Probabilistic Methods For Bioinformatics

Book Description :

The Bayesian network is one of the most important architectures for representing and reasoning with multivariate probability distributions. When used in conjunction with specialized informatics, possibilities of real-world applications are achieved. Probabilistic Methods for BioInformatics explains the application of probability and statistics, in particular Bayesian networks, to genetics. This book provides background material on probability, statistics, and genetics, and then moves on to discuss Bayesian networks and applications to bioinformatics. Rather than getting bogged down in proofs and algorithms, probabilistic methods used for biological information and Bayesian networks are explained in an accessible way using applications and case studies. The many useful applications of Bayesian networks that have been developed in the past 10 years are discussed. Forming a review of all the significant work in the field that will arguably become the most prevalent method in biological data analysis. Unique coverage of probabilistic reasoning methods applied to bioinformatics data--those methods that are likely to become the standard analysis tools for bioinformatics. Shares insights about when and why probabilistic methods can and cannot be used effectively; Complete review of Bayesian networks and probabilistic methods with a practical approach.

Book Description :

Probabilistic Modelling in Bioinformatics and Medical Informatics has been written for researchers and students in statistics, machine learning, and the biological sciences. The first part of this book provides a self-contained introduction to the methodology of Bayesian networks. The following parts demonstrate how these methods are applied in bioinformatics and medical informatics. All three fields - the methodology of probabilistic modeling, bioinformatics, and medical informatics - are evolving very quickly. The text should therefore be seen as an introduction, offering both elementary tutorials as well as more advanced applications and case studies.

Book Description :

Download Probabilistic Methods for Bionformatics book written by Richard E. Neapolitan, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

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Biological research and recent technological advances have resulted in an enormous increase in research data that require large storage capacities, powerful computing resources, and accurate data analysis algorithms. Bioinformatics is the field that provides these resources to life science researchers. The Swiss Institute of Bioinformatics (SIB), which has celebrated its 10th anniversary in 2008, is an institution of national importance, recognized worldwide for its state-of-the-art work. Organized as a federation of bioinformatics research groups from Swiss universities and research institutes, the SIB provides services to the life science community that are highly appreciated worldwide, and coordinates research and education in bioinformatics nationwide. The SIB plays a central role in life science research both in Switzerland and abroad by developing extensive and high-quality bioinformatics resources that are essential for all life scientists. Knowledge developed by SIB members in areas such as genomics, proteomics, and systems biology is directly transformed by academia and industry into innovative solutions to improve global health. Such an astounding concentration of talent in a given field is unusual and unique in Switzerland. This book provides an insight into some of the key areas of activity in bioinformatics in Switzerland. With contributions from SIB members, it covers both research work and major infrastructure efforts in genome and gene expression analysis, investigations on proteins and proteomes, evolutionary bioinformatics, and modeling of biological systems.

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Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

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The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

