Synchronization of Arbitrarily Switched Boolean Networks

Finite-Horizon Optimal Control of Boolean Control Networks: A Unified Graph-Theoretical Approach

This article investigates the finite-horizon optimal control (FHOC) problem of Boolean control networks (BCNs) from a graph theory perspective. We first formulate two general problems to unify various special cases studied in the literature: 1) the horizon length is a priori fixed and 2) the horizon length is unspecified but finite for given destination states. Notably, both problems can incorporate time-variant costs, which are rarely considered in existing work, and a variety of constraints. The existence of an optimal control sequence is analyzed under mild assumptions. Motivated by BCNs' finite state space and control space, we approach the two general problems intuitively and efficiently under a graph-theoretical framework. A weighted state transition graph and its time-expanded variants are developed, and the equivalence between the FHOC problem and the shortest-path (SP) problem in specific graphs is established rigorously. Two algorithms are developed to find the SP and construct the optimal control sequence for the two problems with reduced computational complexity, though technically, a classical SP algorithm in graph theory is sufficient for all problems. Compared with existing algebraic methods, our graph-theoretical approach can achieve state-of-the-art time efficiency while targeting the most general problems. Furthermore, our approach is the first one capable of solving Problem 2) with time-variant costs. Finally, a genetic network in the bacterium E. coli and a signaling network involved in human leukemia are used to validate the effectiveness of our approach. The results of two common tasks for both networks show that our approach can dramatically reduce the running time. Python implementation of our algorithms is available at GitHub https://github.com/ShuhuaGao/FHOC.

Policy Iteration Approach to the Infinite Horizon Average Optimal Control of Probabilistic Boolean Networks

This article studies the optimal control of probabilistic Boolean control networks (PBCNs) with the infinite horizon average cost criterion. By resorting to the semitensor product (STP) of matrices, a nested optimality equation for the optimal control problem of PBCNs is proposed. The Laurent series expression technique and the Jordan decomposition method derive a novel policy iteration-type algorithm, where finite iteration steps can provide the optimal state feedback law, which is presented. Finally, the intervention problem of the probabilistic Ara operon in E. coil, as a biological application, is solved to demonstrate the effectiveness and feasibility of the proposed theoretical approach and algorithms.

Target Controllability in Multilayer Networks via Minimum-Cost Maximum-Flow Method

In this article, to maximize the dimension of controllable subspace, we consider target controllability problem with maximum covered nodes set in multiplex networks. We call such an issue as maximum-cost target controllability problem. Likewise, minimum-cost target controllability problem is also introduced which is to find minimum covered node set and driver node set. To address these two issues, we first transform them into a minimum-cost maximum-flow problem based on graph theory. Then an algorithm named target minimum-cost maximum-flow (TMM) is proposed. It is shown that the proposed TMM ensures the target nodes in multiplex networks to be controlled with the minimum number of inputs as well as the maximum (minimum) number of covered nodes. Simulation results on Erdős-Rényi (ER-ER) networks, scale-free (SF-SF) networks, and real-life networks illustrate satisfactory performance of the TMM.

Stability and Stabilization in Probability of Probabilistic Boolean Networks

This article studies the stability in probability of probabilistic Boolean networks and stabilization in the probability of probabilistic Boolean control networks. To simulate more realistic cellular systems, the probability of stability/stabilization is not required to be a strict one. In this situation, the target state is indefinite to have a probability of transferring to itself. Thus, it is a challenging extension of the traditional probability-one problem, in which the self-transfer probability of the target state must be one. Some necessary and sufficient conditions are proposed via the semitensor product of matrices. Illustrative examples are also given to show the effectiveness of the derived results.

