State Estimation for Delayed Genetic Regulatory Networks With Reaction-Diffusion Terms

Single-Cell RNA-Seq Debiased Clustering via Batch Effect Disentanglement

A variety of single-cell RNA-seq (scRNA-seq) clustering methods has achieved great success in discovering cellular phenotypes. However, it remains challenging when the data confounds with batch effects brought by different experimental conditions or technologies. Namely, the data partitions would be biased toward these nonbiological factors. Meanwhile, the batch differences are not always much smaller than true biological variations, hindering the cooperation of batch integration and clustering methods. To overcome this challenge, we propose single-cell RNA-seq debiased clustering (SCDC), an end-to-end clustering method that is debiased toward batch effects by disentangling the biological and nonbiological information from scRNA-seq data during data partitioning. In six analyses, SCDC qualitatively and quantitatively outperforms both the state-of-the-art clustering and batch integration methods in handling scRNA-seq data with batch effects. Furthermore, SCDC clusters data with a linearly increasing running time with respect to cell numbers and a fixed graphics processing unit (GPU) memory consumption, making it scalable to large datasets. The code will be released on Github.

Observer-based resilient dissipativity control for discrete-time memristor-based neural networks with unbounded or bounded time-varying delays

This work focuses on the issue of observer-based resilient dissipativity control of discrete-time memristor-based neural networks (DTMBNNs) with unbounded or bounded time-varying delays. Firstly, the Luenberger observer is designed, and additionally based on the observed states, the observer-based resilient controller is proposed. An augmented system is presented by considering both the error system and the DTMBNNs with the controller. Secondly, a novel sufficient extended exponential dissipativity condition is obtained for the augmented system with unbounded time-varying delays by proposing a system solutions-based estimation approach. This method is based on system solutions and without constructing any Lyapunov-Krasovskii functionals (LKF), thereby reducing the complexity of theoretical derivation and computational workload. In addition, an algorithm is proposed to solve the nonlinear inequalities in the sufficient condition. Thirdly, the sufficient extended exponential dissipativity condition for the augmented system with bounded time-varying delays is also obtained. Finally, the effectiveness of the theoretical results is illustrated through two simulation examples.

State estimation for delayed genetic regulatory networks with reaction diffusion terms and Markovian jump

Robust state estimation for delayed genetic regulatory networks with reaction–diffusion terms and uncertainties terms under Dirichlet boundary conditions is addressed in this article. The main purpose of the problem investigation is to design a novel state observer for estimate the true concentrations of mRNA and protein by available measurement outputs. Based on Lyapunov–Krasovskii functions and linear matrix inequalities (LMI), sufficient conditions are given to ensure the robust stability of the estimation error networks. Two examples are presented to illustrate the effectiveness of the proposed approach.

Random periodic sequence of globally mean-square exponentially stable discrete-time stochastic genetic regulatory networks with discrete spatial diffusions

<abstract><p>This paper regards the dual effects of discrete-space and discrete-time in stochastic genetic regulatory networks via exponential Euler difference and central finite difference. Firstly, the global exponential stability of such discrete networks is investigated by using discrete constant variation formulation. In particular, the optimal exponential convergence rate is explored by solving a nonlinear optimization problem under nonlinear constraints, and an implementable computer algorithm for computing the optimal exponential convergence rate is given. Secondly, random periodic sequence for such discrete networks is investigated based on the theory of semi-flow and metric dynamical systems. The researching findings show that the spatial diffusions with nonnegative intensive coefficients have no influence on global mean square boundedness and stability, random periodicity of the networks. This paper is pioneering in considering discrete spatial diffusions, which provides a research basis for future research on genetic regulatory networks.</p></abstract>

State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications

In this paper, state observation of coupled reaction-diffusion genetic regulatory networks (GRNs) with time-varying delays is investigated under Dirichlet boundary conditions. First, the above GRNs are constructed to model gene regulatory properties, where the feedback regulation function of the GRNs is assumed to exhibit the Hill form and a novel method to deal with it is introduced. Then a time-space sampled-data state observer is designed for the mentioned networks and new criteria are established by utilizing the Lyapunov stability theory and the inequality techniques of Halanay et al. Finally, the validity of the theoretical results is proved by numerical examples.

