Bayesian factor analysis is routinely used for dimensionality reduction in modeling of high-dimensional covariance matrices. Factor analytic decompositions express the covariance as a sum of a low rank and diagonal matrix. In practice, Gibbs sampling algorithms are typically used for posterior computation, alternating between updating the latent factors, loadings, and residual variances. In this article, we exploit a blessing of dimensionality to develop a provably accurate pseudo-posterior for the covariance matrix that bypasses the need for Gibbs or other variants of Markov chain Monte Carlo sampling. Our proposed Factor Analysis with BLEssing of dimensionality (FABLE) approach relies on a first-stage singular value decomposition (SVD) to estimate the latent factors, and then defines a jointly conjugate prior for the loadings and residual variances. The accuracy of the resulting pseudo-posterior for the covariance improves with increasing dimensionality. We show that FABLE has excellent performance in high-dimensional covariance matrix estimation, including producing well calibrated credible intervals, both theoretically and through simulation experiments. We also demonstrate the strength of our approach in terms of accurate inference and computational efficiency by applying it to a gene expression data set.
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We present a novel method for training score-based generative models which uses nonlinear noising dynamics to improve learning of structured distributions. Generalizing to a nonlinear drift allows for additional structure to be incorporated into the dynamics, thus making the training better adapted to the data, e.g., in the case of multimodality or (approximate) symmetries. Such structure can be obtained from the data by an inexpensive preprocessing step. The nonlinear dynamics introduces new challenges into training which we address in two ways: 1) we develop a new nonlinear denoising score matching (NDSM) method, 2) we introduce neural control variates in order to reduce the variance of the NDSM training objective. We demonstrate the effectiveness of this method on several examples: a) a collection of low-dimensional examples, motivated by clustering in latent space, b) high-dimensional images, addressing issues with mode collapse, small training sets, and approximate symmetries, the latter being a challenge for methods based on equivariant neural networks, which require exact symmetries.
Nevanlinna-Pick interpolation problem has been widely studied in recent decades, however, the known algorithm is not simplistic and robust enough. This paper provide a new method to solve the Nevanlinna-Pick interpolation problem with degree constraint. It is based on the covariance extension equation proposed by Byrnes and Lindquist. A reformulation of the Nevanlinna-Pick interpolation problem is achieved and then solved by continuation method. This method need not calculate the initial value and a numerical example illustrates robustness and effciency of the proposed procedure
Inference for functional linear models in the presence of heteroscedastic errors has received insufficient attention given its practical importance; in fact, even a central limit theorem has not been studied in this case. At issue, conditional mean estimates have complicated sampling distributions due to the infinite dimensional regressors, where truncation bias and scaling issues are compounded by non-constant variance under heteroscedasticity. As a foundation for distributional inference, we establish a central limit theorem for the estimated conditional mean under general dependent errors, and subsequently we develop a paired bootstrap method to provide better approximations of sampling distributions. The proposed paired bootstrap does not follow the standard bootstrap algorithm for finite dimensional regressors, as this version fails outside of a narrow window for implementation with functional regressors. The reason owes to a bias with functional regressors in a naive bootstrap construction. Our bootstrap proposal incorporates debiasing and thereby attains much broader validity and flexibility with truncation parameters for inference under heteroscedasticity; even when the naive approach may be valid, the proposed bootstrap method performs better numerically. The bootstrap is applied to construct confidence intervals for centered projections and for conducting hypothesis tests for the multiple conditional means. Our theoretical results on bootstrap consistency are demonstrated through simulation studies and also illustrated with a real data example.
