Algorithms in Bioinformatics

Algorithms in Bioinformatics

An improved model for statistical alignment (I. Mikls, Z. Toroczkai). Improving profile-profile alignments via log average scoring (N. von ohsen, R. Zimmer). False positive s in genomic map assembly and sequence validation (T. Anantharaman, B. Mishra). Boosting EM for radiation hybrid and genetic mapping (T. Schiex, P. Chabrier, M. Bouchez, D. Milan). Placing probes along the genome using pairwise distance data (W. Casey, B. Mishra, M. Wigler). Comparing a Hidden Markov model and a stochastic context-free grammar (A. Jagota, R. B. Lyngso, C. N. S. Pedersen). Assessing the statistical significance of overrepresented oligonucleotides (A. Denise, M. Rgnier, M. vandenbogaert). Pattern matching and pattern discovery algorithms for protein topologies (J. Viksna, D. Gilbert). Computing linking numbers of a filtration (H. Edelsbrusnner, A. Zomorodian). Side chain-positioning as an integer programming problem (O. Eriksson, Y. Zhou, A. Elofsson). A chemical-distance-based test for positive darwinian selection (T. Pupko, R. Sharan, M. Hasegawa, R. Shamir, D. Graur). Finding a maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynominal time (G. Ganapathysaravanabavan, T. Warnow). Experiments in computing sequences of reversals (A. Bergeron, Franois Strasbourg). Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes (Li-San Wang). Finding an optimal inversion median: experimental results (A. C. Siepel, B. M. E. Moret). Analytic solutions for three-taxon MLMC trees with variable rates across sites (B. Chor, M. Hendy, D. Penny). The performance of phylogenetic methods on trees of bounded diameter (L. nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow). (1+E)- approximation of sorting by reversals and transpositions (N. Eriksen). On the practical solution of the reversal median problem (A. Caprara). Algorithms for finding gene clusters (S. Heber, J. Stoye). Determination of binding amino acids based on random peptide array screening data (P. J. van der Veen, L. F. A. Wessels, J. W. Sloostra, R. H. Meloen, M. J. T. Reinders, J. Hellendoorn). A simple hyper-geometric approach for discovering putative transcription factor binding sites (Y. Barash, G. Bejerano, N. Friedman). Comparing assemblies using fragments and mate-pairs (D. H. Huson, A. L. Halpern, Z. Lai, E. W. myers, K. Reinert, G. G. Sutton). Author index.

Algorithms in Bioinformatics

Combinatorial Algorithms for Computers and Calculators - Second Edition

Combinatorial Algorithms for Computers and Calculators - Second Edition

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Combinatorial Algorithms for Computers and Calculators - Second Edition

Small Animal Clinical Diagnosis by Laboratory Methods - Fifth Edition

Small Animal Clinical Diagnosis by Laboratory Methods - Fifth Edition

A quick guide to appropriately selecting and interpreting laboratory tests, Small Animal Clinical Diagnosis by Laboratory Methods, 5th Edition helps you utilize your in-house lab or your specialty reference lab to efficiently make accurate diagnoses without running a plethora of unnecessary and low-yield tests. It provides answers to commonly asked questions relating to laboratory tests, and solutions to frequently encountered problems in small animal diagnosis. For easy reference, information is provided by clinical presentation and abnormalities, and includes hundreds of tables, boxes, key points, and algorithms. This edition, now in full color, is updated with the latest advances in laboratory testing methods and diagnostic problem solving. Written by noted educators Dr. Michael Willard and Dr. Harold Tvedten, this book may be used as an on-the-spot guide to specific problems or conditions as well as a reference for more detailed research on difficult cases.

Small Animal Clinical Diagnosis by Laboratory Methods - Fifth Edition

Digital Self-tuning Controllers

Digital Self-tuning Controllers

A complete course in self-tuning control, beginning with a survey of adaptive control and the formulation of adaptive control problems. Modelling and identification are dealt with before passing on to algebraic design methods. Finally, laboratory verification and experimentation will ground your theoretical knowledge in real plant control. Features: a strong emphasis on practical problem solving with control algorithms clearly laid out in easy-to-follow formats or as MATLAB functions suitable for use in project work; specially written MATLAB toolboxes for the presentation of typical control system and plant properties and ready for use in direct control of real or simulated plants; worked examples and tutorial exercises. This book shows graduate students and advanced undergraduates how to overcome the problems of putting the tools of adaptive control theory into practice. The text will also be of interest to engineers wishing to employ ideas of adaptive control in their designs and plant.

