higher orders. In the second part, we study the several machine learning models from the stochastic analysis viewpoint. Taking the continuous-time limit and using approximate stochastic differential equations (SDE) to analyze stochastic gradients algorithms has become popular in recent years, since it provides many new insights and compact proofs using developed toolkits. We exhibit the power of stochastic analysis in machine learning from two independent projects. In the first project, we consider the asynchronous stochastic gradient descent (ASGD) algorithm that updates iterates with a delay read, which plays an important role in large scale parallel computing. We derive corresponding SDEs to characterize the dynamics of the ASGD algorithm. Based on that, we can further explore algorithmic properties by considering the temperature factors in Langevin type equations, as well as identifying optimal hyper-parameters by using optimal control theory. In the second project, we consider data, model, and stochastic optimization algorithms as an integrated system. On the one side, we focus on comparing resampling and reweighting for correcting sampling biases. On the other side, we propose a combined resampling and reweighting strategy to handle the data feature disparities. Both problems arise as the models are non-convex, and by SDE approaches we explain how stochastic gradient algorithms select the minimum in different regions.

Stochastic Models in Biology

Stochastic Models in Biology PDF Author: Narendra S. Goel
Publisher: Elsevier
ISBN: 1483278107
Category : Science
Languages : en
Pages : 282

Book Description
Stochastic Models in Biology describes the usefulness of the theory of stochastic process in studying biological phenomena. The book describes analysis of biological systems and experiments though probabilistic models rather than deterministic methods. The text reviews the mathematical analyses for modeling different biological systems such as the random processes continuous in time and discrete in state space. The book also discusses population growth and extinction through Malthus' law and the work of MacArthur and Wilson. The text then explains the dynamics of a population of interacting species. The book also addresses population genetics under systematic evolutionary pressures known as deterministic equations and genetic changes in a finite population known as stochastic equations. The text then turns to stochastic modeling of biological systems at the molecular level, particularly the kinetics of biochemical reactions. The book also presents various useful equations such as the differential equation for generating functions for birth and death processes. The text can prove valuable for biochemists, cellular biologists, and researchers in the medical and chemical field who are tasked to perform data analysis.

Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology

Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology PDF Author: David Holcman
Publisher: Springer
ISBN: 3319626272
Category : Mathematics
Languages : en
Pages : 377

Book Description
This book focuses on the modeling and mathematical analysis of stochastic dynamical systems along with their simulations. The collected chapters will review fundamental and current topics and approaches to dynamical systems in cellular biology. This text aims to develop improved mathematical and computational methods with which to study biological processes. At the scale of a single cell, stochasticity becomes important due to low copy numbers of biological molecules, such as mRNA and proteins that take part in biochemical reactions driving cellular processes. When trying to describe such biological processes, the traditional deterministic models are often inadequate, precisely because of these low copy numbers. This book presents stochastic models, which are necessary to account for small particle numbers and extrinsic noise sources. The complexity of these models depend upon whether the biochemical reactions are diffusion-limited or reaction-limited. In the former case, one needs to adopt the framework of stochastic reaction-diffusion models, while in the latter, one can describe the processes by adopting the framework of Markov jump processes and stochastic differential equations. Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology will appeal to graduate students and researchers in the fields of applied mathematics, biophysics, and cellular biology.

Methods and Models in Mathematical Biology

Methods and Models in Mathematical Biology PDF Author: Johannes Müller
Publisher: Springer
ISBN: 3642272517
Category : Mathematics
Languages : en
Pages : 721

Book Description
This book developed from classes in mathematical biology taught by the authors over several years at the Technische Universität München. The main themes are modeling principles, mathematical principles for the analysis of these models and model-based analysis of data. The key topics of modern biomathematics are covered: ecology, epidemiology, biochemistry, regulatory networks, neuronal networks and population genetics. A variety of mathematical methods are introduced, ranging from ordinary and partial differential equations to stochastic graph theory and branching processes. A special emphasis is placed on the interplay between stochastic and deterministic models.

