The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform a statistical operation known as Information Projection or E projection with stochastic mass-action kinetics. Our scheme encodes desired conditional distributions as the equilibrium distributions of reaction systems. To our knowledge this is a first scheme to exploit the inherent stochasticity of reaction networks for information processing. We apply this to the problem of an artificial cell trying to infer its environment from partial observations.
One previous work which has engaged with stochasticity in reaction networks is by @cite_20 . They give a reaction scheme that takes an arbitrary finite probability distribution and encodes it in the stationary distribution of a reaction system. In comparison, we are taking samples from a marginal distribution and encoding the full distribution in terms of the stationary distribution. Thus our scheme allows us to do conditioning and inference.
@cite_20
2039331233 2062626064 2745064379 2951446714
Within systems biology there is an increasing interest in the stochastic behaviour of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformisation technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this study, the authors present an on-the-fly variant of uniformisation, where they improve the original algorithm at the cost of a small approximation error. By means of several examples, the authors show that their approach is particularly well-suited for biochemical reaction networks. We consider the problem of 20 questions with noise for multiple players under the minimum entropy criterion in the setting of stochastic search, with application to target localization. Each player yields a noisy response to a binary query governed by a certain error probability. First, we propose a sequential policy for constructing questions that queries each player in sequence and refines the posterior of the target location. Second, we consider a joint policy that asks all players questions in parallel at each time instant and characterize the structure of the optimal policy for constructing the sequence of questions. This generalizes the single player probabilistic bisection method for stochastic search problems. Third, we prove an equivalence between the two schemes showing that, despite the fact that the sequential scheme has access to a more refined filtration, the joint scheme performs just as well on average. Fourth, we establish convergence rates of the mean-square error and derive error exponents. Finally, we obtain an extension to the case of unknown error probabilities. This framework provides a mathematical model for incorporating a human in the loop for active machine learning systems. 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: Schl "ogl's 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 introduce a novel training principle for probabilistic models that is an alternative to maximum likelihood. The proposed Generative Stochastic Networks (GSN) framework is based on learning the transition operator of a Markov chain whose stationary distribution estimates the data distribution. The transition distribution of the Markov chain is conditional on the previous state, generally involving a small move, so this conditional distribution has fewer dominant modes, being unimodal in the limit of small moves. Thus, it is easier to learn because it is easier to approximate its partition function, more like learning to perform supervised function approximation, with gradients that can be obtained by backprop. We provide theorems that generalize recent work on the probabilistic interpretation of denoising autoencoders and obtain along the way an interesting justification for dependency networks and generalized pseudolikelihood, along with a definition of an appropriate joint distribution and sampling mechanism even when the conditionals are not consistent. GSNs can be used with missing inputs and can be used to sample subsets of variables given the rest. We validate these theoretical results with experiments on two image datasets using an architecture that mimics the Deep Boltzmann Machine Gibbs sampler but allows training to proceed with simple backprop, without the need for layerwise pretraining.