Digital Self-tuning Controllers

Multi-Objective Optimization in Physical Synthesis of Integrated Circuits

Multi-Objective Optimization in Physical Synthesis of Integrated Circuits

This book introduces techniques that advance the capabilities and strength of modern software tools for physical synthesis, with the ultimate goal to improve the quality of leading-edge semiconductor products. It provides a comprehensive introduction to physical synthesis and takes the reader methodically from first principles through state-of-the-art optimizations used in cutting edge industrial tools. It explains how to integrate chip optimizations in novel ways to create powerful circuit transformations that help satisfy performance requirements. Broadens the scope of physical synthesis optimization to include accurate transformations operating between the global and local scales; Integrates groups of related transformations to break circular dependencies and increase the number of circuit elements that can be jointly optimized to escape local minima; Derives several multi-objective optimizations from first observations through complete algorithms and experiments;Describes integrated optimization techniques that ensure a graceful timing closure process and impact nearly every aspect of a typical physical synthesis flow.

Multi-Objective Optimization in Physical Synthesis of Integrated Circuits

FEFLOW

FEFLOW

FEFLOW is an acronym of Finite Element subsurface FLOW simulation system and solves the governing flow, mass and heat transport equations in porous and fractured media by a multidimensional finite element method for complex geometric and parametric situations including variable fluid density, variable saturation, free surface(s), multispecies reaction kinetics, non-isothermal flow and multidiffusive effects. FEFLOW comprises theoretical work, modeling experiences and simulation practice from a period of about 40 years. In this light, the main objective of the present book is to share this achieved level of modeling with all required details of the physical and numerical background with the reader. The book is intended to put advanced theoretical and numerical methods into the hands of modeling practitioners and scientists. It starts with a more general theory for all relevant flow and transport phenomena on the basis of the continuum approach, systematically develops the basic framework for important classes of problems (e.g., multiphase/multispecies non-isothermal flow and transport phenomena, discrete features, aquifer-averaged equations, geothermal processes), introduces finite-element techniques for solving the basic balance equations, in detail discusses advanced numerical algorithms for the resulting nonlinear and linear problems and completes with a number of benchmarks, applications and exercises to illustrate the different types of problems and ways to tackle them successfully (e.g., flow and seepage problems, unsaturated-saturated flow, advective-diffusion transport, saltwater intrusion, geothermal and thermohaline flow).