Latent variable models serve as powerful tools to infer underlying dynamics from observed neural activity. However, due to the absence of ground truth data, prediction benchmarks are often employed as proxies. In this study, we reveal the limitations of the widely-used 'co-smoothing' prediction framework and propose an improved few-shot prediction approach that encourages more accurate latent dynamics. Utilizing a student-teacher setup with Hidden Markov Models, we demonstrate that the high co-smoothing model space can encompass models with arbitrary extraneous dynamics within their latent representations. To address this, we introduce a secondary metric -- a few-shot version of co-smoothing. This involves performing regression from the latent variables to held-out channels in the data using fewer trials. Our results indicate that among models with near-optimal co-smoothing, those with extraneous dynamics underperform in the few-shot co-smoothing compared to 'minimal' models devoid of such dynamics. We also provide analytical insights into the origin of this phenomenon. We further validate our findings on real neural data using two state-of-the-art methods: LFADS and STNDT. In the absence of ground truth, we suggest a proxy measure to quantify extraneous dynamics. By cross-decoding the latent variables of all model pairs with high co-smoothing, we identify models with minimal extraneous dynamics. We find a correlation between few-shot co-smoothing performance and this new measure. In summary, we present a novel prediction metric designed to yield latent variables that more accurately reflect the ground truth, offering a significant improvement for latent dynamics inference.
We propose a new simple and explicit numerical scheme for time-homogeneous stochastic differential equations. The scheme is based on sampling increments at each time step from a skew-symmetric probability distribution, with the level of skewness determined by the drift and volatility of the underlying process. We show that as the step-size decreases the scheme converges weakly to the diffusion of interest. We then consider the problem of simulating from the limiting distribution of an ergodic diffusion process using the numerical scheme with a fixed step-size. We establish conditions under which the numerical scheme converges to equilibrium at a geometric rate, and quantify the bias between the equilibrium distributions of the scheme and of the true diffusion process. Notably, our results do not require a global Lipschitz assumption on the drift, in contrast to those required for the Euler--Maruyama scheme for long-time simulation at fixed step-sizes. Our weak convergence result relies on an extension of the theory of Milstein \& Tretyakov to stochastic differential equations with non-Lipschitz drift, which could also be of independent interest. We support our theoretical results with numerical simulations.
Characteristic formulae give a complete logical description of the behaviour of processes modulo some chosen notion of behavioural semantics. They allow one to reduce equivalence or preorder checking to model checking, and are exactly the formulae in the modal logics characterizing classic behavioural equivalences and preorders for which model checking can be reduced to equivalence or preorder checking. This paper studies the complexity of determining whether a formula is characteristic for some finite, loop-free process in each of the logics providing modal characterizations of the simulation-based semantics in van Glabbeek's branching-time spectrum. Since characteristic formulae in each of those logics are exactly the consistent and prime ones, it presents complexity results for the satisfiability and primality problems, and investigates the boundary between modal logics for which those problems can be solved in polynomial time and those for which they become computationally hard. Amongst other contributions, this article also studies the complexity of constructing characteristic formulae in the modal logics characterizing simulation-based semantics, both when such formulae are presented in explicit form and via systems of equations.
Epidemics are inherently stochastic, and stochastic models provide an appropriate way to describe and analyse such phenomena. Given temporal incidence data consisting of, for example, the number of new infections or removals in a given time window, a continuous-time discrete-valued Markov process provides a natural description of the dynamics of each model component, typically taken to be the number of susceptible, exposed, infected or removed individuals. Fitting the SEIR model to time-course data is a challenging problem due incomplete observations and, consequently, the intractability of the observed data likelihood. Whilst sampling based inference schemes such as Markov chain Monte Carlo are routinely applied, their computational cost typically restricts analysis to data sets of no more than a few thousand infective cases. Instead, we develop a sequential inference scheme that makes use of a computationally cheap approximation of the most natural Markov process model. Crucially, the resulting model allows a tractable conditional parameter posterior which can be summarised in terms of a set of low dimensional statistics. This is used to rejuvenate parameter samples in conjunction with a novel bridge construct for propagating state trajectories conditional on the next observation of cumulative incidence. The resulting inference framework also allows for stochastic infection and reporting rates. We illustrate our approach using synthetic and real data applications.
