Download or read book Analysis of Molecular Expression Patterns and Integration with Other Knowledge Bases Using Probabilistic Bayesian Network Models written by and published by . This book was released on 2000 with total page 5 pages. Available in PDF, EPUB and Kindle. Book excerpt: How can molecular expression experiments be interpreted with greater than ten to the fourth measurements per chip? How can one get the most quantitative information possible from the experimental data with good confidence? These are important questions whose solutions require an interdisciplinary combination of molecular and cellular biology, computer science, statistics, and complex systems analysis. The explosion of data from microarray techniques present the problem of interpreting the experiments. The availability of large-scale knowledge bases provide the opportunity to maximize the information extracted from these experiments. We have developed new methods of discovering biological function, metabolic pathways, and regulatory networks from these data and knowledge bases. These techniques are applicable to analyses for biomedical engineering, clinical, and fundamental cell and molecular biology studies. Our approach uses probabilistic, computational methods that give quantitative interpretations of data in a biological context. We have selected Bayesian statistical models with graphical network representations as a framework for our methods. As a first step, we use a nave Bayesian classifier to identify statistically significant patterns in gene expression data. We have developed methods which allow us to (a) characterize which genes or experiments distinguish each class from the others, (b) cross-index the resulting classes with other databases to assess biological meaning of the classes, and (c) display a gross overview of cellular dynamics. We have developed a number of visualization tools to convey the results. We report here our methods of classification and our first attempts at integrating the data and other knowledge bases together with new visualization tools. We demonstrate the utility of these methods and tools by analysis of a series of yeast cDNA microarray data and to a set of cancerous/normal sample data from colon cancer patients. We discuss extending our methods to inferring biological pathways and networks using more complex dynamic Bayesian networks.
Download or read book Knowledge Based Bioinformatics written by Gil Alterovitz and published by John Wiley & Sons. This book was released on 2011-04-20 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is an increasing need throughout the biomedical sciences for a greater understanding of knowledge-based systems and their application to genomic and proteomic research. This book discusses knowledge-based and statistical approaches, along with applications in bioinformatics and systems biology. The text emphasizes the integration of different methods for analysing and interpreting biomedical data. This, in turn, can lead to breakthrough biomolecular discoveries, with applications in personalized medicine. Key Features: Explores the fundamentals and applications of knowledge-based and statistical approaches in bioinformatics and systems biology. Helps readers to interpret genomic, proteomic, and metabolomic data in understanding complex biological molecules and their interactions. Provides useful guidance on dealing with large datasets in knowledge bases, a common issue in bioinformatics. Written by leading international experts in this field. Students, researchers, and industry professionals with a background in biomedical sciences, mathematics, statistics, or computer science will benefit from this book. It will also be useful for readers worldwide who want to master the application of bioinformatics to real-world situations and understand biological problems that motivate algorithms.
Download or read book Bayesian Analysis of Gene Expression Data written by Bani K. Mallick and published by John Wiley & Sons. This book was released on 2009-07-20 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of high-throughput genetic experimentation is evolving rapidly, with the advent of new technologies and new venues for data mining. Bayesian methods play a role central to the future of data and knowledge integration in the field of Bioinformatics. This book is devoted exclusively to Bayesian methods of analysis for applications to high-throughput gene expression data, exploring the relevant methods that are changing Bioinformatics. Case studies, illustrating Bayesian analyses of public gene expression data, provide the backdrop for students to develop analytical skills, while the more experienced readers will find the review of advanced methods challenging and attainable. This book: Introduces the fundamentals in Bayesian methods of analysis for applications to high-throughput gene expression data. Provides an extensive review of Bayesian analysis and advanced topics for Bioinformatics, including examples that extensively detail the necessary applications. Accompanied by website featuring datasets, exercises and solutions. Bayesian Analysis of Gene Expression Data offers a unique introduction to both Bayesian analysis and gene expression, aimed at graduate students in Statistics, Biomedical Engineers, Computer Scientists, Biostatisticians, Statistical Geneticists, Computational Biologists, applied Mathematicians and Medical consultants working in genomics. Bioinformatics researchers from many fields will find much value in this book.
Download or read book Bayesian Networks and Influence Diagrams A Guide to Construction and Analysis written by Uffe B. Kjærulff and published by Springer Science & Business Media. This book was released on 2012-11-30 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis, Second Edition, provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. This new edition contains six new sections, in addition to fully-updated examples, tables, figures, and a revised appendix. Intended primarily for practitioners, this book does not require sophisticated mathematical skills or deep understanding of the underlying theory and methods nor does it discuss alternative technologies for reasoning under uncertainty. The theory and methods presented are illustrated through more than 140 examples, and exercises are included for the reader to check his or her level of understanding. The techniques and methods presented for knowledge elicitation, model construction and verification, modeling techniques and tricks, learning models from data, and analyses of models have all been developed and refined on the basis of numerous courses that the authors have held for practitioners worldwide.
