arXiv subjects

Matti Vihola

Publications and source records attributed to Matti Vihola.

At least 19 recordsLinked to original sources

arXiv2026

Adaptive Riemannian Manifold Hamiltonian Monte Carlo with Hierarchical Metric

Hamiltonian Monte Carlo (HMC) and its dynamic extensions, such as the No-U-Turn Sampler (NUTS), are powerful Markov chain Monte Carlo methods for sampling from complex, high-dimensional probability distributions. Riemannian manifold Hamiltonian Monte Carlo (RMHMC) extends HMC by allowing the mass matrix to depend on position, which can substantially improve mixing but also makes implementation considerably more challenging. In this paper, we study an adaptive hierarchical version of RMHMC that is well suited to many hierarchical sampling problems. A key feature of hierarchical RMHMC is that, unlike general RMHMC, it admits a closed-form explicit leapfrog integrator, enabling efficient implementation and direct use within dynamic HMC methods such as NUTS. We introduce an adaptive scheme that automatically tunes the parameters of the hierarchical mass matrix during simulation. Importantly, the target density need not exhibit any hierarchical or block structure; the hierarchy is instead imposed on the mass matrix as a modeling device to capture the local geometry of the target distribution. Numerical experiments demonstrate appealing empirical performance in high-dimensional Bayesian inference problems.

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arXiv2026

On the complexity of standard and waste-free SMC samplers

We establish finite sample bounds for the error of standard and waste-free SMC samplers. Our results cover estimates of both expectations and normalising constants of the target distributions. We consider first an arbitrary sequence of distributions, and then specialise our results to tempering sequences. We use our results to derive the complexity of SMC samplers with respect to the parameters of the problem, such as $T$, the number of target distributions, in the general case, or $d$, the dimension of the ambient space, in the tempering case. We use these bounds to derive practical recommendations for the implementation of SMC samplers for end users.

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arXiv2025

Iterated sampling importance resampling with adaptive number of proposals

Iterated sampling importance resampling (i-SIR) is a Markov chain Monte Carlo (MCMC) algorithm which is based on $N$ independent proposals. As $N$ grows, its samples become nearly independent, but with an increased computational cost. We discuss a method which finds an approximately optimal number of proposals $N$ in terms of the asymptotic efficiency. The optimal $N$ depends on both the mixing properties of the i-SIR chain and the (parallel) computing costs. Our method for finding an appropriate $N$ is based on an approximate asymptotic variance of the i-SIR, which has similar properties as the i-SIR asymptotic variance, and a generalised i-SIR transition having fractional `number of proposals.' These lead to an adaptive i-SIR algorithm, which tunes the number of proposals automatically during sampling. Our experiments demonstrate that our approximate efficiency and the adaptive i-SIR algorithm have promising empirical behaviour. We also present new theoretical results regarding the i-SIR, such as the convexity of asymptotic variance in the number of proposals, which can be of independent interest.

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arXiv2024

An invitation to adaptive Markov chain Monte Carlo convergence theory

Adaptive Markov chain Monte Carlo (MCMC) algorithms, which automatically tune their parameters based on past samples, have proved extremely useful in practice. The self-tuning mechanism makes them `non-Markovian', which means that their validity cannot be ensured by standard Markov chains theory. Several different techniques have been suggested to analyse their theoretical properties, many of which are technically involved. The technical nature of the theory may make the methods unnecessarily unappealing. We discuss one technique -- based on a martingale decomposition -- with uniformly ergodic Markov transitions. We provide an accessible and self-contained treatment in this setting, and give detailed proofs of the results discussed in the paper, which only require basic understanding of martingale theory and general state space Markov chain concepts. We illustrate how our conditions can accomodate different types of adaptation schemes, and can give useful insight to the requirements which ensure their validity.

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arXiv2023

Mixing time of the conditional backward sampling particle filter

The conditional backward sampling particle filter (CBPF) is a powerful Markov chain Monte Carlo sampler for general state space hidden Markov model (HMM) smoothing. It was proposed as an improvement over the conditional particle filter (CPF), which has an $O(T^2)$ complexity under a general `strong' mixing assumption, where $T$ is the time horizon. Empirical evidence of the superiority of the CBPF over the CPF has never been theoretically quantified. We show that the CBPF has $O(T \log T)$ time complexity under strong mixing: its mixing time is upper bounded by $O(\log T)$, for any sufficiently large number of particles $N$ independent of $T$. This $O(\log T)$ mixing time is optimal. To prove our main result, we introduce a novel coupling of two CBPFs, which employs a maximal coupling of two particle systems at each time instant. The coupling is implementable and we use it to construct unbiased, finite variance, estimates of functionals which have arbitrary dependence on the latent state's path, with a total expected cost of $O(T \log T)$. We use this to construct unbiased estimates of the HMM's score function, and also investigate other couplings which can exhibit improved behaviour. We demonstrate our methods on financial and calcium imaging applications.

