This work covers sequence-based protein homology detection, a fundamental and challenging bioinformatics problem with a variety of real-world applications. The text first surveys a few popular homology detection methods, such as Position-Specific Scoring Matrix (PSSM) and Hidden Markov Model (HMM) based methods, and then describes a novel Markov Random Fields (MRF) based method developed by the authors. MRF-based methods are much more sensitive than HMM- and PSSM-based methods for remote homolog detection and fold recognition, as MRFs can model long-range residue-residue interaction. The text also describes the installation, usage and result interpretation of programs implementing the MRF-based method.

This book provides the reader with the mathematical framework required to fully explore the potential of small quantum information processing devices. As decoherence will continue to limit their size, it is essential to master the conceptual tools which make such investigations possible. A strong emphasis is given to information measures that are essential for the study of devices of finite size, including Renyi entropies and smooth entropies. The presentation is self-contained and includes rigorous and concise proofs of the most important properties of these measures. The first chapters will introduce the formalism of quantum mechanics, with particular emphasis on norms and metrics for quantum states. This is necessary to explore quantum generalizations of Renyi divergence and conditional entropy, information measures that lie at the core of information theory. The smooth entropy framework is discussed next and provides a natural means to lift many arguments from information theory to the quantum setting. Finally selected applications of the theory to statistics and cryptography are discussed. The book is aimed at graduate students in Physics and Information Theory. Mathematical fluency is necessary, but no prior knowledge of quantum theory is required.

This book collects the refereed proceedings of the First International Conference onon Algorithms and Discrete Applied Mathematics, CALDAM 2015, held in Kanpur, India, in February 2015. The volume contains 26 full revised papers from 58 submissions along with 2 invited talks presented at the conference. The workshop covered a diverse range of topics on algorithms and discrete mathematics, including computational geometry, algorithms including approximation algorithms, graph theory and computational complexity.

This book presents selected papers from the 3rd International Workshop on Computational Engineering held in Stuttgart from October 6 to 10, 2014, bringing together innovative contributions from related fields with computer science and mathematics as an important technical basis among others. The workshop discussed the state of the art and the further evolution of numerical techniques for simulation in engineering and science. We focus on current trends in numerical simulation in science and engineering, new requirements arising from rapidly increasing parallelism in computer architectures, and novel mathematical approaches. Accordingly, the chapters of the book particularly focus on parallel algorithms and performance optimization, coupled systems, and complex applications and optimization.

This book is devoted to the state-of-the-art in all aspects of fireworks algorithm (FWA), with particular emphasis on the efficient improved versions of FWA. It describes the most substantial theoretical analysis including basic principle and implementation of FWA and modeling and theoretical analysis of FWA. It covers exhaustively the key recent significant research into the improvements of FWA so far. In addition, the book describes a few advanced topics in the research of FWA, including multi-objective optimization (MOO), discrete FWA (DFWA) for combinatorial optimization, and GPU-based FWA for parallel implementation. In sequels, several successful applications of FWA on non-negative matrix factorization (NMF), text clustering, pattern recognition, and seismic inversion problem, and swarm robotics, are illustrated in details, which might shed new light on more real-world applications in future. Addressing a multidisciplinary topic, it will appeal to researchers and professionals in the areas of metahuristics, swarm intelligence, evolutionary computation, complex optimization solving, etc.

The LNCS journal Transactions on Large-Scale Data- and Knowledge-Centered Systems focuses on data management, knowledge discovery, and knowledge processing, which are core and hot topics in computer science. Since the 1990s, the Internet has become the main driving force behind application development in all domains. An increase in the demand for resource sharing across different sites connected through networks has led to an evolution of data- and knowledge-management systems from centralized systems to decentralized systems enabling large-scale distributed applications providing high scalability. Current decentralized systems still focus on data and knowledge as their main resource. Feasibility of these systems relies basically on P2P (peer-to-peer) techniques and the support of agent systems with scaling and decentralized control. Synergy between grids, P2P systems, and agent technologies is the key to data- and knowledge-centered systems in large-scale environments. This, the 16th issue of Transactions on Large-Scale Data- and Knowledge-Centered Systems, contains extended and revised versions of 7 papers, selected from the 30 papers presented at the International Conference on Advanced Computing and Applications, ACOMP 2013, held October 23-25, 2013, in Ho Chi Minh City, Vietnam. Topics covered include data engineering, information retrieval, query processing and optimization, energy-efficient resource allocation, and security and privacy.