Download or read book Modeling and Learning Realistic Genetic Interactions Using Dynamic Bayesian Network and Information Theory written by Nizamul Morshed and published by . This book was released on 2013 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deciphering genetic interactions is of fundamental importance in computational systems biology, with wide applications in a number of other associated areas. Realistic modeling of these interactions poses novel challenges while dealing with the problem. Further, learning these interactions using computational methods becomes increasingly complex with the adoption of advanced and more realistic modeling techniques. In this thesis, we propose methods to address this challenge using a graphical model having sound probabilistic underpinnings, commonly known as dynamic Bayesian networks. Inference of genetic interactions is usually carried out using DNA microarray data. This data provides snapshots of mRNA expression levels of a large number of genes from a single experiment. However, the number of samples from such experiments is small, and additionally, they contain missing values and noise. Bayesian networks are considered as one of the most promising ways by which these issues can be tackled. However, traditional Bayesian networks have their own limitations; for example, they neither take time information into account nor can they capture feedback. Further, accurate determination of the direction of regulation requires a significant number of tests to be performed. Dynamic Bayesian networks (DBN) are extensions of Bayesian networks that can effectively address these limitations. In this thesis, we develop novel techniques for gene regulatory network reconstruction using DBN based modeling approach. We start with a basic DBN based model, and improve it so that it can represent and model both instantaneous and time-delayed genetic interactions. Initially, we aim to detect the occurrence of instantaneous and single-step time-delayed interactions, and subsequently this approach is further extended to model the instantaneous and multi-step time-delayed interactions. This approach of modeling both instantaneous and multi-step time-delayed genetic interactions is superior to traditional DBN based GRN reconstruction techniques, where only the time delayed interactions are learnt.%, thereby advancing the state of the art for modeling genetic regulations using DBNs.In addition to modeling interactions, one needs a learning mechanism for inferring genetic interactions. To facilitate detection of nonlinear gene to gene interactions (in addition to linear interactions), which are prevalent in all genetic networks, we propose using well known properties, including fundamental results related to information theoretic measures for testing conditional independence relations in a DBN. This enables us to formulate efficient learning techniques for reconstructing GRNs. Using these theoretical underpinnings, we first implement simple hill-climbing techniques that enable detection of various types of interactions among genes. Subsequently, we use these results to devise novel score and search based evolutionary computation techniques, which can effectively explore a significantly larger search space. We carry out investigations using both synthetic networks as well as real-life networks. For real-life network study, we use four different microarray data sources, covering three organisms, namely, yeast, E. coli and cyanobacteria. We use networks of varying sizes, ranging from five-gene small networks (yeast) to large scale networks of cyanobacteria (730 genes). The evaluation of the performance is carried out using four widely used performance measures. For some networks where we do not have sufficient information for calculating these performance measures, we use literature mining for performing comparative evaluations of the proposed approaches. For the large scale network of cyanobacteria, we use gene ontology (GO) based analysis of gene functionalities, in addition to degree distribution analysis of the inferred network.Due to the inherent difficulties associated with inferring GRNs using DNA microarray data, it is often supplemented by other sources of data; for example, genomic data and protein-protein interaction data. In this thesis, we propose a framework that jointly learns the structure of a GRN and a protein-protein interaction network (PPIN). Using this process, the GRN reconstruction technique can effectively make use of the vast wealth of knowledge available from these external sources of data. This knowledge is fed to the GRN reconstruction process probabilistically, thereby enabling it to weigh each different data source according to the reliability of that source. The approach is applied on yeast networks where four different interaction data sources and a number of genomic data sources are used. Together with the novel modeling and learning techniques proposed in this thesis, the probabilistic integration of different types of knowledge sources and the co-learning of GRN with PPIN represents a significant step towards the reconstruction of GRNs using DBNs.
Download or read book Probabilistic Modeling in Bioinformatics and Medical Informatics written by Dirk Husmeier and published by Springer Science & Business Media. This book was released on 2005-02 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written for researchers and students in statistics, machine learning, and the biological sciences. This book provides a self-contained introduction to the methodology of Bayesian networks. It offers both elementary tutorials as well as more advanced applications and case studies.
