Probabilistic Boolean Networks

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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.

Current Developments in Mathematical Biology

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Publisher : World Scientific
ISBN 13 : 9812700153
Total Pages : 181 pages
Book Rating : 4.8/5 (127 download)

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Book Synopsis Current Developments in Mathematical Biology by : Kazem Mahdavi

Download or read book Current Developments in Mathematical Biology written by Kazem Mahdavi and published by World Scientific. This book was released on 2007 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of papers on various areas of current interest in mathematical biology, such as epidemic disease modeling, including the effects of vaccination and strain replacement; immunology, such as T-Cell dynamics and the mechanism of phagocytosis; knot theory; DNA computation; and Boolean networks.

Analysis and Control of Boolean Networks

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Publisher : Springer Science & Business Media
ISBN 13 : 0857290975
Total Pages : 474 pages
Book Rating : 4.8/5 (572 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 Science & Business Media. This book was released on 2010-11-23 with total page 474 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.

Dynamics of Boolean Networks

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Publisher :
ISBN 13 :
Total Pages : 110 pages
Book Rating : 4.:/5 (51 download)

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Book Synopsis Dynamics of Boolean Networks by : Florian Greil

Download or read book Dynamics of Boolean Networks written by Florian Greil and published by . This book was released on 2009 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Annealed Dynamics of Boolean Networks

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Publisher :
ISBN 13 : 9789521516580
Total Pages : 108 pages
Book Rating : 4.5/5 (165 download)

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Book Synopsis Annealed Dynamics of Boolean Networks by : Pauli Rämö

Download or read book Annealed Dynamics of Boolean Networks written by Pauli Rämö and published by . This book was released on 2006 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Information Processing and Biological Systems

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Publisher : Springer Science & Business Media
ISBN 13 : 3642196217
Total Pages : 234 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis Information Processing and Biological Systems by : Samuli Niiranen

Download or read book Information Processing and Biological Systems written by Samuli Niiranen and published by Springer Science & Business Media. This book was released on 2011-03-10 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living beings require constant information processing for survival. In cells, information is being processed and propagated at various levels, from the gene regulatory network to chemical pathways, to the interaction with the environment. How this is achieved and how information is coded is still poorly understood. For example, what a cell interprets as information in the temporal level of an mRNA and what is interpreted as noise remains an open question. Recently, information theoretical methods and other tools, developed in the context of engineering and natural sciences, have been applied to study diverse biological processes. This book covers the latest findings on how information is processed in various biological processes, ranging from information processing and propagation in gene regulatory networks to information processing in natural language. An overview is presented of the state-of-the-art in information processing in biological systems and the opinion of current leaders in this research field on future research directions.

An Introduction to Semi-tensor Product of Matrices and Its Applications

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Author :
Publisher : World Scientific
ISBN 13 : 9814374695
Total Pages : 610 pages
Book Rating : 4.8/5 (143 download)

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Book Synopsis An Introduction to Semi-tensor Product of Matrices and Its Applications by : Dai-Zhan Cheng

Download or read book An Introduction to Semi-tensor Product of Matrices and Its Applications written by Dai-Zhan Cheng and published by World Scientific. This book was released on 2012 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: A generalization of Conventional Matrix Product (CMP), called the Semi-Tensor Product (STP), is proposed. It extends the CMP to two arbitrary matrices and maintains all fundamental properties of CMP. In addition, it has a pseudo-commutative property, which makes it more superior to CMP. The STP was proposed by the authors to deal with higher-dimensional data as well as multilinear mappings. After over a decade of development, STP has been proven to be a powerful tool in dealing with nonlinear and logical calculations.This book is a comprehensive introduction to the theory of STP and its various applications, including logical function, fuzzy control, Boolean networks, analysis and control of nonlinear systems, amongst others.

Dynamics of Complex Autonomous Boolean Networks

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Publisher : Springer
ISBN 13 : 3319135783
Total Pages : 208 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Dynamics of Complex Autonomous Boolean Networks by : David P. Rosin

Download or read book Dynamics of Complex Autonomous Boolean Networks written by David P. Rosin and published by Springer. This book was released on 2014-12-31 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis focuses on the dynamics of autonomous Boolean networks, on the basis of Boolean logic functions in continuous time without external clocking. These networks are realized with integrated circuits on an electronic chip as a field programmable gate array (FPGA) with roughly 100,000 logic gates, offering an extremely flexible model system. It allows fast and cheap design cycles and large networks with arbitrary topologies and coupling delays. The author presents pioneering results on theoretical modeling, experimental realization, and selected applications. In this regard, three classes of novel dynamic behavior are investigated: (i) Chaotic Boolean networks are proposed as high-speed physical random number generators with high bit rates. (ii) Networks of periodic Boolean oscillators are home to long-living transient chimera states, i.e., novel patterns of coexisting domains of spatially coherent (synchronized) and incoherent (desynchronized) dynamics. (iii) Excitable networks exhibit cluster synchronization and can be used as fast artificial Boolean neurons whose spiking patterns can be controlled. This work presents the first experimental platform for large complex networks, which will facilitate exciting future developments.

