Algorithms For Analysis Inference And Control Of Boolean Networks

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Algorithms For Analysis, Inference, And Control Of Boolean Networks

Author : Akutsu Tatsuya
Publisher : World Scientific
ISBN 13 : 9813233443
Total Pages : 228 pages
Book Rating : 4.8/5 (132 download)

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Book Synopsis Algorithms For Analysis, Inference, And Control Of Boolean Networks by : Akutsu Tatsuya

Download or read book Algorithms For Analysis, Inference, And Control Of Boolean Networks written by Akutsu Tatsuya and published by World Scientific. This book was released on 2018-02-13 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Boolean network (BN) is a mathematical model of genetic networks and other biological networks. Although extensive studies have been done on BNs from a viewpoint of complex systems, not so many studies have been undertaken from a computational viewpoint. This book presents rigorous algorithmic results on important computational problems on BNs, which include inference of a BN, detection of singleton and periodic attractors in a BN, and control of a BN. This book also presents algorithmic results on fundamental computational problems on probabilistic Boolean networks and a Boolean model of metabolic networks. Although most contents of the book are based on the work by the author and collaborators, other important computational results and techniques are also reviewed or explained. Contents: Preliminaries Boolean Networks Detection of Attractors Detection of Singleton Attractors Detection of Periodic Attractors Identification of Boolean Networks Control of Boolean Networks Predecessor and Observability Problems Semi-Tensor Product Approach Analysis of Metabolic Networks Probabilistic Boolean Networks Identification of Probabilistic Boolean Networks Control of Probabilistic Boolean Networks Readership: Graduate students and researchers working on string theory and related topics. Keywords: Boolean Networks;Bioinformatics;Systems Biology;Combinatorial Algorithms;AttractorsReview: Key Features: Unique book focusing on computational aspects of Boolean networks Provide computational foundations on Boolean networks Contain recent and up-to-date results on algorithms for Boolean networks

Probabilistic Boolean Networks

Author : Ilya Shmulevich
Publisher : SIAM
ISBN 13 : 0898716926
Total Pages : 276 pages
Book Rating : 4.8/5 (987 download)

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Book Synopsis Probabilistic Boolean Networks by : Ilya Shmulevich

Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-21 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

Analysis and Control of Boolean Networks

Author : Daizhan Cheng
Publisher : Springer
ISBN 13 : 9781447126119
Total Pages : 472 pages
Book Rating : 4.1/5 (261 download)

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Book Synopsis Analysis and Control of Boolean Networks by : Daizhan Cheng

Download or read book Analysis and Control of Boolean Networks written by Daizhan Cheng and published by Springer. This book was released on 2013-01-27 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Analysis and Control of Boolean Networks presents a systematic new approach to the investigation of Boolean control networks. The fundamental tool in this approach is a novel matrix product called the semi-tensor product (STP). Using the STP, a logical function can be expressed as a conventional discrete-time linear system. In the light of this linear expression, certain major issues concerning Boolean network topology – fixed points, cycles, transient times and basins of attractors – can be easily revealed by a set of formulae. This framework renders the state-space approach to dynamic control systems applicable to Boolean control networks. The bilinear-systemic representation of a Boolean control network makes it possible to investigate basic control problems including controllability, observability, stabilization, disturbance decoupling etc.

Algebraic Biology

Author : Katsuhisa Horimoto
Publisher : Springer Science & Business Media
ISBN 13 : 3540851003
Total Pages : 256 pages
Book Rating : 4.5/5 (48 download)

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Book Synopsis Algebraic Biology by : Katsuhisa Horimoto

Download or read book Algebraic Biology written by Katsuhisa Horimoto and published by Springer Science & Business Media. This book was released on 2008-07-18 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the Third International Conference on Algebraic Biology, AB 2008, held at the Castle of Hagenberg, Austria in July 2008 as part of the RISC Summer 2008, organized by the Research Institute for Symbolic Computation. The 14 revised full papers presented together with 3 tutorial lectures were carefully reviewed and selected from 27 submissions. The conference is the interdisciplinary forum for the presentation of research on all aspects of applications of symbolic computation (computer algebra, computational logic, and related methods) to various issues in biology and life sciences as well as other problems in biology being approached with symbolic methods.

Algorithms for Computational Biology

Author : Jesper Jansson
Publisher : Springer
ISBN 13 : 3319919385
Total Pages : 155 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis Algorithms for Computational Biology by : Jesper Jansson

Download or read book Algorithms for Computational Biology written by Jesper Jansson and published by Springer. This book was released on 2018-06-20 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 5th InternationalConference on Algorithms for Computational Biology, AlCoB 2018, held in Hong Kong, China, in June 2018. The 11 full papers presented together with 1 invited paper were carefully reviewed and selected from 20 submissions. They are organized in the following topical sections: Phylogenetics, Sequence Rearrangement and Analysis, Systems Biology and Other Biological Processes.

