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Register a new userSlack Reactants: A State-Space Truncation Framework to Estimate Quantitative Behavior of the Chemical Master Equation
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State space truncation methods are widely used to approximate solutions of the chemical master equation. While most methods of this kind focus on truncating the state space directly, in this work we propose modifying the underlying chemical reaction network by introducing emph{slack reactants} that indirectly truncate the state space. More specifically, slack reactants introduce an expanded chemical reaction network and impose a truncation scheme based on user defined properties, such as mass-conservation. This network structure allows us to prove inheritance of special properties of the original model, such as irreducibility and complex balancing. We use the network structure imposed by slack reactants to prove the convergence of the stationary distribution and first arrival times. We then provide examples comparing our method with the stationary finite state projection and finite buffer methods. Our slack reactant system appears to be more robust than some competing methods with respect to calculating first arrival times.
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The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with uncontrolled errors. Here, we introduce mathematical programming approaches that yield approximations of these distributions with computable error bounds which enable the verification of their accuracy. First, we use semidefinite programming to compute increasingly tighter upper and lower bounds on the moments of the stationary distributions for networks with rational propensities. Second, we use these moment bounds to formulate linear programs that yield convergent upper and lower bounds on the stationary distributions themselves, their marginals and stationary averages. The bounds obtained also provide a computational test for the uniqueness of the distribution. In the unique case, the bounds form an approximation of the stationary distribution with a computable bound on its error. In the non-unique case, our approach yields converging approximations of the ergodic distributions. We illustrate our methodology through several biochemical examples taken from the literature: Schlogls model for a chemical bifurcation, a two-dimensional toggle switch, a model for bursty gene expression, and a dimerisation model with multiple stationary distributions.
We present results of existence, regularity and uniqueness of solutions of the master equation associated with the mean field planning problem in the finite state space case, in the presence of a common noise. The results hold under monotonicity assumptions, which are used crucially in the different proofs of the paper. We also make a link with the trajectories induced by the solution of the master equation and start a discussion on the case of boundary conditions.
Mean field games (MFGs) describe the limit, as $n$ tends to infinity, of stochastic differential games with $n$ players interacting with one another through their common empirical distribution. Under suitable smoothness assumptions that guarantee uniqueness of the MFG equilibrium, a form of law of large of numbers (LLN), also known as propagation of chaos, has been established to show that the MFG equilibrium arises as the limit of the sequence of empirical measures of the $n$-player game Nash equilibria, including the case when player dynamics are driven by both idiosyncratic and common sources of noise. The proof of convergence relies on the so-called master equation for the value function of the MFG, a partial differential equation on the space of probability measures. In this work, under additional assumptions, we establish a functional central limit theorem (CLT) that characterizes the limiting fluctuations around the LLN limit as the unique solution of a linear stochastic PDE. The key idea is to use the solution to the master equation to construct an associated McKean-Vlasov interacting $n$-particle system that is sufficiently close to the Nash equilibrium dynamics of the $n$-player game for large $n$. We then derive the CLT for the latter from the CLT for the former. Along the way, we obtain a new multidimensional CLT for McKean-Vlasov systems. We also illustrate the broader applicability of our methodology by applying it to establish a CLT for a specific linear-quadratic example that does not satisfy our main assumptions, and we explicitly solve the resulting stochastic PDE in this case.
We use a simple N-player stochastic game with idiosyncratic and common noises to introduce the concept of Master Equation originally proposed by Lions in his lectures at the Coll`ege de France. Controlling the limit N tends to the infinity of the explicit solution of the N-player game, we highlight the stochastic nature of the limit distributions of the states of the players due to the fact that the random environment does not average out in the limit, and we recast the Mean Field Game (MFG) paradigm in a set of coupled Stochastic Partial Differential Equations (SPDEs). The first one is a forward stochastic Kolmogorov equation giving the evolution of the conditional distributions of the states of the players given the common noise. The second is a form of stochastic Hamilton Jacobi Bellman (HJB) equation providing the solution of the optimization problem when the flow of conditional distributions is given. Being highly coupled, the system reads as an infinite dimensional Forward Backward Stochastic Differential Equation (FBSDE). Uniqueness of a solution and its Markov property lead to the representation of the solution of the backward equation (i.e. the value function of the stochastic HJB equation) as a deterministic function of the solution of the forward Kolmogorov equation, function which is usually called the decoupling field of the FBSDE. The (infinite dimensional) PDE satisfied by this decoupling field is identified with the textit{master equation}. We also show that this equation can be derived for other large populations equilibriums like those given by the optimal control of McKean-Vlasov stochastic differential equations. The paper is written more in the style of a review than a technical paper, and we spend more time and energy motivating and explaining the probabilistic interpretation of the Master Equation, than identifying the most general set of assumptions under which our claims are true.
Purpose: To develop an automated machine-learning-based method for the discovery of rapid and quantitative chemical exchange saturation transfer (CEST) MR fingerprinting acquisition and reconstruction protocols. Methods: An MR physics governed AI system was trained to generate optimized acquisition schedules and the corresponding quantitative reconstruction neural-network. The system (termed AutoCEST) is composed of a CEST saturation block, a spin dynamics module, and a deep reconstruction network, all differentiable and jointly connected. The method was validated using a variety of chemical exchange phantoms and an in-vivo mouse brain at 9.4T. Results: The acquisition times for AutoCEST optimized schedules ranged from 35-71s, with a quantitative image reconstruction time of only 29 ms. The resulting exchangeable proton concentration maps for the phantoms were in good agreement with the known solute concentrations for AutoCEST sequences (mean absolute error = 2.42 mM; Pearsons r=0.992 , p$<$0.0001), but not for an unoptimized sequence (mean absolute error = 65.19 mM; Pearsons r=-0.161, p=0.522). Similarly, improved exchange rate agreement was observed between AutoCEST and quantification of exchange using saturation power (QUESP) methods (mean absolute error: 35.8 Hz, Pearsons r=0.971, p$<$0.0001) compared to an unoptimized schedule and QUESP (mean absolute error = 58.2 Hz; Pearsons r=0.959, p$<$0.0001). The AutoCEST in-vivo mouse brain semi-solid proton volume-fractions were lower in the cortex (12.21$pm$1.37%) compared to the white-matter (19.73 $pm$ 3.30%), as expected, and the amide proton volume-fraction and exchange rates agreed with previous reports. Conclusion: AutoCEST can automatically generate optimized CEST/MT acquisition protocols that can be rapidly reconstructed into quantitative exchange parameter maps.
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