Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called PolII, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e., the asymmetric exclusion processes in the hydrodynamic limit, assuming a Gaussian process prior for the PolII progression rate as a latent variable. Our framework allows us to infer the speed of PolIIs during transcription given their spatial distribution, whilst avoiding the explicit inversion of the system's dynamics. The results may have implications for the understanding of gene expression.
Bayesian inference provides a framework to combine an arbitrary number of model components with shared parameters, allowing joint uncertainty estimation and the use of all available data sources. However, misspecification of any part of the model might propagate to all other parts and lead to unsatisfactory results. Cut distributions have been proposed as a remedy, where the information is prevented from flowing along certain directions. We consider cut distributions from an asymptotic perspective, find the equivalent of the Laplace approximation, and notice a lack of frequentist coverage for the associate credible regions. We propose algorithms based on the Posterior Bootstrap that deliver credible regions with the nominal frequentist asymptotic coverage. The algorithms involve numerical optimization programs that can be performed fully in parallel. The results and methods are illustrated in various settings, such as causal inference with propensity scores and epidemiological studies.
In this work we propose a formal system for fuzzy algebraic reasoning. The sequent calculus we define is based on two kinds of propositions, capturing equality and existence of terms as members of a fuzzy set. We provide a sound semantics for this calculus and show that there is a notion of free model for any theory in this system, allowing us (with some restrictions) to recover models as Eilenberg-Moore algebras for some monad. We will also prove a completeness result: a formula is derivable from a given theory if and only if it is satisfied by all models of the theory. Finally, leveraging results by Milius and Urbat, we give HSP-like characterizations of subcategories of algebras which are categories of models of particular kinds of theories.
We study the entropic Gromov-Wasserstein and its unbalanced version between (unbalanced) Gaussian distributions with different dimensions. When the metric is the inner product, which we refer to as inner product Gromov-Wasserstein (IGW), we demonstrate that the optimal transportation plans of entropic IGW and its unbalanced variant are (unbalanced) Gaussian distributions. Via an application of von Neumann's trace inequality, we obtain closed-form expressions for the entropic IGW between these Gaussian distributions. Finally, we consider an entropic inner product Gromov-Wasserstein barycenter of multiple Gaussian distributions. We prove that the barycenter is a Gaussian distribution when the entropic regularization parameter is small. We further derive a closed-form expression for the covariance matrix of the barycenter.
Generalised Bayesian inference updates prior beliefs using a loss function, rather than a likelihood, and can therefore be used to confer robustness against possible mis-specification of the likelihood. Here we consider generalised Bayesian inference with a Stein discrepancy as a loss function, motivated by applications in which the likelihood contains an intractable normalisation constant. In this context, the Stein discrepancy circumvents evaluation of the normalisation constant and produces generalised posteriors that are either closed form or accessible using standard Markov chain Monte Carlo. On a theoretical level, we show consistency, asymptotic normality, and bias-robustness of the generalised posterior, highlighting how these properties are impacted by the choice of Stein discrepancy. Then, we provide numerical experiments on a range of intractable distributions, including applications to kernel-based exponential family models and non-Gaussian graphical models.
We analyze the information geometric structure of time reversibility for parametric families of irreducible transition kernels of Markov chains. We define and characterize reversible exponential families of Markov kernels, and show that irreducible and reversible Markov kernels form both a mixture family and, perhaps surprisingly, an exponential family in the set of all stochastic kernels. We propose a parametrization of the entire manifold of reversible kernels, and inspect reversible geodesics. We define information projections onto the reversible manifold, and derive closed-form expressions for the e-projection and m-projection, along with Pythagorean identities with respect to information divergence, leading to some new notion of reversiblization of Markov kernels. We show the family of edge measures pertaining to irreducible and reversible kernels also forms an exponential family among distributions over pairs. We further explore geometric properties of the reversible family, by comparing them with other remarkable families of stochastic matrices. Finally, we show that reversible kernels are, in a sense we define, the minimal exponential family generated by the m-family of symmetric kernels, and the smallest mixture family that comprises the e-family of memoryless kernels.