Multivariate probabilistic verification is concerned with the evaluation of joint probability distributions of vector quantities such as a weather variable at multiple locations or a wind vector for instance. The logarithmic score is a proper score that is useful in this context. In order to apply this score to ensemble forecasts, a choice for the density is required. Here, we are interested in the specific case when the density is multivariate normal with mean and covariance given by the ensemble mean and ensemble covariance, respectively. Under the assumptions of multivariate normality and exchangeability of the ensemble members, a relationship is derived which describes how the logarithmic score depends on ensemble size. It permits to estimate the score in the limit of infinite ensemble size from a small ensemble and thus produces a fair logarithmic score for multivariate ensemble forecasts under the assumption of normality. This generalises a study from 2018 which derived the ensemble size adjustment of the logarithmic score in the univariate case. An application to medium-range forecasts examines the usefulness of the ensemble size adjustments when multivariate normality is only an approximation. Predictions of vectors consisting of several different combinations of upper air variables are considered. Logarithmic scores are calculated for these vectors using ECMWF's daily extended-range forecasts which consist of a 100-member ensemble. The probabilistic forecasts of these vectors are verified against operational ECMWF analyses in the Northern mid-latitudes in autumn 2023. Scores are computed for ensemble sizes from 8 to 100. The fair logarithmic scores of ensembles with different cardinalities are very close, in contrast to the unadjusted scores which decrease considerably with ensemble size. This provides evidence for the practical usefulness of the derived relationships.
The Fisher-Rao distance between two probability distributions of a statistical model is defined as the Riemannian geodesic distance induced by the Fisher information metric. In order to calculate the Fisher-Rao distance in closed-form, we need (1) to elicit a formula for the Fisher-Rao geodesics, and (2) to integrate the Fisher length element along those geodesics. We consider several numerically robust approximation and bounding techniques for the Fisher-Rao distances: First, we report generic upper bounds on Fisher-Rao distances based on closed-form 1D Fisher-Rao distances of submodels. Second, we describe several generic approximation schemes depending on whether the Fisher-Rao geodesics or pregeodesics are available in closed-form or not. In particular, we obtain a generic method to guarantee an arbitrarily small additive error on the approximation provided that Fisher-Rao pregeodesics and tight lower and upper bounds are available. Third, we consider the case of Fisher metrics being Hessian metrics, and report generic tight upper bounds on the Fisher-Rao distances using techniques of information geometry. Uniparametric and biparametric statistical models always have Fisher Hessian metrics, and in general a simple test allows to check whether the Fisher information matrix yields a Hessian metric or not. Fourth, we consider elliptical distribution families and show how to apply the above techniques to these models. We also propose two new distances based either on the Fisher-Rao lengths of curves serving as proxies of Fisher-Rao geodesics, or based on the Birkhoff/Hilbert projective cone distance. Last, we consider an alternative group-theoretic approach for statistical transformation models based on the notion of maximal invariant which yields insights on the structures of the Fisher-Rao distance formula which may be used fruitfully in applications.
Similar to the notion of h-adaptivity, where the discretization resolution is adaptively changed, I propose the notion of model adaptivity, where the underlying model (the governing equations) is adaptively changed in space and time. Specifically, this work introduces a hybrid and adaptive coupling of a 3D bulk fluid flow model with a 2D thin film flow model. As a result, this work extends the applicability of existing thin film flow models to complex scenarios where, for example, bulk flow develops into thin films after striking a surface. At each location in space and time, the proposed framework automatically decides whether a 3D model or a 2D model must be applied. Using a meshless approach for both 3D and 2D models, at each particle, the decision to apply a 2D or 3D model is based on the user-prescribed resolution and a local principal component analysis. When a particle needs to be changed from a 3D model to 2D, or vice versa, the discretization is changed, and all relevant data mapping is done on-the-fly. Appropriate two-way coupling conditions and mass conservation considerations between the 3D and 2D models are also developed. Numerical results show that this model adaptive framework shows higher flexibility and compares well against finely resolved 3D simulations. In an actual application scenario, a 3 factor speed up is obtained, while maintaining the accuracy of the solution.
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