This book explores the two major elements of Hintikka's model of inquiry: underlying game theoretical motivations and the central role of questioning. The chapters build on the Hintikkan tradition extending Hintikka's model and present a wide variety of approaches to the philosophy of inquiry from different directions, ranging from erotetic logic to Lakatosian philosophy, from socio-epistemologic approaches to strategic reasoning and mathematical practice. Hintikka's theory of inquiry is a well-known example of a dynamic epistemic procedure. In an interrogative inquiry, the inquirer is given a theory and a question. He then tries to answer the question based on the theory by posing questions to nature or an oracle. The initial formulation of this procedure by Hintikka is rather broad and informal. This volume introduces a carefully selected responses to the issues discussed by Hintikka. The articles in the volume were contributed by various authors associated with a research project on Hintikka's interrogative theory of inquiry conducted in the Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST) of Paris, including those who visited to share their insight.

The most crucial ability for machine learning and data science is mathematical logic for grasping their essence rather than knowledge and experience. This textbook approaches the essence of machine learning and data science by considering math problems and building Python programs. As the preliminary part, Chapter 1 provides a concise introduction to linear algebra, which will help novices read further to the following main chapters. Those succeeding chapters present essential topics in statistical learning: linear regression, classification, resampling, information criteria, regularization, nonlinear regression, decision trees, support vector machines, and unsupervised learning. Each chapter mathematically formulates and solves machine learning problems and builds the programs. The body of a chapter is accompanied by proofs and programs in an appendix, with exercises at the end of the chapter. Because the book is carefully organized to provide the solutions to the exercises in each chapter, readers can solve the total of 100 exercises by simply following the contents of each chapter. This textbook is suitable for an undergraduate or graduate course consisting of about 12 lectures. Written in an easy-to-follow and self-contained style, this book will also be perfect material for independent learning.

This book presents theories and the main useful techniques of the Finite Element Method (FEM), with an introduction to FEM and many case studies of its use in engineering practice. It supports engineers and students to solve primarily linear problems in mechanical engineering, with a main focus on static and dynamic structural problems. Readers of this text are encouraged to discover the proper relationship between theory and practice, within the finite element method: Practice without theory is blind, but theory without practice is sterile. Beginning with elasticity basic concepts and the classical theories of stressed materials, the work goes on to apply the relationship between forces, displacements, stresses and strains on the process of modeling, simulating and designing engineered technical systems. Chapters discuss the finite element equations for static, eigenvalue analysis, as well as transient analyses. Students and practitioners using commercial FEM software will find this book very helpful. It uses straightforward examples to demonstrate a complete and detailed finite element procedure, emphasizing the differences between exact and numerical procedures.

The first part of this book covers the key concepts of cryptography on an undergraduate level, from encryption and digital signatures to cryptographic protocols. Essential techniques are demonstrated in protocols for key exchange, user identification, electronic elections and digital cash. In the second part, more advanced topics are addressed, such as the bit security of one-way functions and computationally perfect pseudorandom bit generators. The security of cryptographic schemes is a central topic. Typical examples of provably secure encryption and signature schemes and their security proofs are given. Though particular attention is given to the mathematical foundations, no special background in mathematics is presumed. The necessary algebra, number theory and probability theory are included in the appendix. Each chapter closes with a collection of exercises. In the second edition the authors added a complete description of the AES, an extended section on cryptographic hash functions, and new sections on random oracle proofs and public-key encryption schemes that are provably secure against adaptively-chosen-ciphertext attacks. The third edition is a further substantive extension, with new topics added, including: elliptic curve cryptography; Paillier encryption; quantum cryptography; the new SHA-3 standard for cryptographic hash functions; a considerably extended section on electronic elections and Internet voting; mix nets; and zero-knowledge proofs of shuffles. The book is appropriate for undergraduate and graduate students in computer science, mathematics, and engineering.

This work explores the scope and flexibility afforded by integrated quantum photonics, both in terms of practical problem-solving, and for the pursuit of fundamental science. The author demonstrates and fully characterizes a two-qubit quantum photonic chip, capable of arbitrary two-qubit state preparation. Making use of the unprecedented degree of reconfigurability afforded by this device, a novel variation on Wheeler's delayed choice experiment is implemented, and a new technique to obtain nonlocal statistics without a shared reference frame is tested. Also presented is a new algorithm for quantum chemistry, simulating the helium hydride ion. Finally, multiphoton quantum interference in a large Hilbert space is demonstrated, and its implications for computational complexity are examined.