FEFLOW

Nature-Inspired Algorithms for Optimisation

Nature-Inspired Algorithms for Optimisation

Sect. I. Introduction — Why Is Optimization Difficult? / Thomas Weise, Michael Zapf, Raymond Chiong, Antonio J. Nebro — The Rationale behind Seeking Inspiration from Nature / Kent C.B. Steer, Andrew Wirth, Saman K. Halgamuge — Sect. II. Evolutionary Intelligence — The Evolutionary-Gradient-Search Procedure in Theory and Practice / Ralf Salomon, Dirk V. Arnold — The Evolutionary Transition Algorithm: Evolving Complex Solutions out of Simpler Ones / Tom Lenaerts, Anne Defaweux, Jano van Hemert — A Model-Assisted Memetic Algorithm for Expensive Optimization Problems / Yoel Tenne — A Self-Adaptive Mixed Distribution Based Uni-variate Estimation of Distribution Algorithm for Large Scale Global Optimization / Yu Wang, Bin Li — Differential Evolution with Fitness Diversity Self-Adaptation / Ville Tirronen, Ferrante Neri — Central Pattern Generators: Optimisation and Application / Leena N. Patel — Sect. III. Collective Intelligence — Fish School Search / Carmelo J.A. Bastos Filho … [et al.] — Magnifier Particle Swarm Optimization / Ying Tan, Junqi Zhang — Improved Particle Swarm Optimization in Constrained Numerical Search Spaces / Efren Mezura-Montes, Jorge Isacc Flore-Mendoza — Applying River Formation Dynamics to Solve NP-Complete Problems / Pablo Rabanal, Ismael Rodriguez, Fernando Rubio — Sect. IV. Social-Natural Intelligence — Algorithms Inspired in Social Phenomena / Antonio Neme, Sergio Hernandez — Artificial Immune Systems for Optimization / Heder S. Bernardino, Helio J.C. Barbosa — Sect. V. Multi-Objective Optimisation — Ranking Methods in Many-objective Evolutionary Algorithms / Antonio Lopez Jaimes, Luis Vicente Santana Quintero, Carlos A. Coello Coello — On the Effect of Applying a Steady-State Selection Scheme in the Multi-Objective Genetic Algorithm NSGA-II / Antonio J. Nebro, Juan J. Durillo — Improving the Performance of Multiobjective Evolutionary Optimization Algorithms using Coevolutionary Learning /Tse Guan Tan, Jason Teo — Evolutionary Optimization for Multiobjective Portfolio Selection Under Markowitzs Model with Application to the Caracas Stock Exchange / Feijoo Colomine Duran, Carlos Cotta, Antonio J. Fernandez.

Nature-Inspired Algorithms for Optimisation

Markov Networks in Evolutionary Computation

Markov Networks in Evolutionary Computation

Markov networks and other probabilistic graphical modes have recently received an upsurge in attention from Evolutionary computation community, particularly in the area of Estimation of distribution algorithms (EDAs). EDAs have arisen as one of the most successful experiences in the application of machine learning methods in optimization, mainly due to their efficiency to solve complex real-world optimization problems and their suitability for theoretical analysis.This book focuses on the different steps involved in the conception, implementation and application of EDAs that use Markov networks, and undirected models in general. It can serve as a general introduction to EDAs but covers also an important current void in the study of these algorithms by explaining the specificities and benefits of modeling optimization problems by means of undirected probabilistic models. All major developments to date in the progressive introduction of Markov networks based EDAs are reviewed in the book. Hot current research trends and future perspectives in the enhancement and applicability of EDAs are also covered. The contributions included in the book address topics as relevant as the application of probabilistic-based fitness models, the use of belief propagation algorithms in EDAs and the application of Markov network based EDAs to real-world optimization problems. The book should be of interest to researchers and practitioners from areas such as optimization, evolutionary computation, and machine learning.

Markov Networks in Evolutionary Computation

Numerical Methods for Controlled Stochastic Delay Systems

Numerical Methods for Controlled Stochastic Delay Systems

The Markov chain approximation methods are widely used for the numerical solution of nonlinear stochastic control problems in continuous time. This book extends the methods to stochastic systems with delays. Because such problems are infinite-dimensional, many new issues arise in getting good numerical approximations and in the convergence proofs. Useful forms of numerical algorithms and system approximations are developed in this work, and the convergence proofs are given. All of the usual cost functions are treated as well as singular and impulsive controls. A major concern is on representations and approximations that use minimal memory. Featuring numerical algorithms and examples with applications to control and modern communications systems, this book is the first on the subject and will be of great interest to all those who work with stochastic delay equations and whose main interest is in either the use of the algorithms or in the underlying mathematics. An excellent resource for graduate students, researchers, and practitioners, the work may be used as a graduate-level textbook for a special topics course or seminar on numerical methods in stochastic control.

Numerical Methods for Controlled Stochastic Delay Systems

Treatment of Pediatric Neurologic Disorders

Treatment of Pediatric Neurologic Disorders

This reference discusses state-of-the-art methods for the management of children with conditions affecting the nervous system-providing over 80 chapters that outline direct, logical approaches to numerous pediatric neurologic disorders using clear tables, algorithms, and figures for quick reference to key material.