Global Asymptotic Stability of Competitive Neural Networks with Reaction-Diffusion Terms and Mixed Delays

In this article, a new competitive neural network (CNN) with reaction-diffusion terms and mixed delays is proposed. Because this network system contains reaction-diffusion terms, it belongs to a partial differential system, which is different from the existing classic CNNs. First, taking into account the spatial diffusion effect, we introduce spatial diffusion for CNNs. Furthermore, since the time delay has an essential influence on the properties of the system, we introduce mixed delays including time-varying discrete delays and distributed delays for CNNs. By constructing suitable Lyapunov–Krasovskii functionals and virtue of the theories of delayed partial differential equations, we study the global asymptotic stability for the considered system. The effectiveness and correctness of the proposed CNN model with reaction-diffusion terms and mixed delays are verified by an example. Finally, some discussion and conclusions for recent developments of CNNs are given.

Finite-Time H∞ State Estimation for PDT-Switched Genetic Regulatory Networks With Randomly Occurring Uncertainties

This article is concerned with the problem of finite-time H_∞ state estimation for switched genetic regulatory networks with randomly occurring uncertainties. The persistent dwell-time switching rule, as a more versatile class of switching rules, is considered in this paper. Besides, several random variables that obey the Bernoulli distribution are used to represent randomly occurring uncertainties. The overriding purpose of this article is to design an estimator to ensure that the estimation error system is stochastically finite-time bounded and satisfies the H_∞ performance. Based on this, sufficient conditions for the explicit form of the estimator gains can be obtained by the Lyapunov method. Finally, a numerical example is given to verify the correctness and feasibility of the proposed method.

A Novel Coupled Reaction-Diffusion System for Explainable Gene Expression Profiling

Machine learning (ML)-based algorithms are playing an important role in cancer diagnosis and are increasingly being used to aid clinical decision-making. However, these commonly operate as 'black boxes' and it is unclear how decisions are derived. Recently, techniques have been applied to help us understand how specific ML models work and explain the rational for outputs. This study aims to determine why a given type of cancer has a certain phenotypic characteristic. Cancer results in cellular dysregulation and a thorough consideration of cancer regulators is required. This would increase our understanding of the nature of the disease and help discover more effective diagnostic, prognostic, and treatment methods for a variety of cancer types and stages. Our study proposes a novel explainable analysis of potential biomarkers denoting tumorigenesis in non-small cell lung cancer. A number of these biomarkers are known to appear following various treatment pathways. An enhanced analysis is enabled through a novel mathematical formulation for the regulators of mRNA, the regulators of ncRNA, and the coupled mRNA-ncRNA regulators. Temporal gene expression profiles are approximated in a two-dimensional spatial domain for the transition states before converging to the stationary state, using a system comprised of coupled-reaction partial differential equations. Simulation experiments demonstrate that the proposed mathematical gene-expression profile represents a best fit for the population abundance of these oncogenes. In future, our proposed solution can lead to the development of alternative interpretable approaches, through the application of ML models to discover unknown dynamics in gene regulatory systems.

Sampled-Data State Estimation of Reaction Diffusion Genetic Regulatory Networks via Space-Dividing Approaches

A novel state estimator is designed for genetic regulatory networks with reaction-diffusion terms in this study. First, the diffusion space (where mRNA and protein exist) is divided into several parts and only a point, a line, or a plane, etc., is measured in every subspace to reduce the measurement cost effectively. Then, samplers and network-induced time delay are considered to meet the network transmission requirement. A new criterion to ensure that the estimation error converges to zero is established by using the Lyapunov functional combined with Wirtinger's inequality, reciprocally convex approach, and Halanay's inequality; furthermore, the estimator's parameters are derived by solving linear matrix inequalities. Finally, two simulation examples (including one-dimensional and two-dimensional spaces) are presented to demonstrate the developed scheme's applicability.

