Generating probabilistic Boolean networks from a prescribed transition probability matrix

2009 ◽  
Vol 3 (6) ◽  
pp. 453-464 ◽  
Author(s):  
W.-K. Ching ◽  
X. Chen ◽  
N.-K. Tsing
Keyword(s):  
Transition Probability ◽  
Transition Probability Matrix ◽  
Boolean Networks ◽  
Probabilistic Boolean Networks

On Construction of Sparse Probabilistic Boolean Networks

2012 ◽  
Vol 2 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Xi Chen ◽  
Hao Jiang ◽  
Wai-Ki Ching
Keyword(s):  
Objective Function ◽  
Stationary Distribution ◽  
Transition Probability ◽  
Additional Term ◽  
Control Policy ◽  
Transition Probability Matrix ◽  
Boolean Networks ◽  
Entropy Rate ◽  
Sparse Solution ◽  
Probabilistic Boolean Networks

AbstractIn this paper we envisage building Probabilistic Boolean Networks (PBNs) from a prescribed stationary distribution. This is an inverse problem of huge size that can be subdivided into two parts — viz. (i) construction of a transition probability matrix from a given stationary distribution (Problem ST), and (ii) construction of a PBN from a given transition probability matrix (Problem TP). A generalized entropy approach has been proposed for Problem ST and a maximum entropy rate approach for Problem TP respectively. Here we propose to improve both methods, by considering a new objective function based on the entropy rate with an additional term of La-norm that can help in getting a sparse solution. A sparse solution is useful in identifying the major component Boolean networks (BNs) from the constructed PBN. These major BNs can simplify the identification of the network structure and the design of control policy, and neglecting non-major BNs does not change the dynamics of the constructed PBN to a large extent. Numerical experiments indicate that our new objective function is effective in finding a better sparse solution.

Construction of Probabilistic Boolean Networks from a Prescribed Transition Probability Matrix: A Maximum Entropy Rate Approach

2011 ◽  
Vol 1 (2) ◽  
pp. 132-154 ◽  
Author(s):  
Xi Chen ◽  
Wai-Ki Ching ◽  
Xiao-Shan Chen ◽  
Yang Cong ◽  
Nam-Kiu Tsing
Keyword(s):  
Inverse Problem ◽  
Maximum Entropy ◽  
Regulatory Networks ◽  
Transition Probability ◽  
Transition Probability Matrix ◽  
Boolean Networks ◽  
Genetic Regulatory Networks ◽  
Genomic Research ◽  
Long Run ◽  
Probabilistic Boolean Networks

AbstractModeling genetic regulatory networks is an important problem in genomic research. Boolean Networks (BNs) and their extensions Probabilistic Boolean Networks (PBNs) have been proposed for modeling genetic regulatory interactions. In a PBN, its steady-state distribution gives very important information about the long-run behavior of the whole network. However, one is also interested in system synthesis which requires the construction of networks. The inverse problem is ill-posed and challenging, as there may be many networks or no network having the given properties, and the size of the problem is huge. The construction of PBNs from a given transition-probability matrix and a given set of BNs is an inverse problem of huge size. We propose a maximum entropy approach for the above problem. Newton's method in conjunction with the Conjugate Gradient (CG) method is then applied to solving the inverse problem. We investigate the convergence rate of the proposed method. Numerical examples are also given to demonstrate the effectiveness of our proposed method.

On Generating Optimal Sparse Probabilistic Boolean Networks with Maximum Entropy from a Positive Stationary Distribution

2012 ◽  
Vol 2 (4) ◽  
pp. 353-372 ◽  
Author(s):  
Hao Jiang ◽  
Xi Chen ◽  
Yushan Qiu ◽  
Wai-Ki Ching
Keyword(s):  
Maximum Entropy ◽  
Stationary Distribution ◽  
Sparse Matrix ◽  
Transition Probability ◽  
Transition Probability Matrix ◽  
Boolean Networks ◽  
Efficiency And Effectiveness ◽  
Probabilistic Boolean Networks ◽  
Transition Probability Matrices ◽  
Probability Matrices