This book opens the door to a new interesting and ambitious world of reversible and quantum computing research. It presents the state of the art required to travel around that world safely. Top world universities, companies and government institutions are in a race of developing new methodologies, algorithms and circuits on reversible logic, quantum logic, reversible and quantum computing and nano-technologies. In this book, twelve reversible logic synthesis methodologies are presented for the first time in a single literature with some new proposals. Also, the sequential reversible logic circuitries are discussed for the first time in a book. Reversible logic plays an important role in quantum computing. Any progress in the domain of reversible logic can be directly applied to quantum logic. One of the goals of this book is to show the application of reversible logic in quantum computing. A new implementation of wavelet and multiwavelet transforms using quantum computing is performed for this purpose. Researchers in academia or industry and graduate students, who work in logic synthesis, quantum computing, nano-technology, and low power VLSI circuit design, will be interested in this book.

The authors describe systematic methods for uncovering scientific laws a priori, on the basis of intuition, or "Gedanken Experiments". Mathematical expressions of scientific laws are, by convention, constrained by the rule that their form must be invariant with changes of the units of their variables. This constraint makes it possible to narrow down the possible forms of the laws. It is closely related to, but different from, dimensional analysis. It is a mathematical book, largely based on solving functional equations. In fact, one chapter is an introduction to the theory of functional equations.

This volume features key contributions from the International Conference on Pattern Recognition Applications and Methods, (ICPRAM 2012,) held in Vilamoura, Algarve, Portugal from February 6th-8th, 2012. The conference provided a major point of collaboration between researchers, engineers and practitioners in the areas of Pattern Recognition, both from theoretical and applied perspectives, with a focus on mathematical methodologies. Contributions describe applications of pattern recognition techniques to real-world problems, interdisciplinary research, and experimental and theoretical studies which yield new insights that provide key advances in the field. This book will be suitable for scientists and researchers in optimization, numerical methods, computer science, statistics and for differential geometers and mathematical physicists.

This textbook provides an accessible introduction to the most important features of Fortran 2008. Features: presents a complete discussion of all the basic features needed to write complete Fortran programs; makes extensive use of examples and case studies to illustrate the practical use of features of Fortran 08, and supplies simple problems for the reader; provides a detailed exploration of control constructs, modules, procedures, arrays, character strings, data structures and derived types, pointer variables, and object-oriented programming; includes coverage of such major new features in Fortran 08 as coarrays, submodules, parameterized derived types, and derived-type input and output; highlights the topic of modules as the framework for organizing data and procedures for a Fortran program; investigates the excellent input/output facilities available in Fortran; contains appendices listing the many intrinsic procedures and providing a brief informal syntax specification for the language.

A complete and systematic introduction to the fundamentals of the hyperequational theory of universal algebra, offering the newest results on solid varieties of semirings and semigroups. The book aims to develop the theory of solid varieties as a system of mathematical discourse that is applicable in several concrete situations. A unique feature of this book is the use of Galois connections to integrate different topics.

This book constitutes the thoroughly refereed post-conference proceedings of the 17th Brazilian Symposium on Formal Methods, SBMF 2014, held in Maceio, Brazil, in September/October 2014. The 9 revised full papers presented together with 2 invited talks were carefully reviewed and selected from 34 submissions. SBMF is an event devoted to the dissemination of the development and use of formal methods for the construction of high quality computational systems, aiming to promote opportunities for researchers with interests in formal methods to discuss the recent advances in this area.

This book brings together historical notes, reviews of research developments, fresh ideas on how to make VC (Vapnik-Chervonenkis) guarantees tighter, and new technical contributions in the areas of machine learning, statistical inference, classification, algorithmic statistics, and pattern recognition. The contributors are leading scientists in domains such as statistics, mathematics, and theoretical computer science, and the book will be of interest to researchers and graduate students in these domains.

Data science has never had more influence on the world. Large companies are now seeing the benefit of employing data scientists to interpret the vast amounts of data that now exists. However, the field is so new and is evolving so rapidly that the analysis produced can be haphazard at best. The 9 Pitfalls of Data Science shows us real-world examples of what can go wrong. Written to be an entertaining read, this invaluable guide investigates the all too common mistakes of data scientists - who can be plagued by lazy thinking, whims, hunches, and prejudices - and indicates how they have been at the root of many disasters, including the Great Recession. Gary Smith and Jay Cordes emphasise how scientific rigor and critical thinking skills are indispensable in this age of Big Data, as machines often find meaningless patterns that can lead to dangerous false conclusions. The 9 Pitfalls of Data Science is loaded with entertaining tales of both successful and misguided approaches to interpreting data, both grand successes and epic failures. These cautionary tales will not only help data scientists be more effective, but also help the public distinguish between good and bad data science.