Treatment of Pediatric Neurologic Disorders

Algorithms on Trees and Graphs

Algorithms on Trees and Graphs

Graph algorithms is a well-established subject in mathematics and computer science. Beyond classical application fields, like approximation, combinatorial optimization, graphics, and operations research, graph algorithms have recently attracted increased attention from computational molecular biology and computational chemistry. Centered around the fundamental issue of graph isomorphism, this text goes beyond classical graph problems of shortest paths, spanning trees, flows in networks, and matchings in bipartite graphs. Advanced algorithmic results and techniques of practical relevance are presented in a coherent and consolidated way. This book introduces graph algorithms on an intuitive basis followed by a detailed exposition in a literate programming style, with correctness proofs as well as worst-case analyses. Furthermore, full C++ implementations of all algorithms presented are given using the LEDA library of efficient data structures and algorithms. Numerous illustrations, examples, and exercises, and a comprehensive bibliography support students and professionals in using the book as a text and source of reference

Algorithms on Trees and Graphs

Algebra, Geometry and Software Systems

Algebra, Geometry and Software Systems

The book contains surveys and research papers on mathematical software and algorithms. The common thread is that the field of mathematical applications lies on the border between algebra and geometry. Topics include polyhedral geometry, elimination theory, algebraic surfaces, Gr’obner bases, triangulations of point sets and the mutual relationship. This diversity is accompanied by the abundance of available software systems which often handle only special mathematical aspects. Therefore the volumes other focus is on solutions towards the integration of mathematical software systems. This includes low-level and XML based high-level communication channels as well as general frameworks for modular systems.

Algebra, Geometry and Software Systems

Advanced Planning in Supply Chains

Advanced Planning in Supply Chains

Advanced Planning Systems (APS) are a key enabler of the supply chain management. However, APS are highly complex and difficult to comprehend. This book provides students with valuable insights into the capabilities of state-of-the-art APS and bridges the gap between theory (model building and solution algorithms), software implementation, and adaptation to a specific business case. Our business case named Frutado provides a unifying framework for illustrating the different planning tasks that arise in a company from demand planning to the distribution of goods that are addressed by APS. In addition, the book guides through interactive learning units which have been created and recorded for each module of SAPs APS. Learning units can be downloaded free of charge ready to be displayed in a web browser. Together, the textbook and the learning units provide the required skills to better understand the concepts, models, and algorithms underlying todays APS.

Advanced Planning in Supply Chains

A Guide to Data Compression Methods, Volume 1

A Guide to Data Compression Methods, Volume 1

Many faces of modern computing – from archiving data to coding theory to image processing rely heavily on data compression. This new and practical guide explains the process of compressing all types of computer data, as well as the use of significant methods and algorithms. Its purpose is to succinctly describe both the principles underlying the field of data compression and how to use the key methods effectively. A Guide to Data Compression Methods concentrates on general concepts and methods and describes them with a minimal amount of mathematical detail. It presents the main approaches to data compression, describes the most important algorithms, and includes straightforward examples. Statistical, dictionary, and wavelet methodologies are addressed in specific chapters, as well as image, video, and audio compression. The reader can expect to gain a basic understanding of the key algorithms and methods used to compress data for storage and transmission. Topics and features: All core methods are clearly explained with realistic examples, and some computer code is included Accessible presentation, with only minimum computer and mathematics technical background Discussion of wavelet methods and JPEG 2000 Appendix lists all algorithms presented in the book This book is an invaluable practical reference and guide for all practitioners and professionals in computer science, software engineering, and programming.

A Guide to Data Compression Methods, Volume 1

Data Structures and Algorithms in C++, Fourth Edition

Data Structures and Algorithms in C++, Fourth Edition

Strengthen your understanding of data structures and their algorithms for the foundation you need to successfully design, implement and maintain virtually any software system. Theoretical, yet practical, DATA STRUCUTRES AND ALGORITHMS IN C++, 4E by experienced author Adam Drosdek highlights the fundamental connection between data structures and their algorithms, giving equal weight to the practical implementation of data structures and the theoretical analysis of algorithms and their efficiency. This edition provides critical new coverage of treaps, k-d trees and k-d B-trees, generational garbage collection, and other advanced topics such as sorting methods and a new hashing technique. Abundant C++ code examples and a variety of case studies provide valuable insights into data structures implementation. DATA STRUCTURES AND ALGORITHMS IN C++ provides the balance of theory and practice to prepare readers for a variety of applications in a modern, object-oriented paradigm.