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Advances in computers and biotechnology have had a profound impact on biomedical research, and as a result complex data sets can now be generated to address extremely complex biological questions. Correspondingly, advances in the statistical methods necessary to analyze such data are following closely behind the advances in data generation methods. The statistical methods required by bioinformatics present many new and difficult problems for the research community. This book provides an introduction to some of these new methods. The main biological topics treated include sequence analysis, BLAST, microarray analysis, gene finding, and the analysis of evolutionary processes. The main statistical techniques covered include hypothesis testing and estimation, Poisson processes, Markov models and Hidden Markov models, and multiple testing methods. The second edition features new chapters on microarray analysis and on statistical inference, including a discussion of ANOVA, and discussions of the statistical theory of motifs and methods based on the hypergeometric distribution. Much material has been clarified and reorganized. The book is written so as to appeal to biologists and computer scientists who wish to know more about the statistical methods of the field, as well as to trained statisticians who wish to become involved with bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, but with an emphasis on material relevant to later chapters and often not covered in standard introductory texts. Later chapters should be immediately accessible to the trained statistician. Sufficient mathematical background consists of introductory courses in calculus and linear algebra. The basic biological concepts that are used are explained, or can be understood from the context, and standard mathematical concepts are summarized in an Appendix. Problems are provided at the end of each chapter allowing the reader to develop aspects of the theory outlined in the main text. Warren J. Ewens holds the Christopher H. Brown Distinguished Professorship at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics. He is a senior editor of Annals of Human Genetics and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceedings of the Royal Society B and SIAM Journal in Mathematical Biology. He is a fellow of the Royal Society and the Australian Academy of Science. Gregory R. Grant is a senior bioinformatics researcher in the University of Pennsylvania Computational Biology and Informatics Laboratory. He obtained his Ph.D. in number theory from the University of Maryland in 1995 and his Masters in Computer Science from the University of Pennsylvania in 1999. Comments on the first edition: "This book would be an ideal text for a postgraduate course...[and] is equally well suited to individual study.... I would recommend the book highly." (Biometrics) "Ewens and Grant have given us a very welcome introduction to what is behind those pretty [graphical user] interfaces." (Naturwissenschaften) "The authors do an excellent job of presenting the essence of the material without getting bogged down in mathematical details." (Journal American Statistical Association) "The authors have restructured classical material to a great extent and the new organization of the different topics is one of the outstanding services of the book." (Metrika)

Book Description :

This reference serves as a reader-friendly guide to every basic tool and skill required in the mathematical library and helps mathematicians find resources in any format in the mathematics literature. It lists a wide range of standard texts, journals, review articles, newsgroups, and Internet and database tools for every major subfield in mathemati

Book Description :

The first edition of this popular textbook, Contemporary Artificial Intelligence, provided an accessible and student friendly introduction to AI. This fully revised and expanded update, Artificial Intelligence: With an Introduction to Machine Learning, Second Edition, retains the same accessibility and problem-solving approach, while providing new material and methods. The book is divided into five sections that focus on the most useful techniques that have emerged from AI. The first section of the book covers logic-based methods, while the second section focuses on probability-based methods. Emergent intelligence is featured in the third section and explores evolutionary computation and methods based on swarm intelligence. The newest section comes next and provides a detailed overview of neural networks and deep learning. The final section of the book focuses on natural language understanding. Suitable for undergraduate and beginning graduate students, this class-tested textbook provides students and other readers with key AI methods and algorithms for solving challenging problems involving systems that behave intelligently in specialized domains such as medical and software diagnostics, financial decision making, speech and text recognition, genetic analysis, and more.

Book Description :

The notion of artificial intelligence (AI) often sparks thoughts of characters from science fiction, such as the Terminator and HAL 9000. While these two artificial entities do not exist, the algorithms of AI have been able to address many real issues, from performing medical diagnoses to navigating difficult terrain to monitoring possible failures

Book Description :

Logic is a field studied mainly by researchers and students of philosophy, mathematics and computing. Inductive logic seeks to determine the extent to which the premisses of an argument entail its conclusion, aiming to provide a theory of how one should reason in the face of uncertainty. It has applications to decision making and artificial intelligence, as well as how scientists should reason when not in possession of the full facts. In this book, Jon Williamson embarks on a quest to find a general, reasonable, applicable inductive logic (GRAIL), all the while examining why pioneers such as Ludwig Wittgenstein and Rudolf Carnap did not entirely succeed in this task. Along the way he presents a general framework for the field, and reaches a new inductive logic, which builds upon recent developments in Bayesian epistemology (a theory about how strongly one should believe the various propositions that one can express). The book explores this logic in detail, discusses some key criticisms, and considers how it might be justified. Is this truly the GRAIL? Although the book presents new research, this material is well suited to being delivered as a series of lectures to students of philosophy, mathematics, or computing and doubles as an introduction to the field of inductive logic

Book Description :