The computational cost of usual Monte Carlo methods for sampling a posteriori laws in Bayesian inference scales linearly with the number of data points. One option to reduce it to a fraction of this cost is to resort to mini-batching in conjunction with unadjusted discretizations of Langevin dynamics, in which case only a random fraction of the data is used to estimate the gradient. However, this leads to an additional noise in the dynamics and hence a bias on the invariant measure which is sampled by the Markov chain. We advocate using the so-called Adaptive Langevin dynamics, which is a modification of standard inertial Langevin dynamics with a dynamical friction which automatically corrects for the increased noise arising from mini-batching. We investigate the practical relevance of the assumptions underpinning Adaptive Langevin (constant covariance for the estimation of the gradient), which are not satisfied in typical models of Bayesian inference, and quantify the bias induced by minibatching in this case. We also show how to extend AdL in order to systematically reduce the bias on the posterior distribution by considering a dynamical friction depending on the current value of the parameter to sample.
Robust statistical data modelling under potential model mis-specification often requires leaving the parametric world for the nonparametric. In the latter, parameters are infinite dimensional objects such as functions, probability distributions or infinite vectors. In the Bayesian nonparametric approach, prior distributions are designed for these parameters, which provide a handle to manage the complexity of nonparametric models in practice. However, most modern Bayesian nonparametric models seem often out of reach to practitioners, as inference algorithms need careful design to deal with the infinite number of parameters. The aim of this work is to facilitate the journey by providing computational tools for Bayesian nonparametric inference. The article describes a set of functions available in the \R package BNPdensity in order to carry out density estimation with an infinite mixture model, including all types of censored data. The package provides access to a large class of such models based on normalized random measures, which represent a generalization of the popular Dirichlet process mixture. One striking advantage of this generalization is that it offers much more robust priors on the number of clusters than the Dirichlet. Another crucial advantage is the complete flexibility in specifying the prior for the scale and location parameters of the clusters, because conjugacy is not required. Inference is performed using a theoretically grounded approximate sampling methodology known as the Ferguson & Klass algorithm. The package also offers several goodness of fit diagnostics such as QQ-plots, including a cross-validation criterion, the conditional predictive ordinate. The proposed methodology is illustrated on a classical ecological risk assessment method called the Species Sensitivity Distribution (SSD) problem, showcasing the benefits of the Bayesian nonparametric framework.
In this paper, we propose a probabilistic physics-guided framework, termed Physics-guided Deep Markov Model (PgDMM). The framework is especially targeted to the inference of the characteristics and latent structure of nonlinear dynamical systems from measurement data, where it is typically intractable to perform exact inference of latent variables. A recently surfaced option pertains to leveraging variational inference to perform approximate inference. In such a scheme, transition and emission functions of the system are parameterized via feed-forward neural networks (deep generative models). However, due to the generalized and highly versatile formulation of neural network functions, the learned latent space is often prone to lack physical interpretation and structured representation. To address this, we bridge physics-based state space models with Deep Markov Models, thus delivering a hybrid modeling framework for unsupervised learning and identification for nonlinear dynamical systems. Specifically, the transition process can be modeled as a physics-based model enhanced with an additive neural network component, which aims to learn the discrepancy between the physics-based model and the actual dynamical system being monitored. The proposed framework takes advantage of the expressive power of deep learning, while retaining the driving physics of the dynamical system by imposing physics-driven restrictions on the side of the latent space. We demonstrate the benefits of such a fusion in terms of achieving improved performance on illustrative simulation examples and experimental case studies of nonlinear systems. Our results indicate that the physics-based models involved in the employed transition and emission functions essentially enforce a more structured and physically interpretable latent space, which is essential to generalization and prediction capabilities.
We develop an inference method for a (sub)vector of parameters identified by conditional moment restrictions, which are implied by economic models such as rational behavior and Euler equations. Building on Bierens (1990), we propose penalized maximum statistics and combine bootstrap inference with model selection. Our method is optimized to be powerful against a set of local alternatives of interest by solving a data-dependent max-min problem for tuning parameter selection. We demonstrate the efficacy of our method by a proof of concept using two empirical examples: rational unbiased reporting of ability status and the elasticity of intertemporal substitution.
This paper presents and analyzes a discontinuous Galerkin method for the compressible three-phase flow problem in porous media. We use a first order time extrapolation which allows us to solve the equations implicitly and sequentially. We show that the discrete problem is well-posed, and obtain a priori error estimates. Our numerical results validate the theoretical results, i.e. the algorithm converges with first order, under different setups that involve variable density and effects of gravity.