Discrete-Time and Discrete-Space Dynamical Systems

Author : Kuize Zhang
Publisher : Springer
ISBN 13 : 3030259722
Total Pages : 222 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Discrete-Time and Discrete-Space Dynamical Systems by : Kuize Zhang

Download or read book Discrete-Time and Discrete-Space Dynamical Systems written by Kuize Zhang and published by Springer. This book was released on 2019-08-06 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discrete-Time and Discrete-Space Dynamical Systems provides a systematic characterization of the similarities and differences of several types of discrete-time and discrete-space dynamical systems, including: Boolean control networks; nondeterministic finite-transition systems; finite automata; labelled Petri nets; and cellular automata. The book's perspective is primarily based on topological properties though it also employs semitensor-product and graph-theoretic methods where appropriate. It presents a series of fundamental results: invertibility, observability, detectability, reversiblity, etc., with applications to systems biology. Academic researchers with backgrounds in applied mathematics, engineering or computer science and practising engineers working with discrete-time and discrete-space systems will find this book a helpful source of new understanding for this increasingly important class of systems. The basic results to be found within are of fundamental importance for further study of related problems such as automated synthesis and safety control in cyber-physical systems using formal methods.

Boolean Systems

Author : Serban E. Vlad
Publisher : Elsevier
ISBN 13 : 032395569X
Total Pages : 458 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Boolean Systems by : Serban E. Vlad

Download or read book Boolean Systems written by Serban E. Vlad and published by Elsevier. This book was released on 2023-01-06 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Boolean functions may be iterated either asynchronously, when their coordinates are computed independently of each other, or synchronously, when their coordinates are computed at the same time. In Boolean Systems: Topics in Asynchronicity, a book addressed to mathematicians and computer scientists interested in Boolean systems and their use in modelling, author Serban E. Vlad presents a consistent and original mathematical theory of the discrete-time Boolean asynchronous systems. The purpose of the book is to set forth the concepts of such a theory, resulting from the synchronous Boolean system theory and mostly from the synchronous real system theory, by analogy, and to indicate the way in which known synchronous deterministic concepts generate new asynchronous nondeterministic concepts. The reader will be introduced to the dependence on the initial conditions, periodicity, path-connectedness, topological transitivity, and chaos. A property of major importance is invariance, which is present in five versions. In relation to it, the reader will study the maximal invariant subsets, the minimal invariant supersets, the minimal invariant subsets, connectedness, separation, the basins of attraction, and attractors. The stability of the systems and their time-reversal symmetry end the topics that refer to the systems without input. The rest of the book is concerned with input systems. The most consistent chapters of this part of the book refer to the fundamental operating mode and to the combinational systems (systems without feedback). The chapter Wires, Gates, and Flip-Flops presents a variety of applications. The first appendix addresses the issue of continuous time, and the second one sketches the important theory of Daizhan Cheng, which is put in relation to asynchronicity. The third appendix is a bridge between asynchronicity and the symbolic dynamics of Douglas Lind and Brian Marcus. Presents a consistent and original theory of the discrete-time Boolean asynchronous systems, which are useful for mathematicians and computer scientists interested in Boolean Networks, dynamical systems, and modeling. Studies the flows and equations of evolution, nullclines, dependence on initial conditions, periodicity, path-connectedness, topological transitivity, chaos, nonwandering points, invariance, connectedness, and separation, as well as the basins of attraction, attractors, stability, and time-reversal symmetry. Explains the fundamental operating mode of the input systems and the combinational systems (systems without feedback). Includes a chapter of applications of the Boolean systems and their modeling techniques. Makes use of the unbounded delay model of computation of the Boolean functions.

Algebraic Biology

Author : Katsuhisa Horimoto
Publisher : Springer
ISBN 13 : 3540851011
Total Pages : 245 pages
Book Rating : 4.5/5 (48 download)

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Book Synopsis Algebraic Biology by : Katsuhisa Horimoto

Download or read book Algebraic Biology written by Katsuhisa Horimoto and published by Springer. This book was released on 2008-07-30 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the proceedings of the Third International Conference on Algebraic Biology (AB 2008). Jointly organized by the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, and the Research Institute for Symbolic Computation (RISC), Hagenberg, Austria, it was held from July 31 to August 2, 2008 in the Castle of Hagenberg. Algebraic biology is an interdisciplinary forum for research on all aspects of applying symbolic computation in biology. The ?rst conference on algebraic biology (AB 2005) was held November 28–30, 2005 in Tokyo, the second during July 2–4, 2007 in Hagenberg. The AB conference series is intended as a bridge between life sciences and symbolic computation: On the one hand, new insights inbiologyarefoundbypowerfulsymbolicmethods;ontheotherhand,biological problems suggestnew algebraicstructures andalgorithms.While this pro?le has been established in the previous proceedings, the papers in the present volume demonstrate the continuous growth of algebraic biology. We received 27 submissions from 14 countries (Australia, Austria, Canada, China, Colombia, France, Germany, Italy, Japan, Norway, Russia, Switzerland, UK, USA), and 14 papers were accepted for publication. Each submission was assigned to at least three ProgramCommittee members, who carefully reviewed the papers, in many cases with the help of external referees. The reviews were discussedby the ProgramCommittee for oneweekvia the EasyChairconference management system.