Hybrid systems are models for complex physical systems and have become a widely used concept for understanding their behavior. Many applications are safety-critical, including car, railway, and air traffic control, robotics, physical-chemical process control, and biomedical devices. Hybrid systems analysis studies how we can build computerized controllers for physical systems which are guaranteed to meet their design goals. The author gives a unique, logic-based perspective on hybrid systems analysis. It is the first book that leverages the power of logic for hybrid systems. The author develops a coherent logical approach for systematic hybrid systems analysis, covering its theory, practice, and applications. It is further shown how the developed verification techniques can be used to study air traffic and railway control systems. This book is intended for researchers, postgraduates, and professionals who are interested in hybrid systems analysis, cyberphysical or embedded systems design, logic and theorem proving, or transportation and automation.

The field of quantum computing has experienced rapid development and many different experimental and theoretical groups have emerged worldwide.This book presents the key elements of quantum computation and communication theories and their implementation in an easy-to-read manner for readers coming from physics, mathematics and computer science backgrounds. Integrating both theoretical aspects and experimental verifications of developing quantum computers, the author explains why particular mathematical methods, physical models and realistic implementations might provide critical steps towards achieving the final goal - constructing quantum computers and quantum networks. The book serves as an excellent introduction for new researchers and also provides a useful review for specialists in the field

The Fortran 2003 Handbook is a definitive and comprehensive guide to Fortran 2003 and its use. Fortran 2003, the latest standard version of Fortran, has many excellent features that assist the programmer in writing efficient, portable and maintainable programs. This all-inclusive volume offers a reader-friendly, easy-to-follow and informal description of Fortran 2003, and has been developed to provide not only a readable explanation of features, but also some rationale for the inclusion of features and their use. This highly versatile handbook is intended for anyone who wants a comprehensive survey of Fortran 2003.

Learning spaces offer a rigorous mathematical foundation for practical systems of educational technology. Learning spaces generalize partially ordered sets and are special cases of knowledge spaces. The various structures are investigated from the standpoints of combinatorial properties and stochastic processes. Leaning spaces have become the essential structures to be used in assessing students' competence of various topics. A practical example is offered by ALEKS, a Web-based, artificially intelligent assessment and learning system in mathematics and other scholarly fields. At the heart of ALEKS is an artificial intelligence engine that assesses each student individually and continously. The book is of interest to mathematically oriented readers in education, computer science, engineering, and combinatorics at research and graduate levels. Numerous examples and exercises are included, together with an extensive bibliography.

On the occasion of his 60th birthday in October 2009, friends, collaborators, and admirers of Wolfgang Dahmen have organized this volume which touches on va- ous of his research interests. This volume will provide an easy to read excursion into many important topics in applied and computational mathematics. These include nonlinear and adaptive approximation, multivariate splines, subdivision schemes, multiscale and wavelet methods, numerical schemes for partial differential and boundary integral equations, learning theory, and high-dimensional integrals. College Station, Texas, USA Ronald A. DeVore Paderborn, Germany Angela Kunoth June 2009 vii Acknowledgements We are deeply grateful to Dr. Martin Peters and Thanh-Ha Le Thi from Springer for realizing this book project and to Frank Holzwarth for technical support. ix Contents Introduction: Wolfgang Dahmen's mathematical work...1 Ronald A. DeVore and Angela Kunoth 1 Introduction ...1 2 The early years: Classical approximation theory...2 3 Bonn, Bielefeld, Berlin, and multivariate splines ...2 3. 1 Computer aided geometric design ...3 3. 2 Subdivision and wavelets ...4 4 Wavelet and multiscale methods for operator equations...5 4. 1 Multilevel preconditioning ...5 4. 2 Compression of operators...5 5 Adaptive solvers ...6 6 Constructionandimplementation...7 7 Hyperbolic partial differential equations and conservation laws ...8 8 Engineering collaborations ...9 9 Thepresent ...9 10 Finalremarks...10 Publications by Wolfgang Dahmen (as of summer 2009)...10 The way things were in multivariate splines: A personal view...19 Carl de Boor 1 Tensor product spline interpolation...19 2 Quasiinterpolation ...20 3 MultivariateB-splines ...21 4 Kergininterpolation ...

In real electronic systems, voltage and current signals are not necessarily of a periodical quantity, due to the presence of nonharmonic components or/and possible stochastic variation. This book presents in three parts methods for analyzing and processing and reconstructing complex signals. The first part of this book is dedicated to the problem of measurements of the basic electric quantities in electric utilities, both from the aspect of accuracy of this type of measurements and the possibilities of simple and practical realization. The second part presents a reconstruction of trigonometric polynomials, a specific class of band-limited signals, from a number of integrated values of input signals. The third part deals with the problem of estimating the value of the active power of the ac signal in the presence of subharmonics and interharmonics. The analysis makes use of the most general model of the voltage and current signal, i.e. the most complex spectral content that can be expected to appear in practice.