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Analysis And Control Of Boolean Networks

Analysis And Control Of Boolean Networks

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Author by : Daizhan Cheng
Languange Used : en
Release Date : 2010-11-23
Publisher by : Springer Science & Business Media

ISBN : 9780857290977

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....



Algorithms For Analysis Inference And Control Of Boolean Networks

Algorithms For Analysis Inference And Control Of Boolean Networks

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Author by : Tatsuya Akutsu
Languange Used : en
Release Date : 2018-02-14
Publisher by : World Scientific

ISBN : 9789813233447

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....



Observer Design For Control And Fault Diagnosis Of Boolean Networks

Observer Design For Control And Fault Diagnosis Of Boolean Networks

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Author by : Zhihua Zhang
Languange Used : en
Release Date : 2021-12-11
Publisher by : Springer Nature

ISBN : 9783658359294

Boolean control networks (BCNs) are a kind of parameter-free model, which can be used to approximate the qualitative behavior of biological systems. After converting into a model similar to the standard discrete-time state-space model, control-theoretic problems of BCNs can be studied. In control theory, state observers can provide state estimation for any other applications. Reconstructibility condition is necessary for the existence of state observers. In this thesis explicit and recursive methods have been developed for reconstructibility analysis. Then, an approach to design Luenberger-like observer has been proposed, which works in a two-step process (i.e. predict and update). If a BCN is reconstructible, then an accurate state estimate can be provided by the observer no later than the minimal reconstructibility index. For a wide range of applications the approach has been extended to enable design of unknown input observer, distributed observers and reduced-order observer. The performance of the observers has been evaluated thoroughly. Furthermore, methods for output tracking control and fault diagnosis of BCNs have been developed. Finally, the developed schemes are tested with numerical examples....



Analysis And Control Of Finite Valued Systems

Analysis And Control Of Finite Valued Systems

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Author by : Haitao Li
Languange Used : en
Release Date : 2018-05-11
Publisher by : CRC Press

ISBN : 9781351368292

A comprehensive work in finite-value systems that covers the latest achievements using the semi-tensor product method, on various kinds of finite-value systems. These results occupy the highest position in the analysis and control of this field. It not only covers all aspects of research in finite-value systems, but also presents the mathematical derivation for each conclusion in depth. The book contains examples to provide a better understanding of the practical applications of finite-value systems. It will serve as a textbook for graduate students of Cybernetics, Mathematical, and Biology, and a reference for readers interested in the theory of finite-value systems....



Probabilistic Boolean Networks

Probabilistic Boolean Networks

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Author by : Ilya Shmulevich
Languange Used : en
Release Date : 2010-01-21
Publisher by : SIAM

ISBN : 9780898716924

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



Probabilistic Boolean Networks

Probabilistic Boolean Networks

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Author by : Ilya Shmulevich
Languange Used : en
Release Date : 2010-01-01
Publisher by : SIAM

ISBN : 9780898717631

This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including the relationships between network structure and dynamics, steady-state analysis, and relationships to other model classes." "Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science....



Algebraic Biology

Algebraic Biology

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Author by : Katsuhisa Horimoto
Languange Used : en
Release Date : 2008-07-18
Publisher by : Springer Science & Business Media

ISBN : 9783540851004

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....



Logic Synthesis For Genetic Diseases

Logic Synthesis For Genetic Diseases

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Author by : Pey-Chang Kent Lin
Languange Used : en
Release Date : 2013-10-31
Publisher by : Springer Science & Business Media

ISBN : 9781461494294

This book brings to bear a body of logic synthesis techniques, in order to contribute to the analysis and control of Boolean Networks (BN) for modeling genetic diseases such as cancer. The authors provide several VLSI logic techniques to model the genetic disease behavior as a BN, with powerful implicit enumeration techniques. Coverage also includes techniques from VLSI testing to control a faulty BN, transforming its behavior to a healthy BN, potentially aiding in efforts to find the best candidates for treatment of genetic diseases....



Use Boolean Network To Model And Control Within And Between Person Dynamics

Use Boolean Network To Model And Control Within And Between Person Dynamics

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Author by : Xiao Yang
Languange Used : en
Release Date : 2020
Publisher by :

