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.

In 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.

The sooner and later waiting time problems have been extensively studied and applied in various areas of statistics and applied probability. In this paper, we give a comprehensive study of ordered series and later waiting time distributions of a number of simple patterns with respect to nonoverlapping and overlapping counting schemes in a sequence of Markov dependent multistate trials. Exact distributions and probability generating functions are derived by using the finite Markov chain imbedding technique. Examples are given to illustrate our results.

Consider a sequence of outcomes from Markov dependent two-state (success-failure) trials. In this paper, the exact distributions are derived for three longest-run statistics: the longest failure run, longest success run, and the maximum of the two. The method of finite Markov chain imbedding is used to obtain these exact distributions, and their bounds and large deviation approximation are also studied. Numerical comparisons among the exact distributions, bounds, and approximations are provided to illustrate the theoretical results. With some modifications, we show that the results can be easily extended to Markov dependent multistate trials.

Probability generation functions of waiting time distributions of runs and patterns have been used successfully in various areas of statistics and applied probability. In this paper, we provide a simple way to obtain the probability generating functions for waiting time distributions of compound patterns by using the finite Markov chain imbedding method. We also study the characters of waiting time distributions for compound patterns. A computer algorithm based on Markov chain imbedding technique has been developed for automatically computing the distribution, probability generating function, and mean of waiting time for a compound pattern.

Let be the scan statistic of window size r for a sequence of n bistate trials . The scan statistic Sn(r) has been successfully used in various fields of applied probability and statistics, and its distribution has been studied extensively in the literature. Currently, all existing formulae for the distribution of Sn(r) are rather complex, and they can only be numerically implemented when is a sequence of Bernoulli trials, the window size r is less than 20 and the length of the sequence n is not too large. Hence, these formulae have been limiting the practical applications of the scan statistic. In this article, we derive a simple and effective formula for the distribution of Sn(r) via the finite Markov chain embedding technique to overcome some of the limitations of the existing complex formulae. This new formula can be applied when is either a sequence of Bernoulli trials or a sequence of Markov dependent bistate trials. Selected numerical examples are given to illustrate our results.

In this paper we consider a class of reliability structures which can be efficiently described through (imbedded in) finite Markov chains. Some general results are provided for the reliability evaluation and generating functions of such systems. Finally, it is shown that a great variety of well known reliability structures can be accommodated in this general framework, and certain properties of those structures are obtained on using their Markov chain imbedding description.

We give formulas for updating both the steady-state probability distribution and the fundamental matrices of a singularly perturbed Markov chain. This formula generalizes Schweitzer's regular perturbation formulas to the case of singular perturbations.

Let Y1, · ··, Yn be a finite Markov chain and let f be a binary value function defined over the state space of the Y's. We study the reliability of general series system having the structure function φ (Y) = min {f(Y1), · ··, f(Yn)} and show that, under certain regularity conditions, the reliability of the system tends to a constant c (1 ≥ c ≥ 0), where c often has the form c = exp {–λ}.

A direct proof of the expression for the limit probability generating function (p.g.f.) of the sum of Markov Bernoulli random variables is outlined. This depends on the larger eigenvalue of the transition probability matrix of their Markov chain.