Abstract.To understand a genetic regulatory network, two popular mathematical models, Boolean Networks (BNs) and its extension Probabilistic Boolean Networks (PBNs) have been proposed. Here we address the problem of constructing a sparse Probabilistic Boolean Network (PBN) from a prescribed positive stationary distribution. A sparse matrix is more preferable, as it is easier to study and identify the major components and extract the crucial information hidden in a biological network. The captured network construction problem is both ill-posed and computationally challenging. We present a novel method to construct a sparse transition probability matrix from a given stationary distribution. A series of sparse transition probability matrices can be determined once the stationary distribution is given. By controlling the number of nonzero entries in each column of the transition probability matrix, a desirable sparse transition probability matrix in the sense of maximum entropy can be uniquely constructed as a linear combination of the selected sparse transition probability matrices (a set of sparse irreducible matrices). Numerical examples are given to demonstrate both the efficiency and effectiveness of the proposed method.

On calculating extinction probabilities for branching processes in random environments

1969 ◽  
Vol 6 (03) ◽  
pp. 478-492 ◽  
Author(s):  
William E. Wilkinson
Keyword(s):  
Generating Functions ◽  
Infinite Sequence ◽  
Branching Processes ◽  
Transition Probability ◽  
Transition Probability Matrix ◽  
Random Environments ◽  
Real Numbers ◽  
Discrete Time Markov Chain ◽  
Extinction Probabilities ◽  
Image Position

Consider a discrete time Markov chain {Zn } whose state space is the non-negative integers and whose transition probability matrix ║Pij ║ possesses the representation where {Pr }, r = 1,2,…, is a finite or denumerably infinite sequence of non-negative real numbers satisfying , and , is a corresponding sequence of probability generating functions. It is assumed that Z 0 = k, a finite positive integer.

Further enhancement on H∞ sliding mode control design for singular Markovian jump systems with partly known transition probabilities

2021 ◽  
pp. 107754632198920
Author(s):  
Zeinab Fallah ◽  
Mahdi Baradarannia ◽  
Hamed Kharrati ◽  
Farzad Hashemzadeh
Keyword(s):  
Transition Probabilities ◽  
Sliding Mode ◽  
Transition Probability ◽  
Transition Probability Matrix ◽  
Linear Matrix ◽  
Sliding Mode Controller ◽  
Sliding Surface ◽  
Markovian Jump ◽  
Markovian Jump System ◽  
Singular Markovian Jump Systems

This study considers the designing of the H ∞ sliding mode controller for a singular Markovian jump system described by discrete-time state-space realization. The system under investigation is subject to both matched and mismatched external disturbances, and the transition probability matrix of the underlying Markov chain is considered to be partly available. A new sufficient condition is developed in terms of linear matrix inequalities to determine the mode-dependent parameter of the proposed quasi-sliding surface such that the stochastic admissibility with a prescribed H ∞ performance of the sliding mode dynamics is guaranteed. Furthermore, the sliding mode controller is designed to assure that the state trajectories of the system will be driven onto the quasi-sliding surface and remain in there afterward. Finally, two numerical examples are given to illustrate the effectiveness of the proposed design algorithms.

Asynchronous quadratic control for constrained hidden markov jump linear systems with incomplete MTPM and MOCPM

2021 ◽  
Author(s):  
Jin Zhu ◽  
Kai Xia ◽  
Geir E Dullerud
Keyword(s):  
Linear Systems ◽  
Controller Design ◽  
Hidden Markov ◽  
Transition Probability ◽  
Original System ◽  
Transition Probability Matrix ◽  
Markov Jump ◽  
Jump Linear Systems ◽  
Weighting Matrix ◽  
Markov Jump Linear Systems

Abstract This paper investigates the quadratic optimal control problem for constrained Markov jump linear systems with incomplete mode transition probability matrix (MTPM). Considering original system mode is not accessible, observed mode is utilized for asynchronous controller design where mode observation conditional probability matrix (MOCPM), which characterizes the emission between original modes and observed modes is assumed to be partially known. An LMI optimization problem is formulated for such constrained hidden Markov jump linear systems with incomplete MTPM and MOCPM. Based on this, a feasible state-feedback controller can be designed with the application of free-connection weighting matrix method. The desired controller, dependent on observed mode, is an asynchronous one which can minimize the upper bound of quadratic cost and satisfy restrictions on system states and control variables. Furthermore, clustering observation where observed modes recast into several clusters, is explored for simplifying the computational complexity. Numerical examples are provided to illustrate the validity.

Sign in / Sign up

Export Citation Format

Share Document