Download or read book Gene Expression Data Analysis written by Pankaj Barah and published by CRC Press. This book was released on 2021-11-08 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Development of high-throughput technologies in molecular biology during the last two decades has contributed to the production of tremendous amounts of data. Microarray and RNA sequencing are two such widely used high-throughput technologies for simultaneously monitoring the expression patterns of thousands of genes. Data produced from such experiments are voluminous (both in dimensionality and numbers of instances) and evolving in nature. Analysis of huge amounts of data toward the identification of interesting patterns that are relevant for a given biological question requires high-performance computational infrastructure as well as efficient machine learning algorithms. Cross-communication of ideas between biologists and computer scientists remains a big challenge. Gene Expression Data Analysis: A Statistical and Machine Learning Perspective has been written with a multidisciplinary audience in mind. The book discusses gene expression data analysis from molecular biology, machine learning, and statistical perspectives. Readers will be able to acquire both theoretical and practical knowledge of methods for identifying novel patterns of high biological significance. To measure the effectiveness of such algorithms, we discuss statistical and biological performance metrics that can be used in real life or in a simulated environment. This book discusses a large number of benchmark algorithms, tools, systems, and repositories that are commonly used in analyzing gene expression data and validating results. This book will benefit students, researchers, and practitioners in biology, medicine, and computer science by enabling them to acquire in-depth knowledge in statistical and machine-learning-based methods for analyzing gene expression data. Key Features: An introduction to the Central Dogma of molecular biology and information flow in biological systems A systematic overview of the methods for generating gene expression data Background knowledge on statistical modeling and machine learning techniques Detailed methodology of analyzing gene expression data with an example case study Clustering methods for finding co-expression patterns from microarray, bulkRNA, and scRNA data A large number of practical tools, systems, and repositories that are useful for computational biologists to create, analyze, and validate biologically relevant gene expression patterns Suitable for multidisciplinary researchers and practitioners in computer science and the biological sciences
Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-01 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including the relationships between network structure and dynamics, steady-state analysis, and relationships to other model classes." "Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science.
Download or read book Enhanced Bayesian Network Models for Spatial Time Series Prediction written by Monidipa Das and published by Springer Nature. This book was released on 2019-11-07 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: This research monograph is highly contextual in the present era of spatial/spatio-temporal data explosion. The overall text contains many interesting results that are worth applying in practice, while it is also a source of intriguing and motivating questions for advanced research on spatial data science. The monograph is primarily prepared for graduate students of Computer Science, who wish to employ probabilistic graphical models, especially Bayesian networks (BNs), for applied research on spatial/spatio-temporal data. Students of any other discipline of engineering, science, and technology, will also find this monograph useful. Research students looking for a suitable problem for their MS or PhD thesis will also find this monograph beneficial. The open research problems as discussed with sufficient references in Chapter-8 and Chapter-9 can immensely help graduate researchers to identify topics of their own choice. The various illustrations and proofs presented throughout the monograph may help them to better understand the working principles of the models. The present monograph, containing sufficient description of the parameter learning and inference generation process for each enhanced BN model, can also serve as an algorithmic cookbook for the relevant system developers.
Download or read book Intelligent Strategies for Pathway Mining written by Qingfeng Chen and published by Springer. This book was released on 2013-12-17 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is organized into thirteen chapters that range over the relevant approaches and tools in data integration, modeling, analysis and knowledge discovery for signaling pathways. Having in mind that the book is also addressed for students, the contributors present the main results and techniques in an easily accessed and understood way together with many references and instances. Chapter 1 presents an introduction to signaling pathway, including motivations, background knowledge and relevant data mining techniques for pathway data analysis. Chapter 2 presents a variety of data sources and data analysis with respect to signaling pathway, including data integration and relevant data mining applications. Chapter 3 presents a framework to measure the inconsistency between heterogenous biological databases. A GO-based (genome ontology) strategy is proposed to associate different data sources. Chapter 4 presents identification of positive regulation of kinase pathways in terms of association rule mining. The results derived from this project could be used when predicting essential relationships and enable a comprehensive understanding of kinase pathway interaction. Chapter 5 presents graphical model-based methods to identify regulatory network of protein kinases. A framework using negative association rule mining is introduced in Chapter 6 to discover featured inhibitory regulation patterns and the relationships between involved regulation factors. It is necessary to not only detect the objects that exhibit a positive regulatory role in a kinase pathway but also to discover those objects that inhibit the regulation. Chapter 7 presents methods to model ncRNA secondary structure data in terms of stems, loops and marked labels, and illustrates how to find matched structure patterns for a given query. Chapter 8 shows an interval-based distance metric for computing the distance between conserved RNA secondary structures. Chapter 9 presents a framework to explore structural and functional patterns of RNA pseudoknot structure according to probability matrix. Chapter 10 presents methods to model miRNA data and identify miRNA interaction of cross-species and within-species. Chapter 11 presents an approach to measure the importance of miRNA site and the adjacent base by using information redundancy and develops a novel measure to identify strongly correlated infrequent itemsets. The discover association rules not only present important structural features in miRNAs, but also promote a comprehensive understanding of regulatory roles of miRNAs. Chapter 12 presents bioinformatics techniques for protein kinase data management and analysis, kinase pathways and drug targets, and describes their potential application in pharmaceutical industry. Chapter 13 presents a summary of the chapters and give a brief discussion to some emerging issues.