Data Structures and Algorithms in C++, Fourth Edition

Inborn Metabolic Diseases - Fifth Edition

Inborn Metabolic Diseases - Fifth Edition

This henceforth classical textbook has become indispensable for those in the front line dealing with metabolic disorders. As with previous editions the book is aimed at all those involved with this specialty including pediatricians, biochemists, dieticians, neurologists, internists, geneticists, psychologists, nurses, and social workers. This 4th edition has been thoroughly updated and revised and John Walter has joined the three other editors. One new chapter on Neonatal screening by tandem MS/MS has been added and several new groups of disorders have been included; for example defects involving the pentose phosphate pathway (polyols metabolism) and disorders of glucose transport. The first chapter presents the clinical approach to inherited metabolic disease using many algorithms and tables and has been entirely revised and extended to include adult metabolic medicine. It now incorporates many new findings particularly in neuroradiology and neurophysiology and emphasises those disorders for which treatment is available. This accessible and practical book can be used either by going directly to the relevant chapter when the diagnosis is already suspected or by referring to Chapter 1 if it is unknown. Despite the numerous updates the book has been maintained at a reasonable size and is published as a single volume of approximately 550 pages divided into 43 Chapters.

Inborn Metabolic Diseases - Fifth Edition

Darwin2K

Darwin2K

Darwin2K: An Evolutionary Approach to Automated Design for Robotics is an essential reference tool for researchers, professionals, and students involved in robot design or in evolutionary synthesis, design, and optimization. It is also necessary for users of Darwin2K. Researchers and hobbyists interested in genetic algorithms and artificial life techniques will find the book interesting.

Darwin2K

Core PHP Programming

Core PHP Programming

Core PHP Programming, Third Edition is the authoritative guide to the new PHP 5 for experienced developers. Top PHP developer Leon Atkinson and PHP 5 contributor/Zend Engine 2 co-creator Zeev Suraski cover every facet of real-world PHP 5 development, from basic syntax to advanced object-oriented development — even design patterns! It’s all here: networking, data structures, regular expressions, math, configuration, graphics, MySQL/PostgreSQL support, XML, algorithms, debugging, optimizationand 650 downloadable code examples, with a Foreword by PHP 5 contributor and Zend Engine 2 co-creator Andi Gutmans!

Core PHP Programming

Inverse Problems in Underwater Acoustics

Inverse Problems in Underwater Acoustics

Inverse problems have a long history in acoustics, optics, electromagnetics and geophysics, but only recently have the signals provided by ocean acoustic sensors become numerous and sophisticated enough to allow for realistic identification of the ocean parameters. Acoustic signals propagating for long distances in the water column and reflections of underwater sound from the ocean boundaries provide novel problems of interpretation and inversion. The chapters in this volume discuss some of the contemporary aspects of these problems. They provide recent and useful results for bottom recognition, inverse scattering in acoustic wave guides, and ocean acoustic tomography, as well as a discussion of some of the new algorithms, such as those related to matched-field processing, that have recently been used for inverting experimental data. Each chapter is by a noted expert in the field and represents the state of the art. The chapters have all been edited to provide a uniform format and level of presentation.

Inverse Problems in Underwater Acoustics

Advanced Bimanual Manipulation

Advanced Bimanual Manipulation

Dexterous and autonomous manipulation is a key technology for the personal and service robots of the future. Advances in Bimanual Manipulation edited by Bruno Siciliano provides the robotics community with the most noticeable results of the four-year European project DEXMART (DEXterous and autonomous dual-arm hand robotic manipulation with sMART sensory-motor skills: A bridge from natural to artificial cognition). The volume covers a host of highly important topics in the field, concerned with modelling and learning of human manipulation skills, algorithms for task planning, human-robot interaction, and grasping, as well as hardware design of dexterous anthropomorphic hands. The results described in this five-chapter collection are believed to pave the way towards the development of robotic systems endowed with dexterous and human-aware dual-arm/hand manipulation skills for objects, operating with a high degree of autonomy in unstructured real-world environments.

Advanced Bimanual Manipulation