Stochastic Biomathematical Models

Stochastic Biomathematical Models PDF Author: Mostafa Bachar
Publisher: Springer
ISBN: 3642321577
Category : Mathematics
Languages : en
Pages : 216

Book Description
Stochastic biomathematical models are becoming increasingly important as new light is shed on the role of noise in living systems. In certain biological systems, stochastic effects may even enhance a signal, thus providing a biological motivation for the noise observed in living systems. Recent advances in stochastic analysis and increasing computing power facilitate the analysis of more biophysically realistic models, and this book provides researchers in computational neuroscience and stochastic systems with an overview of recent developments. Key concepts are developed in chapters written by experts in their respective fields. Topics include: one-dimensional homogeneous diffusions and their boundary behavior, large deviation theory and its application in stochastic neurobiological models, a review of mathematical methods for stochastic neuronal integrate-and-fire models, stochastic partial differential equation models in neurobiology, and stochastic modeling of spreading cortical depression.

Identifiability and Regression Analysis of Biological Systems Models

Identifiability and Regression Analysis of Biological Systems Models PDF Author: Paola Lecca
Publisher: Springer Nature
ISBN: 3030412555
Category : Medical
Languages : en
Pages : 90

Book Description
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.

Nonlinear Models for Repeated Measurement Data

Nonlinear Models for Repeated Measurement Data PDF Author: Marie Davidian
Publisher: Routledge
ISBN: 1351428152
Category : Mathematics
Languages : en
Pages : 360

Book Description
Nonlinear measurement data arise in a wide variety of biological and biomedical applications, such as longitudinal clinical trials, studies of drug kinetics and growth, and the analysis of assay and laboratory data. Nonlinear Models for Repeated Measurement Data provides the first unified development of methods and models for data of this type, with a detailed treatment of inference for the nonlinear mixed effects and its extensions. A particular strength of the book is the inclusion of several detailed case studies from the areas of population pharmacokinetics and pharmacodynamics, immunoassay and bioassay development and the analysis of growth curves.

Statistical Modeling and Machine Learning for Molecular Biology

Statistical Modeling and Machine Learning for Molecular Biology PDF Author: Alan Moses
Publisher: CRC Press
ISBN: 1482258625
Category : Mathematics
Languages : en
Pages : 270

Book Description
Molecular biologists are performing increasingly large and complicated experiments, but often have little background in data analysis. The book is devoted to teaching the statistical and computational techniques molecular biologists need to analyze their data. It explains the big-picture concepts in data analysis using a wide variety of real-world molecular biological examples such as eQTLs, ortholog identification, motif finding, inference of population structure, protein fold prediction and many more. The book takes a pragmatic approach, focusing on techniques that are based on elegant mathematics yet are the simplest to explain to scientists with little background in computers and statistics.

Nonlinear Analysis, Geometry and Applications

Nonlinear Analysis, Geometry and Applications PDF Author: Diaraf Seck
Publisher: Springer Nature
ISBN: 3031526813
Category :
Languages : en
Pages : 410

Book Description


Stochastic Chemical Reaction Systems in Biology

Stochastic Chemical Reaction Systems in Biology PDF Author: Hong Qian
Publisher: Springer Nature
ISBN: 3030862526
Category : Mathematics
Languages : en
Pages : 364

Book Description
This book provides an introduction to the analysis of stochastic dynamic models in biology and medicine. The main aim is to offer a coherent set of probabilistic techniques and mathematical tools which can be used for the simulation and analysis of various biological phenomena. These tools are illustrated on a number of examples. For each example, the biological background is described, and mathematical models are developed following a unified set of principles. These models are then analyzed and, finally, the biological implications of the mathematical results are interpreted. The biological topics covered include gene expression, biochemistry, cellular regulation, and cancer biology. The book will be accessible to graduate students who have a strong background in differential equations, the theory of nonlinear dynamical systems, Markovian stochastic processes, and both discrete and continuous state spaces, and who are familiar with the basic concepts of probability theory.