Download or read book Probabilistic Graphical Models for Genetics Genomics and Postgenomics written by Christine Sinoquet and published by OUP Oxford. This book was released on 2014-09-18 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nowadays bioinformaticians and geneticists are faced with myriad high-throughput data usually presenting the characteristics of uncertainty, high dimensionality and large complexity. These data will only allow insights into this wealth of so-called 'omics' data if represented by flexible and scalable models, prior to any further analysis. At the interface between statistics and machine learning, probabilistic graphical models (PGMs) represent a powerful formalism to discover complex networks of relations. These models are also amenable to incorporating a priori biological information. Network reconstruction from gene expression data represents perhaps the most emblematic area of research where PGMs have been successfully applied. However these models have also created renewed interest in genetics in the broad sense, in particular regarding association genetics, causality discovery, prediction of outcomes, detection of copy number variations, and epigenetics. This book provides an overview of the applications of PGMs to genetics, genomics and postgenomics to meet this increased interest. A salient feature of bioinformatics, interdisciplinarity, reaches its limit when an intricate cooperation between domain specialists is requested. Currently, few people are specialists in the design of advanced methods using probabilistic graphical models for postgenomics or genetics. This book deciphers such models so that their perceived difficulty no longer hinders their use and focuses on fifteen illustrations showing the mechanisms behind the models. Probabilistic Graphical Models for Genetics, Genomics and Postgenomics covers six main themes: (1) Gene network inference (2) Causality discovery (3) Association genetics (4) Epigenetics (5) Detection of copy number variations (6) Prediction of outcomes from high-dimensional genomic data. Written by leading international experts, this is a collection of the most advanced work at the crossroads of probabilistic graphical models and genetics, genomics, and postgenomics. The self-contained chapters provide an enlightened account of the pros and cons of applying these powerful techniques.
Download or read book Bayesian Inference for Gene Expression and Proteomics written by Kim-Anh Do and published by Cambridge University Press. This book was released on 2006-07-24 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Expert overviews of Bayesian methodology, tools and software for multi-platform high-throughput experimentation.
Download or read book Bayesian Networks written by Olivier Pourret and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Networks, the result of the convergence of artificial intelligence with statistics, are growing in popularity. Their versatility and modelling power is now employed across a variety of fields for the purposes of analysis, simulation, prediction and diagnosis. This book provides a general introduction to Bayesian networks, defining and illustrating the basic concepts with pedagogical examples and twenty real-life case studies drawn from a range of fields including medicine, computing, natural sciences and engineering. Designed to help analysts, engineers, scientists and professionals taking part in complex decision processes to successfully implement Bayesian networks, this book equips readers with proven methods to generate, calibrate, evaluate and validate Bayesian networks. The book: Provides the tools to overcome common practical challenges such as the treatment of missing input data, interaction with experts and decision makers, determination of the optimal granularity and size of the model. Highlights the strengths of Bayesian networks whilst also presenting a discussion of their limitations. Compares Bayesian networks with other modelling techniques such as neural networks, fuzzy logic and fault trees. Describes, for ease of comparison, the main features of the major Bayesian network software packages: Netica, Hugin, Elvira and Discoverer, from the point of view of the user. Offers a historical perspective on the subject and analyses future directions for research. Written by leading experts with practical experience of applying Bayesian networks in finance, banking, medicine, robotics, civil engineering, geology, geography, genetics, forensic science, ecology, and industry, the book has much to offer both practitioners and researchers involved in statistical analysis or modelling in any of these fields.
Download or read book Probabilistic Graphical Models written by Linda C. van der Gaag and published by Springer. This book was released on 2014-09-11 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 7th International Workshop on Probabilistic Graphical Models, PGM 2014, held in Utrecht, The Netherlands, in September 2014. The 38 revised full papers presented in this book were carefully reviewed and selected from 44 submissions. The papers cover all aspects of graphical models for probabilistic reasoning, decision making, and learning.
Download or read book Bayesian Networks in R written by Radhakrishnan Nagarajan and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.
Download or read book Probabilistic Methods for Bioinformatics written by Richard E. Neapolitan and published by Morgan Kaufmann. This book was released on 2009-06-12 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Bayesian Networks and Decision Graphs written by Thomas Dyhre Nielsen and published by Springer. This book was released on 2010-11-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a brand new edition of an essential work on Bayesian networks and decision graphs. It is an introduction to probabilistic graphical models including Bayesian networks and influence diagrams. The reader is guided through the two types of frameworks with examples and exercises, which also give instruction on how to build these models. Structured in two parts, the first section focuses on probabilistic graphical models, while the second part deals with decision graphs, and in addition to the frameworks described in the previous edition, it also introduces Markov decision process and partially ordered decision problems.