Foundations of Algorithms, Fifth Edition offers a well-balanced presentation of algorithm design, complexity analysis of algorithms, and computational complexity. Ideal for any computer science students with a background in college algebra and discrete structures, the text presents mathematical concepts using standard English and simple notation to maximize accessibility and user-friendliness. Concrete examples, appendices reviewing essential mathematical concepts, and a student-focused approach reinforce theoretical explanations and promote learning and retention. C++ and Java pseudocode help students better understand complex algorithms. A chapter on numerical algorithms includes a review of basic number theory, Euclid's Algorithm for finding the greatest common divisor, a review of modular arithmetic, an algorithm for solving modular linear equations, an algorithm for computing modular powers, and the new polynomial-time algorithm for determining whether a number is prime. The revised and updated Fifth Edition features an all-new chapter on genetic algorithms and genetic programming, including approximate solutions to the traveling salesperson problem, an algorithm for an artificial ant that navigates along a trail of food, and an application to financial trading. With fully updated exercises and examples throughout and improved instructor resources including complete solutions, an Instructor's Manual and PowerPoint lecture outlines, Foundations of Algorithms is an essential text for undergraduate and graduate courses in the design and analysis of algorithms. Key features include: • The only text of its kind with a chapter on genetic algorithms • Use of C++ and Java pseudocode to help students better understand complex algorithms • No calculus background required • Numerous clear and student-friendly examples throughout the text • Fully updated exercises and examples throughout • Improved instructor resources, including complete solutions, an Instructor's Manual, and PowerPoint lecture outlines

Book Description :

This book constitutes the refereed proceedings of the 11th European Conference on Symbolic and Quantitative Approaches to Reasoning with Uncertainty, ECSQARU 2011, held in Belfast, UK, in June/July 2011. The 60 revised full papers presented together with 3 invited talks were carefully reviewed and selected from 108 submissions. The papers are organized in topical sections on argumentation; Bayesian networks and causal networks; belief functions; belief revision and inconsistency handling; classification and clustering; default reasoning and logics for reasoning under uncertainty; foundations of reasoning and decision making under uncertainty; fuzzy sets and fuzzy logic; implementation and applications of uncertain systems; possibility theory and possibilistic logic; and uncertainty in databases.

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Data Structures & Theory of Computation

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An introduction to machine learning methods and their applications to problems in bioinformatics Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. From an internationally recognized panel of prominent researchers in the field, Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics. Coverage includes: feature selection for genomic and proteomic data mining; comparing variable selection methods in gene selection and classification of microarray data; fuzzy gene mining; sequence-based prediction of residue-level properties in proteins; probabilistic methods for long-range features in biosequences; and much more. Machine Learning in Bioinformatics is an indispensable resource for computer scientists, engineers, biologists, mathematicians, researchers, clinicians, physicians, and medical informaticists. It is also a valuable reference text for computer science, engineering, and biology courses at the upper undergraduate and graduate levels.

Book Description :

This book constitutes the refereed proceedings of the Fourth International Workshop on Pattern Recognition in Bioinformatics, PRIB 2009, held in Sheffield, UK, in September 2009. The 38 revised full papers presented were carefully reviewed and selected from numerous submissions. The topics covered by these papers range from image analysis for biomedical data to systems biology. The conference aims at crating a focus for the development and application of pattern recognition techniques in the biological domain.

Book Description :

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Book Description :

Computational methods are playing an ever increasing role in cell biology. This volume of Methods in Cell Biology focuses on Computational Methods in Cell Biology and consists of two parts: (1) data extraction and analysis to distill models and mechanisms, and (2) developing and simulating models to make predictions and testable hypotheses. Focuses on computational methods in cell biology Split into 2 parts--data extraction and analysis to distill models and mechanisms, and developing and simulating models to make predictions and testable hypotheses Emphasizes the intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment

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"Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses"--Provided by publisher.

Book Description :

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.