Chengqi Zhang

Qingfeng Chen

Baoshan Chen

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.

Model and Pattern Identification

Intelligent Strategies for Pathway Mining

Shichao Zhang

The present volume arose from the need for a comprehensive coverage of the state of the art in security protocol analysis. It aims to serve as an overall course-aid and to provide self-study material for researchers and students in formal methods theory and applications in e-commerce, data analysis and data mining. The volume will also be useful to anyone interested in secure e-commerce. The book is organized in eight chapters covering the main approaches and tools in formal methods for security protocol analysis. It starts with an introductory chapter presenting the fundamentals and background knowledge with respect to formal methods and security protocol analysis. Chapter 2 provides an overview of related work in this area, including basic concepts and terminology. Chapters 3 and 4 show a logical framework and a model checker for analyzing secure transaction protocols. Chapter 5 explains how to deal with uncertainty issues in secure messages, including inconsistent messages and conflicting beliefs in messages. Chapter 6 integrates data mining with security protocol analysis, and Chapter 7 develops a new technique for detecting collusion attack in security protocols. Chapter 8 gives a summary of the chapters and presents a brief discussion of some emerging issues in the field.

Qingfeng Chen

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