ISBN : OCLC:1198444979

This body of work introduces and forwards a Boolean network-based method for studying psychological dynamics, both within-person and between-persons. I outline the Boolean network method, provide a guide for implementation, and illustrate how the method is applied in two empirical settings -- study of children's self-regulation, and study of group-therapy processes. The work highlights the utility of the method for obtaining intuitive descriptions of individual or group processes and deriving strategies for directing the individual or group towards desired outcomes. Developmental science is making use of dynamical system methods to explain the mechanisms of change driving human development and to predict how and when individuals or groups will change. A natural next step is to understand how to intervene when problematic patterns or change arise. Although psychological researchers have proposed and explored use of network methods to design interventions, applications are sparse. My aim is to enrich the repertoire of methods researchers can use to learn about and direct individuals' and groups' psychological functioning, and in doing so to prompt further use of network methods for modeling behavior change. In Chapter 1, I outline the motivation for introducing a Boolean network method that can be used to describe psychological systems and design interventions that may optimize how those systems function. Although a number of researchers have outlined the possibility of using dynamical system methods to guide psychological processes to desired levels, methods for deriving control strategies have remained theoretical. In this chapter, I identify a gap in the research on methods for analysis of developmental and psychological change processes -- specifically, the sparsity of empirical applications of control system design despite its theoretical importance -- and introduce how a Boolean network control method (Kauffman, 1969; 1993) can address this gap. Second, I briefly explain why network control is useful for guiding developmental processes, and how methods at the overlap between dynamical systems methods and network analysis can be used to develop that guidance. Third, I clarify how within- and between-person dynamics are conceptualized in this project, and how the definitions used here are analogous to other terms used in psychology. Fourth, I explain why the same dynamical system method can be used to describe both within- and between-person dynamics. I then briefly outline two empirical studies where I demonstrate how the Boolean network method can be applied to study and control of both within- and between-person dynamics. In Chapter 2, I revisit how dynamical system methods are used to model the nonlinear dynamics of multivariate systems. Despite the interest and advancement of control theory to direct psychological dynamics toward desired goals, control has been less studied and rarely applied in nonlinear psychological systems. We introduce the Boolean network method to address this gap. This method is useful because it can be used to model the nonlinear dynamics in multivariate systems and to develop network control strategies that might be used to manage the system toward a desired state. The Boolean network method is a discrete-time dynamical system method, and we introduce this method in three steps: (1) inference of the temporal relations between multiple binary variables as Boolean functions and construction of Boolean networks in which the binary variables are nodes and the Boolean functions are edges, (2) extraction of attractors based on the inferred dynamics and assignment of desirability for each attractor, and (3) design of network control to direct a psychological system toward a desired attractor by identifying how the Boolean network needs to be updated. To demonstrate how the Boolean network can describe and prescribe control for emotion regulation dynamics, we applied this method to an observational dataset of children's regulation of anger using bidding and/or distraction behavior (N = 120, T = 480 seconds). Network control strategies were designed to move the child into attractors where anger is OFF. The sample shows heterogeneous emotion regulation dynamics across children in 22 distinct Boolean networks, and heterogeneous control strategies regarding which behavior to perturb and how to perturb it. The presentation and illustration forward the Boolean network method as a novel method to describe nonlinear dynamics in multivariate psychological systems and a control method to guide nonlinear psychological systems toward desired goals. In Chapter 3, I revisit theories suggesting group processes can induce desired or undesired behavior change in individuals in a group because they are under social influence. Empirical modeling of group processes often assumes the social influence is assimilative only, and network-based interventions that aim to manage group processes and promote desired behavior change does not apply when the social network is fully connected. We introduce the Boolean network method to address these two gaps because it allows both assimilative and repulsive social influence to be modeled simultaneously, and prescribes network control strategies by changing a few group members' behavior regardless of network topology. The Boolean network method is a dynamical system method that models the group-specific temporal relations between group members' behavior as a Boolean network, and also allows for control theory to design group management strategies and direct the groups toward desired behavior. The Boolean network method is applied to empirical data of individuals' self-disclosure behavior in multi-week therapy groups (N = 155, 18 groups, T = 10~16 weeks), to model and manage group-specific processes of self-disclosure. Results show the method can estimate each group member's self-disclosure with error rate of 0.14 (SD = 0.10). Both assimilative and repulsive social influence are found in 14 out of 18 groups. Group-specific network control strategies were designed to elicit the majority of the group self-disclose by encouraging a few group members' self-disclose behavior. This example illustrates the Boolean network as a flexible method that allows for modeling of assimilative and repulsive social influences that simultaneously operate in a group process and design of strategies that can be used to direct the group process to desired states (without manipulating the social ties). This dissertation introduces and forwards the Boolean network method as a method that can be used to describe and control a system's trajectory. The final chapter, Chapter 4, summarizes the contribution of this dissertation in terms of method innovation, theory, data, and potential applications, and begins to elaborate how the method might be extended further. To our knowledge, this is the first application of the Boolean network method in describing and controlling nonlinear psychological processes. The Boolean network method follows the long-standing tradition of using dynamical system methods to explain, model, and predict how complex psychological systems operate and change over time. This dissertation adds to that literature by providing the methodological steps and empirical examples that will enable control system design for nonlinear within- and between-person dynamics. Our demonstration emphasizes the appeal of this method for both theory and practice -- providing simple descriptions and explanations of system dynamics and system control strategies. Altogether, this dissertation forwards and provides access to a useful tool that can help researchers discover, understand, and shape many different kinds of psychological dynamics....



Analysis And Identification Of Boolean Networks Using Harmonic Analysis

Analysis And Identification Of Boolean Networks Using Harmonic Analysis

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Author by : Steffen Schober
Languange Used : en
Release Date : 2011
Publisher by :

ISBN : 3862471810

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