Tractable Learning and Inference for Large-Scale Probabilistic Boolean Networks

Probabilistic Boolean networks (PBNs) have previously been proposed so as to gain insights into complex dynamical systems. However, identification of large networks and their underlying discrete Markov chain which describes their temporal evolution still remains a challenge. In this paper, we introduce an equivalent representation for PBNs, the stochastic conjunctive normal form network (SCNFN), which enables a scalable learning algorithm and helps predict long-run dynamic behavior of large-scale systems. State-of-the-art methods turn out to be 400 times slower for middle-sized networks (i.e., containing 100 nodes) and incapable of terminating for large networks (i.e., containing 1000 nodes) compared to the SCNFN-based learning, when attempting to achieve comparable accuracy. In addition, in contrast to the currently used methods which introduce strict restrictions on the structure of the learned PBNs, the hypothesis space of our training paradigm is the set of all possible PBNs. Moreover, SCNFNs enable efficient sampling so as to statistically infer multistep transition probabilities which can provide information on the activity levels of individual nodes in the long run. Extensive experimental results showcase the scalability of the proposed approach both in terms of sample and runtime complexity. In addition, we provide examples to study large and complex cell signaling networks to show the potential of our model. Finally, we suggest several directions for future research on model variations, theoretical analysis, and potential applications of SCNFNs.

Fast-Time Stability of Temporal Boolean Networks

In real systems, most of the biological functionalities come from the fact that the connections are not active all the time. Based on the fact, temporal Boolean networks (TBNs) are proposed in this paper, and the fast-time stability is analyzed via semi-tensor product (STP) of matrices and incidence matrices. First, the algebraic form of a TBN is obtained based on the STP method, and one necessary and sufficient condition for global fast-time stability is presented. Moreover, incidence matrices are used to obtain several sufficient conditions, which reduce the computational complexity from O(n2ⁿ) (exponential type) to O(n⁴) (polynomial type) compared with the STP method. In addition, the global fast-time stabilization of TBNs is considered, and pinning controllers are designed based on the neighbors of controlled nodes rather than all the nodes. Finally, the local fast-time stability of TBNs is considered based on the incidence matrices as well. Several examples are provided to illustrate the effectiveness of the obtained results.

Function Perturbation Impact on Feedback Stabilization of Boolean Control Networks

Function perturbation analysis of Boolean networks is an important topic in the study of gene regulation due to gene mutation or immeasurable variables. This brief studies the function perturbation impact on feedback stabilization of Boolean control networks (BCNs) by using the algebraic state space representation approach. First, the state feedback stabilization control design of BCNs is recalled and the function perturbation problem is formulated. Second, given a state feedback stabilizer, it is robust to the considered function perturbation if one of the following three cases happens: 1) the block where the function perturbation occurs is different from the block which is affected by the state feedback stabilizer (Case 1); 2) when Case 1 does not happen, the perturbed column converges to the equilibrium faster than the original column (Case 2); 3) when Cases 1 and 2 do not happen, the perturbed column does not belong to the reachable set of the original column (Case 3). Third, when the perturbed column belongs to the reachable set of the original column, a constructive procedure is proposed to modify the given state feedback stabilizer to be robust to the function perturbation. Finally, the obtained new results are applied to the function perturbation analysis of lactose operon in Escherichia coli. The main novelty of this brief is to develop a new theoretical framework for the robustness of feedback controllers of BCNs with respect to function perturbation, which is not solved in the existing literature.

Swarming Behavior of Multiple Euler-Lagrange Systems With Cooperation-Competition Interactions: An Auxiliary System Approach

In this paper, the swarming behavior of multiple Euler-Lagrange systems with cooperation-competition interactions is investigated, where the agents can cooperate or compete with each other and the parameters of the systems are uncertain. The distributed stabilization problem is first studied, by introducing an auxiliary system to each agent, where the common assumption that the cooperation-competition network satisfies the digon sign-symmetry condition is removed. Based on the input-output property of the auxiliary system, it is found that distributed stabilization can be achieved provided that the cooperation subnetwork is strongly connected and the parameters of the auxiliary system are chosen appropriately. Furthermore, as an extension, a distributed consensus tracking problem of the considered multiagent systems is discussed, where the concept of equi-competition is introduced and a new pinning control strategy is proposed based on the designed auxiliary system. Finally, illustrative examples are provided to show the effectiveness of the theoretical analysis.