Boolean Networks as Predictive Models of Emergent Biological Behaviors

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Publisher : Cambridge University Press
ISBN 13 : 1009292943
Total Pages : 118 pages
Book Rating : 4.0/5 (92 download)

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Book Synopsis Boolean Networks as Predictive Models of Emergent Biological Behaviors by : Jordan C. Rozum

Download or read book Boolean Networks as Predictive Models of Emergent Biological Behaviors written by Jordan C. Rozum and published by Cambridge University Press. This book was released on 2024-03-28 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions – from molecules in gene regulatory networks to species in ecological networks – and the often-incomplete state of system knowledge, such as the unknown values of kinetic parameters for biochemical reactions. Boolean networks have emerged as a powerful tool for modeling these systems. This Element provides a methodological overview of Boolean network models of biological systems. After a brief introduction, the authors describe the process of building, analyzing, and validating a Boolean model. They then present the use of the model to make predictions about the system's response to perturbations and about how to control its behavior. The Element emphasizes the interplay between structural and dynamical properties of Boolean networks and illustrates them in three case studies from disparate levels of biological organization.

The Complexity of Boolean Networks

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Publisher :
ISBN 13 :
Total Pages : 526 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis The Complexity of Boolean Networks by : Paul E. Dunne

Download or read book The Complexity of Boolean Networks written by Paul E. Dunne and published by . This book was released on 1988 with total page 526 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Exploring Discrete Dynamics

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Publisher : Luniver Press
ISBN 13 : 1905986319
Total Pages : 538 pages
Book Rating : 4.9/5 (59 download)

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Book Synopsis Exploring Discrete Dynamics by : Andrew Wuensche

Download or read book Exploring Discrete Dynamics written by Andrew Wuensche and published by Luniver Press. This book was released on 2011 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: EXPLORING DISCRETE DYNAMICS is a comprehensive guide to studying cellular automata and discrete dynamical networks with the classic software Discrete Dynamics Laboratory (DDLab). These collective networks are at the core of complexity and emergent self-organisation. With interactive graphics, DDLab is able to explore an huge diversity of behaviour -- mostly terra incognita -- space-time patters, but also basins of attraction, mathematical objects representing the convergent flow in state-space. Applications range within physics, mathematics, biology, cognition, society, economics and computation, and more specifically in neural and genetic networks, artificial life, and a theory of memory.

Handbook on Biological Networks

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Publisher : World Scientific
ISBN 13 : 9812838791
Total Pages : 465 pages
Book Rating : 4.8/5 (128 download)

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Book Synopsis Handbook on Biological Networks by : Stefano Boccaletti

Download or read book Handbook on Biological Networks written by Stefano Boccaletti and published by World Scientific. This book was released on 2010 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networked systems are all around us. The accumulated evidence of systems as complex as a cell cannot be fully understood by studying only their isolated constituents, giving rise to a new area of interest in research ? the study of complex networks. In a broad sense, biological networks have been one of the most studied networks, and the field has benefited from many important contributions. By understanding and modeling the structure of a biological network, a better perception of its dynamical and functional behavior is to be expected. This unique book compiles the most relevant results and novel insights provided by network theory in the biological sciences, ranging from the structure and dynamics of the brain to cellular and protein networks and to population-level biology.

Reviews of Nonlinear Dynamics and Complexity

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Publisher : John Wiley & Sons
ISBN 13 : 9783527407293
Total Pages : 234 pages
Book Rating : 4.4/5 (72 download)

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Book Synopsis Reviews of Nonlinear Dynamics and Complexity by : Heinz Georg Schuster

Download or read book Reviews of Nonlinear Dynamics and Complexity written by Heinz Georg Schuster and published by John Wiley & Sons. This book was released on 2008-06-09 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Adopting a cross-disciplinary approach, the review character of this monograph sets it apart from specialized journals. The editor is advised by a first-class board of international scientists, such that the carefully selected and invited contributions represent the latest and most relevant findings. The resulting review enables both researchers and newcomers in life science, physics, and chemistry to access the most important results in this field, using a common language.

Gene Network Inference

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Publisher : Springer Science & Business Media
ISBN 13 : 3642451616
Total Pages : 135 pages
Book Rating : 4.6/5 (424 download)

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Book Synopsis Gene Network Inference by : Alberto Fuente

Download or read book Gene Network Inference written by Alberto Fuente and published by Springer Science & Business Media. This book was released on 2014-01-03 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.

Algebraic Biology

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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.

Use Boolean Network to Model and Control Within- and Between-Person Dynamics

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Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (119 download)

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Book Synopsis Use Boolean Network to Model and Control Within- and Between-Person Dynamics by : Xiao Yang

Download or read book Use Boolean Network to Model and Control Within- and Between-Person Dynamics written by Xiao Yang and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Complex Systems Dynamics (volume Ii)

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Author :
Publisher : CRC Press
ISBN 13 : 0429717563
Total Pages : 209 pages
Book Rating : 4.4/5 (297 download)

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Book Synopsis Complex Systems Dynamics (volume Ii) by : Gerard Weisbuch

Download or read book Complex Systems Dynamics (volume Ii) written by Gerard Weisbuch and published by CRC Press. This book was released on 2019-03-01 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an accessible introduction to complex systems viewed as networks of automata, using primarily examples drawn from the physics of disordered systems, neural networks, and the origins of life. It is helpful for readers with a university education in science or engineering.