Download or read book Clustering and Network Analysis with Biological Applications written by Konstantin Voevodski and published by . This book was released on 2011 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Clustering and network analysis are important areas of research in Computer Science and other disciplines. Clustering is broadly defined as finding sets of similar objects. It has many applications, such as finding groups of similar buyers given their product preferences, and finding groups of similar proteins given their sequences. Network analysis considers data represented by a collection of nodes (vertices), and edges that link these nodes. The structure of the network is studied to find central nodes, identify nodes that are similar to a particular vertex, and find well-connected groups of vertices. The World Wide Web and online social networks are some of the best studied networks today. Network analysis can also be applied to biological networks where nodes are proteins and edges represent relationships or interactions between them. The size of real-world data sets presents many challenges to computational techniques that interpret them. A classic clustering problem is to divide the data set into groups, given the pairwise distances between the objects. However, computing all the pairwise distances may be infeasible if the data set is very large. In this thesis we consider clustering in a limited information setting where we do not know the distances between the objects in advance, and instead must query them during the execution of the algorithm. We present algorithms that find an accurate clustering in this setting using few queries. The networks that we encounter in practice are quite large as well, making computations on the entire network difficult. In this thesis we present techniques for locally exploring networks, which are efficient but still give meaningful information about the local structure of the graph. We develop several tools for locally exploring a network, and show that they give meaningful results when applied to protein networks.

Download or read book Weighted Network Analysis written by Steve Horvath and published by Springer Science & Business Media. This book was released on 2011-04-30 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Download or read book Computational Network Analysis with R written by Matthias Dehmer and published by John Wiley & Sons. This book was released on 2016-12-12 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new title in the well-established "Quantitative Network Biology" series includes innovative and existing methods for analyzing network data in such areas as network biology and chemoinformatics. With its easy-to-follow introduction to the theoretical background and application-oriented chapters, the book demonstrates that R is a powerful language for statistically analyzing networks and for solving such large-scale phenomena as network sampling and bootstrapping. Written by editors and authors with an excellent track record in the field, this is the ultimate reference for R in Network Analysis.

Download or read book Analysis of Biological Networks written by Björn H. Junker and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.

Download or read book Biological Network Analysis written by Pietro Hiram Guzzi and published by Academic Press. This book was released on 2020-05-26 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches

Download or read book Summarizing Biological Networks written by Sourav S. Bhowmick and published by Springer. This book was released on 2017-04-17 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the data mining, systems biology, and bioinformatics computational methods that can be used to summarize biological networks. Specifically, it discusses an array of techniques related to biological network clustering, network summarization, and differential network analysis which enable readers to uncover the functional and topological organization hidden in a large biological network. The authors also examine crucial open research problems in this arena. Academics, researchers, and advanced-level students will find this book to be a comprehensive and exceptional resource for understanding computational techniques and their applications for a summary of biological networks.

Download or read book Recent Advances in Biological Network Analysis written by Byung-Jun Yoon and published by Springer. This book was released on 2022-01-14 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recent advances in the emerging field of computational network biology with special emphasis on comparative network analysis and network module detection. The chapters in this volume are contributed by leading international researchers in computational network biology and offer in-depth insight on the latest techniques in network alignment, network clustering, and network module detection. Chapters discuss the advantages of the respective techniques and present the current challenges and open problems in the field. Recent Advances in Biological Network Analysis: Comparative Network Analysis and Network Module Detection will serve as a great resource for graduate students, academics, and researchers who are currently working in areas relevant to computational network biology or wish to learn more about the field. Data scientists whose work involves the analysis of graphs, networks, and other types of data with topological structure or relations can also benefit from the book's insights.

