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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.
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.
The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.
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 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.
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.
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.
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.
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.