Stability analysis of genetic regulatory networks via a linear parameterization approach

This paper investigates the problem of finite-time stability (FTS) for a class of delayed genetic regulatory networks with reaction-diffusion terms. In order to fully utilize the system information, a linear parameterization method is proposed. Firstly, by applying the Lagrange’s mean-value theorem, the linear parameterization method is applied to transform the nonlinear system into a linear one with time-varying bounded uncertain terms. Secondly, a new generalized convex combination lemma is proposed to dispose the relationship of bounded uncertainties with respect to their boundaries. Thirdly, sufficient conditions are established to ensure the FTS by resorting to Lyapunov Krasovskii theory, convex combination technique, Jensen’s inequality, linear matrix inequality, etc. Finally, the simulation verifications indicate the validity of the theoretical results.

Distributed Dissipative State Estimation for Markov Jump Genetic Regulatory Networks Subject to Round-Robin Scheduling

The distributed dissipative state estimation issue of Markov jump genetic regulatory networks subject to round-robin scheduling is investigated in this paper. The system parameters randomly change in the light of a Markov chain. Each node in sensor networks communicates with its neighboring nodes in view of the prescribed network topology graph. The round-robin scheduling is employed to arrange the transmission order to lessen the likelihood of the occurrence of data collisions. The main goal of the work is to design a compatible distributed estimator to assure that the distributed error system is strictly (Λ ₁,Λ ₂,Λ ₃) - γ -stochastically dissipative. By applying the Lyapunov stability theory and a modified matrix decoupling way, sufficient conditions are derived by solving some convex optimization problems. An illustrative example is given to verify the validity of the provided method.

New Method to Global Exponential Stability Analysis for Switched Genetic Regulatory Networks With Mixed Delays

In this paper, the sufficient conditions for the global exponential stability of the switched genetic regulatory networks with mixed time delays are obtained. The proposed method does not need the construction of Lyapunov-Krasovskii functional, but is directly proceeded by the definition of global exponential stability. The derived sufficient conditions can easily be verified by checking the eigenvalues of a constant matrix or solving several simple linear matrix inequalities. Finally, two numerical examples are presented to illustrate that the obtained global exponential stability criteria are available.

Stability and Oscillation Analysis of a Gene Regulatory Network With Multiple Time Delays and Diffusion Rate

In genetic regulatory networks (GRNs), the diffusion rate of mRNA and protein play a key role in regulatory mechanisms of gene expression, especially in translation and transcription. However, the influence of diffusion rate on oscillatory gene expression is not well understood. In this paper, by considering the diffusion rate of mRNA and protein, a novel GRN is proposed. Then, two basic problems of such network, i.e. stability and oscillation, are solved in detail. Moreover, the properties of oscillation are also investigated. it is found that the total biochemistry reaction time can affect the stability of the positive equilibrium and give rise to the oscillation. The diffusion rate of mRNA and proteins have a major impact on the oscillation properties. Finally, two examples not only verify the theoretical results, but also show that a slight diffusion rate increasing may lead to huge change in oscillatory gene expressions.

A Recursive Approach to Quantized H∞ State Estimation for Genetic Regulatory Networks Under Stochastic Communication Protocols

This paper deals with the finite-horizon quantized H_∞ state estimation problem for a class of discrete time-varying genetic regulatory networks with quantization effects under stochastic communication protocols (SCPs). To better reflect the data-driven flavor of today's biological research, the network measurements (typically gigabytes in size by high-throughput sequencing technologies) are transmitted to a remote state estimator via two independent communication networks of limited bandwidths. To lighten the communication loads and avoid undesired data collisions, the measurement outputs are quantized and then transmitted under two SCPs introduced to schedule the large-scale data transmissions. The purpose of this paper is to design a time-varying state estimator such that the error dynamics of the state estimation satisfies a prescribed H_∞ performance requirement over a finite horizon in the presence of nonlinearities, quantization effects, and SCPs. By utilizing the completing-the-square technique, sufficient conditions are derived to ensure the H_∞ estimation performance and the parameters of the state estimator are designed by solving coupled backward recursive Riccati difference equations. A numerical example is given to illustrate the effectiveness of the design scheme of the proposed state estimator.