Download or read book Advances in Network Analysis and its Applications written by Evangelos Kranakis and published by Springer Science & Business Media. This book was released on 2012-10-24 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: As well as highlighting potentially useful applications for network analysis, this volume identifies new targets for mathematical research that promise to provide insights into network systems theory as well as facilitating the cross-fertilization of ideas between sectors. Focusing on financial, security and social aspects of networking, the volume adds to the growing body of evidence showing that network analysis has applications to transportation, communication, health, finance, and social policy more broadly. It provides powerful models for understanding the behavior of complex systems that, in turn, will impact numerous cutting-edge sectors in science and engineering, such as wireless communication, network security, distributed computing and social networking, financial analysis, and cyber warfare. The volume offers an insider’s view of cutting-edge research in network systems, including methodologies with immense potential for interdisciplinary application. The contributors have all presented material at a series of workshops organized on behalf of Canada’s MITACS initiative, which funds projects and study grants in ‘mathematics for information technology and complex systems’. These proceedings include papers from workshops on financial networks, network security and cryptography, and social networks. MITACS has shown that the partly ghettoized nature of network systems research has led to duplicated work in discrete fields, and thus this initiative has the potential to save time and accelerate the pace of research in a number of areas of network systems research.

Download or read book Clustering Challenges In Biological Networks written by W Art Chaovalitwongse and published by World Scientific. This book was released on 2009-02-11 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a collection of papers dealing with various aspects of clustering in biological networks and other related problems in computational biology. It consists of two parts, with the first part containing surveys of selected topics and the second part presenting original research contributions. This book will be a valuable source of material to faculty, students, and researchers in mathematical programming, data analysis and data mining, as well as people working in bioinformatics, computer science, engineering, and applied mathematics. In addition, the book can be used as a supplement to any course in data mining or computational/systems biology.

Download or read book Statistical and Machine Learning Approaches for Network Analysis written by Matthias Dehmer and published by John Wiley & Sons. This book was released on 2012-06-26 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: Explore the multidisciplinary nature of complex networks through machine learning techniques Statistical and Machine Learning Approaches for Network Analysis provides an accessible framework for structurally analyzing graphs by bringing together known and novel approaches on graph classes and graph measures for classification. By providing different approaches based on experimental data, the book uniquely sets itself apart from the current literature by exploring the application of machine learning techniques to various types of complex networks. Comprised of chapters written by internationally renowned researchers in the field of interdisciplinary network theory, the book presents current and classical methods to analyze networks statistically. Methods from machine learning, data mining, and information theory are strongly emphasized throughout. Real data sets are used to showcase the discussed methods and topics, which include: A survey of computational approaches to reconstruct and partition biological networks An introduction to complex networks—measures, statistical properties, and models Modeling for evolving biological networks The structure of an evolving random bipartite graph Density-based enumeration in structured data Hyponym extraction employing a weighted graph kernel Statistical and Machine Learning Approaches for Network Analysis is an excellent supplemental text for graduate-level, cross-disciplinary courses in applied discrete mathematics, bioinformatics, pattern recognition, and computer science. The book is also a valuable reference for researchers and practitioners in the fields of applied discrete mathematics, machine learning, data mining, and biostatistics.

Download or read book Link Mining Models Algorithms and Applications written by Philip S. Yu and published by Springer Science & Business Media. This book was released on 2010-09-16 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers detailed surveys and systematic discussion of models, algorithms and applications for link mining, focusing on theory and technique, and related applications: text mining, social network analysis, collaborative filtering and bioinformatics.

Download or read book Network Analysis Literacy written by Katharina A. Zweig and published by Springer Science & Business Media. This book was released on 2016-10-26 with total page 546 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a perspective of network analysis as a tool to find and quantify significant structures in the interaction patterns between different types of entities. Moreover, network analysis provides the basic means to relate these structures to properties of the entities. It has proven itself to be useful for the analysis of biological and social networks, but also for networks describing complex systems in economy, psychology, geography, and various other fields. Today, network analysis packages in the open-source platform R and other open-source software projects enable scientists from all fields to quickly apply network analytic methods to their data sets. Altogether, these applications offer such a wealth of network analytic methods that it can be overwhelming for someone just entering this field. This book provides a road map through this jungle of network analytic methods, offers advice on how to pick the best method for a given network analytic project, and how to avoid common pitfalls. It introduces the methods which are most often used to analyze complex networks, e.g., different global network measures, types of random graph models, centrality indices, and networks motifs. In addition to introducing these methods, the central focus is on network analysis literacy – the competence to decide when to use which of these methods for which type of question. Furthermore, the book intends to increase the reader's competence to read original literature on network analysis by providing a glossary and intensive translation of formal notation and mathematical symbols in everyday speech. Different aspects of network analysis literacy – understanding formal definitions, programming tasks, or the analysis of structural measures and their interpretation – are deepened in various exercises with provided solutions. This text is an excellent, if not the best starting point for all scientists who want to harness the power of network analysis for their field of expertise.