Event-Triggered Control for the Disturbance Decoupling Problem of Boolean Control Networks

This paper investigates the disturbance decoupling problem (DDP) of Boolean control networks (BCNs) by event-triggered control. Using the semi-tensor product of matrices, algebraic forms of BCNs can be achieved, based on which, event-triggered controllers are designed to solve the DDP of BCNs. In addition, the DDP of Boolean partial control networks is also derived by event-triggered control. Finally, two illustrative examples demonstrate the effectiveness of proposed methods.

Stability and Guaranteed Cost Analysis of Time-Triggered Boolean Networks

This paper investigates stability and guaranteed cost of time-triggered Boolean networks (BNs) based on the semitensor product of matrices. The time triggering is generated by mode-dependent average dwell-time switching signals in the BNs. With the help of the copositive Lyapunov function, a sufficient condition is derived to ensure that the considered network is globally stable under a designed average dwell-time switching signal. Subsequently, an infinite time cost function is further discussed and its bound is presented according to the obtained stability result. Numerical examples are finally given to show the feasibility of the theoretical results.

Model Approximation for Switched Genetic Regulatory Networks

The model approximation problem is studied in this paper for switched genetic regulatory networks (GRNs) with time-varying delays. We focus on constructing a reduced-order model to approximate the high-order GRNs considered under the switching signal subject to certain constraints, such that the approximation error system between the original and reduced-order systems is exponentially stable with a disturbance attenuation performance. The stability conditions and the disturbance attenuation performance are established by utilizing two integral inequality bounding techniques and the average dwell-time method for the approximation error system. Then, the solvability conditions for the reduced-order models for the GRNs are also established using the projection method. Furthermore, the model approximation problem can be transferred into a sequential minimization problem that is subject to linear matrix inequality constraints by using the cone complementarity algorithm. Finally, several examples are provided to illustrate the effectiveness and the advantages of the proposed methods.

Single-Input Pinning Controller Design for Reachability of Boolean Networks

This brief is concerned with the problem of a single-input pinning control design for reachability of Boolean networks (BNs). Specifically, the transition matrix of a BN is designed to steer the BN from an initial state to a desirable one. In addition, some nodes are selected as the pinning nodes by solving some logical matrix equations. Furthermore, a single-input pinning control algorithm is given. Eventually, a genetic regulatory network is provided to demonstrate the effectiveness and feasibility of the developed method.

Synchronization for the Realization-Dependent Probabilistic Boolean Networks

This paper investigates the synchronization problem for the realization-dependent probabilistic Boolean networks (PBNs) coupled unidirectionally in the drive-response configuration. The realization of the response PBN is assumed to be uniquely determined by the realization signal generated by the drive PBN at each discrete time instant. First, the drive-response PBNs are expressed in their algebraic forms based on the semitensor product method, and then, a necessary and sufficient condition is presented for the synchronization of the PBNs. Second, by resorting to a newly defined matrix operator, the reachable set from any initial state is expressed by a column vector. Consequently, an easily computable algebraic criterion is derived assuring the synchronization of the drive-response PBNs. Finally, three illustrative examples are employed to demonstrate the applicability and usefulness of the developed theoretical results.

Identifying a Probabilistic Boolean Threshold Network From Samples

This paper studies the problem of exactly identifying the structure of a probabilistic Boolean network (PBN) from a given set of samples, where PBNs are probabilistic extensions of Boolean networks. Cheng et al. studied the problem while focusing on PBNs consisting of pairs of AND/OR functions. This paper considers PBNs consisting of Boolean threshold functions while focusing on those threshold functions that have unit coefficients. The treatment of Boolean threshold functions, and triplets and -tuplets of such functions, necessitates a deepening of the theoretical analyses. It is shown that wide classes of PBNs with such threshold functions can be exactly identified from samples under reasonable constraints, which include: 1) PBNs in which any number of threshold functions can be assigned provided that all have the same number of input variables and 2) PBNs consisting of pairs of threshold functions with different numbers of input variables. It is also shown that the problem of deciding the equivalence of two Boolean threshold functions is solvable in pseudopolynomial time but remains co-NP complete.