Noise can speed Markov chain Monte Carlo estimation and quantum annealing

The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model

Diffusion models are widely applied in population genetics, but their approximate solutions may not accurately capture the exact stochastic process. Nevertheless, this practice was necessary due to computing limitations, particularly for large populations. In this article, we develop the exact Markov chain algebra (MCA) for a discrete haploid multi-allelic Wright-Fisher model (MA-WFM) with a full mutation matrix to address this challenge. A special case of nonzero mutations between multiple alleles have not been captured by previous bi-allelic models. We formulated the mean allele frequencies for asymptotic equilibrium analytically for the tri- and quad-allelic case. We also evaluated the exact time-dependent Markov model numerically, presenting it concisely in terms of diffusion variables. The convergence with increasing population size to a diffusion limit is demonstrated for the population composition distribution. Our model shows that there will never be exact irreversible extinction when there are nonzero mutation rates into each allele and never be an exact irreversible fixation when there are nonzero mutation rates out of each allele. We only present results where there is no complete extinction and no complete fixation. Finally, we present detailed computations for the full Markov process, exposing the behavior near the boundaries for the compositional domains, which are non-singular boundaries according to diffusion theory.

Generalized fluctuation-dissipation theorem for non-Markovian reaction networks

Intracellular biochemical networks often display large fluctuations in the molecule numbers or the concentrations of reactive species, making molecular approaches necessary for system descriptions. For Markovian reaction networks, the fluctuation-dissipation theorem (FDT) has been well established and extensively used in fast evaluation of fluctuations in reactive species. For non-Markovian reaction networks, however, the similar FDT has not been established so far. Here, we present a generalized FDT (gFDT) for a large class of non-Markovian reaction networks where general intrinsic-event waiting-time distributions account for the effect of intrinsic noise and general stochastic reaction delays represent the impact of extrinsic noise from environmental perturbations. The starting point is a generalized chemical master equation (gCME), which describes the probabilistic behavior of an equivalent Markovian reaction network and identifies the structure of the original non-Markovian reaction network in terms of stoichiometries and effective transition rates (extensions of common reaction propensity functions). From this formulation follows directly the solution of the linear noise approximation of the stationary gCME for all the components in the non-Markovian reaction network. While the gFDT can quickly trace noisy sources in non-Markovian reaction networks, example analysis verifies its effectiveness.

A Study on Computational Algorithms in the Estimation of Parameters for a Class of Beta Regression Models

Beta regressions describe the relationship between a response that assumes values in the zero-one range and covariates. These regressions are used for modeling rates, ratios, and proportions. We study computational aspects related to parameter estimation of a class of beta regressions for the mean with fixed precision by maximizing the log-likelihood function with heuristics and other optimization methods. Through Monte Carlo simulations, we analyze the behavior of ten algorithms, where four of them present satisfactory results. These are the differential evolutionary, simulated annealing, stochastic ranking evolutionary, and controlled random search algorithms, with the latter one having the best performance. Using the four algorithms and the optim function of R, we study sets of parameters that are hard to be estimated. We detect that this function fails in most cases, but when it is successful, it is more accurate and faster than the others. The annealing algorithm obtains satisfactory estimates in viable time with few failures so that we recommend its use when the optim function fails.