Download or read book Networks of Networks in Biology written by Narsis A. Kiani and published by Cambridge University Press. This book was released on 2021-04 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces network inspired approaches for the analysis and integration of large, heterogeneous data sets in the life sciences.

Download or read book Complex Networks and Their Applications VIII written by Hocine Cherifi and published by Springer Nature. This book was released on 2019-11-25 with total page 992 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights cutting-edge research in the field of network science, offering scientists, researchers, students, and practitioners a unique update on the latest advances in theory and a multitude of applications. It presents the peer-reviewed proceedings of the Eighth International Conference on Complex Networks and their Applications (COMPLEX NETWORKS 2019), which took place in Lisbon, Portugal, on December 10–12, 2019. The carefully selected papers cover a wide range of theoretical topics such as network models and measures; community structure, and network dynamics; diffusion, epidemics, and spreading processes; resilience and control as well as all the main network applications, including social and political networks; networks in finance and economics; biological and neuroscience networks; and technological networks.

Download or read book The Influence of Technology on Social Network Analysis and Mining written by Tansel Özyer and published by Springer Science & Business Media. This book was released on 2013-03-15 with total page 652 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of social networks was originated in social and business communities. In recent years, social network research has advanced significantly; the development of sophisticated techniques for Social Network Analysis and Mining (SNAM) has been highly influenced by the online social Web sites, email logs, phone logs and instant messaging systems, which are widely analyzed using graph theory and machine learning techniques. People perceive the Web increasingly as a social medium that fosters interaction among people, sharing of experiences and knowledge, group activities, community formation and evolution. This has led to a rising prominence of SNAM in academia, politics, homeland security and business. This follows the pattern of known entities of our society that have evolved into networks in which actors are increasingly dependent on their structural embedding General areas of interest to the book include information science and mathematics, communication studies, business and organizational studies, sociology, psychology, anthropology, applied linguistics, biology and medicine.

Download or read book An Introduction to Systems Biology written by Uri Alon and published by CRC Press. This book was released on 2019-07-12 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: Praise for the first edition: ... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. – Nature [This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. ... Alon’s book should become a standard part of the training of graduate students. – Physics Today Written for students and researchers, the second edition of this best-selling textbook continues to offer a clear presentation of design principles that govern the structure and behavior of biological systems. It highlights simple, recurring circuit elements that make up the regulation of cells and tissues. Rigorously classroom-tested, this edition includes new chapters on exciting advances made in the last decade. Features: Includes seven new chapters The new edition has 189 exercises, the previous edition had 66 Offers new examples relevant to human physiology and disease

Download or read book Data Clustering Theory Algorithms and Applications Second Edition written by Guojun Gan and published by SIAM. This book was released on 2020-11-10 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data clustering, also known as cluster analysis, is an unsupervised process that divides a set of objects into homogeneous groups. Since the publication of the first edition of this monograph in 2007, development in the area has exploded, especially in clustering algorithms for big data and open-source software for cluster analysis. This second edition reflects these new developments, covers the basics of data clustering, includes a list of popular clustering algorithms, and provides program code that helps users implement clustering algorithms. Data Clustering: Theory, Algorithms and Applications, Second Edition will be of interest to researchers, practitioners, and data scientists as well as undergraduate and graduate students.