Application Of Omics, Ai And Blockchain In Bioinformatics Research

Author : Jeffrey J P Tsai
Publisher : World Scientific
ISBN 13 : 9811203598
Total Pages : 207 pages
Book Rating : 4.8/5 (112 download)

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Book Synopsis Application Of Omics, Ai And Blockchain In Bioinformatics Research by : Jeffrey J P Tsai

Download or read book Application Of Omics, Ai And Blockchain In Bioinformatics Research written by Jeffrey J P Tsai and published by World Scientific. This book was released on 2019-10-14 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the increasing availability of omics data and mounting evidence of the usefulness of computational approaches to tackle multi-level data problems in bioinformatics and biomedical research in this post-genomics era, computational biology has been playing an increasingly important role in paving the way as basis for patient-centric healthcare.Two such areas are: (i) implementing AI algorithms supported by biomedical data would deliver significant benefits/improvements towards the goals of precision medicine (ii) blockchain technology will enable medical doctors to securely and privately build personal healthcare records, and identify the right therapeutic treatments and predict the progression of the diseases.A follow-up in the publication of our book Computation Methods with Applications in Bioinformatics Analysis (2017), topics in this volume include: clinical bioinformatics, omics-based data analysis, Artificial Intelligence (AI), blockchain, big data analytics, drug discovery, RNA-seq analysis, tensor decomposition and Boolean network.

Multi-Agent Systems

Author : Dorothea Baumeister
Publisher : Springer Nature
ISBN 13 : 3031206142
Total Pages : 462 pages
Book Rating : 4.0/5 (312 download)

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Book Synopsis Multi-Agent Systems by : Dorothea Baumeister

Download or read book Multi-Agent Systems written by Dorothea Baumeister and published by Springer Nature. This book was released on 2022-12-10 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes thoroughly refereed and revised selected papers from the proceedings of 19th European Conference on Multi-Agent Systems, EUMAS 2022, held in Düsseldorf, Germany, during September 14–16, 2022. The 23 full papers included in this book were carefully reviewed and selected from 36 submissions. The book also contains 6 short summaries of talks from PhD students at the PhD day. The papers deal with current topics in the research and development of multi-agent systems.

An Introduction to the Analysis of Algorithms

Author : Michael Soltys
Publisher : World Scientific
ISBN 13 : 9814401153
Total Pages : 211 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis An Introduction to the Analysis of Algorithms by : Michael Soltys

Download or read book An Introduction to the Analysis of Algorithms written by Michael Soltys and published by World Scientific. This book was released on 2012 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: A successor to the first edition, this updated and revised book is a great companion guide for students and engineers alike, specifically software engineers who design reliable code. While succinct, this edition is mathematically rigorous, covering the foundations of both computer scientists and mathematicians with interest in algorithms. Besides covering the traditional algorithms of Computer Science such as Greedy, Dynamic Programming and Divide & Conquer, this edition goes further by exploring two classes of algorithms that are often overlooked: Randomised and Online algorithms with emphasis placed on the algorithm itself. The coverage of both fields are timely as the ubiquity of Randomised algorithms are expressed through the emergence of cryptography while Online algorithms are essential in numerous fields as diverse as operating systems and stock market predictions. While being relatively short to ensure the essentiality of content, a strong focus has been placed on self-containment, introducing the idea of pre/post-conditions and loop invariants to readers of all backgrounds. Containing programming exercises in Python, solutions will also be placed on the book's website.

Boolean Functions

Author : Yves Crama
Publisher : Cambridge University Press
ISBN 13 : 1139498630
Total Pages : 711 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Boolean Functions by : Yves Crama

Download or read book Boolean Functions written by Yves Crama and published by Cambridge University Press. This book was released on 2011-05-16 with total page 711 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by prominent experts in the field, this monograph provides the first comprehensive, unified presentation of the structural, algorithmic and applied aspects of the theory of Boolean functions. The book focuses on algebraic representations of Boolean functions, especially disjunctive and conjunctive normal form representations. This framework looks at the fundamental elements of the theory (Boolean equations and satisfiability problems, prime implicants and associated short representations, dualization), an in-depth study of special classes of Boolean functions (quadratic, Horn, shellable, regular, threshold, read-once functions and their characterization by functional equations) and two fruitful generalizations of the concept of Boolean functions (partially defined functions and pseudo-Boolean functions). Several topics are presented here in book form for the first time. Because of the depth and breadth and its emphasis on algorithms and applications, this monograph will have special appeal for researchers and graduate students in discrete mathematics, operations research, computer science, engineering and economics.