Prescribed Performance Model-Free Adaptive Integral Sliding Mode Control for Discrete-Time Nonlinear Systems

This paper studies the data-driven prescribed performance control (PPC) problem for a class of discrete-time nonlinear systems in the presence of tracking error constraints. By using the equivalent dynamic linearization technique and constructing a novel transformed error strategy, an adaptive integral sliding mode controller is designed such that the tracking error converges to a predefined neighborhood. Meanwhile, the presented control scheme can effectively ensure that the convergence rate is less than a predefined value and maximum overshoot is not smaller than a preselected constant. In addition, better tracking performance can be achieved by regulating the design parameters appropriately, which is more preferable in the practical application. Contrary to the existing PPC results, the new proposed control law does not use either the plant structure or any knowledge of system dynamics. The efficiency of the proposed control approach is shown with two simulated examples.

Stability Analysis of Genetic Regulatory Networks With General Random Disturbances

This paper establishes the stability criteria for genetic regulatory networks with random disturbances. We assume the nonlinear feedback regulation function to satisfy the sector-like condition and the random perturbation to have a finite second-order moment. First, under the globally Lipschitz condition, the existence and uniqueness of solution to random genetic regulatory networks are considered by exploiting an iterative approximation method. Then, by feat of the random analysis method and matrix technique, sufficient conditions are given to guarantee the noise-to-state stability in mean and globally asymptotic stability in probability, respectively. At last, two simulation examples are exploited in order to verify the validity of the proposed theory.

Reduced- and Full-Order Observers for Delayed Genetic Regulatory Networks

This paper is centered upon the state estimation for delayed genetic regulatory networks. Our aim is at estimating the concentrations of mRNAs and proteins by designing reduced-order and full-order state observers based on available network outputs. We introduce a Lyapunov-Krasovskii functional including quadruplicate integrals, and estimate its derivative by employing the Wirtinger-type integral inequalities, reciprocal convex technique, and convex technique. From which, delay-dependent sufficient conditions, in the form of linear matrix inequalities (LMIs), are investigated to ensure that the resultant error system is asymptotically stable. One can verify these conditions by utilizing the MATLAB Toolboxes LMI or YALMIP. In addition, the gains of reduced-order and full-order observers are represented by the feasible solutions of the LMIs, and thereby, the concrete expressions of the desired reduced-order and full-order state observers are presented. Finally, the simulation results of a numerical example are demonstrated, which explains the validity of the proposed method.

State Estimation for Discrete Time-Delayed Genetic Regulatory Networks With Stochastic Noises Under the Round-Robin Protocols

This paper investigates the problem of state estimation for discrete time-delayed genetic regulatory networks with stochastic process noises and bounded exogenous disturbances under the Round-Robin (RR) protocols. The network measurement outputs obtained by two groups of sensors are transmitted to two remote sub-estimators via two independent communication channels, respectively. To lighten the communication loads of the networks and reduce the occurrence rate of data collisions, two RR protocols are utilized to orchestrate the transmission orders of sensor nodes in two groups, respectively. The error dynamics of the state estimation is governed by a switched system with periodic switching parameters. By constructing a transmission-order-dependent Lyapunov-like functional and utilizing the up-to-date discrete Wirtinger-based inequality together with the reciprocally convex approach, sufficient conditions are established to guarantee the exponentially ultimate boundedness of the estimation error dynamics in mean square with a prescribed upper bound on the decay rate. An asymptotic upper bound of the outputs of the estimation errors in mean square is derived and the estimator parameters are then obtained by minimizing such an upper bound subject to linear matrix inequality constraints. The repressilator model is utilized to illustrate the effectiveness of the designed estimator.