Algorithms for Computational Biology

Author : María Botón-Fernández
Publisher : Springer
ISBN 13 : 3319388274
Total Pages : 187 pages
Book Rating : 4.3/5 (193 download)

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Book Synopsis Algorithms for Computational Biology by : María Botón-Fernández

Download or read book Algorithms for Computational Biology written by María Botón-Fernández and published by Springer. This book was released on 2016-06-11 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016, held inTrujillo, Spain, in June 2016. The 13 full papers presented in this volume were carefully reviewed andselected from 23 submissions. They are organized in the following topical sections: biological networks and modelling; biological structure processing; phylogenetics; and sequence analysis and rearrangement. In addition one invited talk is included.

Logical Modeling of Biological Systems

Author : Luis Fariñas del Cerro
Publisher : John Wiley & Sons
ISBN 13 : 1119015219
Total Pages : 410 pages
Book Rating : 4.1/5 (19 download)

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Book Synopsis Logical Modeling of Biological Systems by : Luis Fariñas del Cerro

Download or read book Logical Modeling of Biological Systems written by Luis Fariñas del Cerro and published by John Wiley & Sons. This book was released on 2014-08-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.

Algorithms

Author : M. H. Alsuwaiyel
Publisher : World Scientific
ISBN 13 : 9814723657
Total Pages : 573 pages
Book Rating : 4.8/5 (147 download)

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Book Synopsis Algorithms by : M. H. Alsuwaiyel

Download or read book Algorithms written by M. H. Alsuwaiyel and published by World Scientific. This book was released on 2016 with total page 573 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Problem solving is an essential part of every scientific discipline. It has two components: (1) problem identification and formulation, and (2) the solution to the formulated problem. One can solve a problem on its own using ad hoc techniques or by following techniques that have produced efficient solutions to similar problems. This requires the understanding of various algorithm design techniques, how and when to use them to formulate solutions, and the context appropriate for each of them. Algorithms: Design Techniques and Analysis advocates the study of algorithm design by presenting the most useful techniques and illustrating them with numerous examples -- emphasizing on design techniques in problem solving rather than algorithms topics like searching and sorting. Algorithmic analysis in connection with example algorithms are explored in detail. Each technique or strategy is covered in its own chapter through numerous examples of problems and their algorithms. Readers will be equipped with problem solving tools needed in advanced courses or research in science and engineering."--Provided by publisher.

Understanding Machine Learning

Author : Shai Shalev-Shwartz
Publisher : Cambridge University Press
ISBN 13 : 1107057132
Total Pages : 415 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Understanding Machine Learning by : Shai Shalev-Shwartz

Download or read book Understanding Machine Learning written by Shai Shalev-Shwartz and published by Cambridge University Press. This book was released on 2014-05-19 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces machine learning and its algorithmic paradigms, explaining the principles behind automated learning approaches and the considerations underlying their usage.

Elements of Causal Inference

Author : Jonas Peters
Publisher : MIT Press
ISBN 13 : 0262037319
Total Pages : 289 pages
Book Rating : 4.2/5 (62 download)

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Book Synopsis Elements of Causal Inference by : Jonas Peters

Download or read book Elements of Causal Inference written by Jonas Peters and published by MIT Press. This book was released on 2017-11-29 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: A concise and self-contained introduction to causal inference, increasingly important in data science and machine learning. The mathematization of causality is a relatively recent development, and has become increasingly important in data science and machine learning. This book offers a self-contained and concise introduction to causal models and how to learn them from data. After explaining the need for causal models and discussing some of the principles underlying causal inference, the book teaches readers how to use causal models: how to compute intervention distributions, how to infer causal models from observational and interventional data, and how causal ideas could be exploited for classical machine learning problems. All of these topics are discussed first in terms of two variables and then in the more general multivariate case. The bivariate case turns out to be a particularly hard problem for causal learning because there are no conditional independences as used by classical methods for solving multivariate cases. The authors consider analyzing statistical asymmetries between cause and effect to be highly instructive, and they report on their decade of intensive research into this problem. The book is accessible to readers with a background in machine learning or statistics, and can be used in graduate courses or as a reference for researchers. The text includes code snippets that can be copied and pasted, exercises, and an appendix with a summary of the most important technical concepts.