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arXiv2023

On the Forgetting of Particle Filters

We study the forgetting properties of the particle filter when its state - the collection of particles - is regarded as a Markov chain. Under a strong mixing assumption on the particle filter's underlying Feynman-Kac model, we find that the particle filter is exponentially mixing, and forgets its initial state in $O(\log N )$ 'time', where $N$ is the number of particles and time refers to the number of particle filter algorithm steps, each comprising a selection (or resampling) and mutation (or prediction) operation. We present an example which shows that this rate is optimal. In contrast to our result, available results to-date are extremely conservative, suggesting $O(\alpha^N)$ time steps are needed, for some $\alpha>1$, for the particle filter to forget its initialisation. We also study the conditional particle filter (CPF) and extend our forgetting result to this context. We establish a similar conclusion, namely, CPF is exponentially mixing and forgets its initial state in $O(\log N )$ time. To support this analysis, we establish new time-uniform $L^p$ error estimates for CPF, which can be of independent interest. We also establish new propagation of chaos type results using our proof techniques, discuss implications to couplings of particle filters and an application to processing out-of-sequence measurements.

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arXiv2023

On the convergence of dynamic implementations of Hamiltonian Monte Carlo and No U-Turn Samplers

There is substantial empirical evidence about the success of dynamic implementations of Hamiltonian Monte Carlo (HMC), such as the No U-Turn Sampler (NUTS), in many challenging inference problems but theoretical results about their behavior are scarce. The aim of this paper is to fill this gap. More precisely, we consider a general class of MCMC algorithms we call dynamic HMC. We show that this general framework encompasses NUTS as a particular case, implying the invariance of the target distribution as a by-product. Second, we establish conditions under which NUTS is irreducible and aperiodic and as a corrolary ergodic. Under conditions similar to the ones existing for HMC, we also show that NUTS is geometrically ergodic. Finally, we improve existing convergence results for HMC showing that this method is ergodic without any boundedness condition on the stepsize and the number of leapfrog steps, in the case where the target is a perturbation of a Gaussian distribution.

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arXiv2023

Simulating counterfactuals

Counterfactual inference considers a hypothetical intervention in a parallel world that shares some evidence with the factual world. If the evidence specifies a conditional distribution on a manifold, counterfactuals may be analytically intractable. We present an algorithm for simulating values from a counterfactual distribution where conditions can be set on both discrete and continuous variables. We show that the proposed algorithm can be presented as a particle filter leading to asymptotically valid inference. The algorithm is applied to fairness analysis in credit-scoring.

stat.ML↗

arXiv2022

On resampling schemes for particle filters with weakly informative observations

We consider particle filters with weakly informative observations (or `potentials') relative to the latent state dynamics. The particular focus of this work is on particle filters to approximate time-discretisations of continuous-time Feynman--Kac path integral models -- a scenario that naturally arises when addressing filtering and smoothing problems in continuous time -- but our findings are indicative about weakly informative settings beyond this context too. We study the performance of different resampling schemes, such as systematic resampling, SSP (Srinivasan sampling process) and stratified resampling, as the time-discretisation becomes finer and also identify their continuous-time limit, which is expressed as a suitably defined `infinitesimal generator.' By contrasting these generators, we find that (certain modifications of) systematic and SSP resampling `dominate' stratified and independent `killing' resampling in terms of their limiting overall resampling rate. The reduced intensity of resampling manifests itself in lower variance in our numerical experiment. This efficiency result, through an ordering of the resampling rate, is new to the literature. The second major contribution of this work concerns the analysis of the limiting behaviour of the entire population of particles of the particle filter as the time discretisation becomes finer. We provide the first proof, under general conditions, that the particle approximation of the discretised continuous-time Feynman--Kac path integral models converges to a (uniformly weighted) continuous-time particle system.

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arXiv2022

Conditional particle filters with bridge backward sampling

Conditional particle filters (CPFs) with backward/ancestor sampling are powerful methods for sampling from the posterior distribution of the latent states of a dynamic model such as a hidden Markov model. However, the performance of these methods deteriorates with models involving weakly informative observations and/or slowly mixing dynamics. Both of these complications arise when sampling finely time-discretised continuous-time path integral models, but can occur with hidden Markov models too. Multinomial resampling, which is commonly employed with CPFs, resamples excessively for weakly informative observations and thereby introduces extra variance. Furthermore, slowly mixing dynamics render the backward/ancestor sampling steps ineffective, leading to degeneracy issues. We detail two conditional resampling strategies suitable for the weakly informative regime: the so-called `killing' resampling and the systematic resampling with mean partial order. To avoid the degeneracy issues, we introduce a generalisation of the CPF with backward sampling that involves auxiliary `bridging' CPF steps that are parameterised by a blocking sequence. We present practical tuning strategies for choosing an appropriate blocking. Our experiments demonstrate that the CPF with a suitable resampling and the developed `bridge backward sampling' can lead to substantial efficiency gains in the weakly informative and slow mixing regime.

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arXiv2021

Hierarchical log Gaussian Cox process for regeneration in uneven-aged forests

We propose a hierarchical log Gaussian Cox process (LGCP) for point patterns, where a set of points x affects another set of points y but not vice versa. We use the model to investigate the effect of large trees to the locations of seedlings. In the model, every point in x has a parametric influence kernel or signal, which together form an influence field. Conditionally on the parameters, the influence field acts as a spatial covariate in the intensity of the model, and the intensity itself is a non-linear function of the parameters. Points outside the observation window may affect the influence field inside the window. We propose an edge correction to account for this missing data. The parameters of the model are estimated in a Bayesian framework using Markov chain Monte Carlo (MCMC) where a Laplace approximation is used for the Gaussian field of the LGCP model. The proposed model is used to analyze the effect of large trees on the success of regeneration in uneven-aged forest stands in Finland.

stat.ME↗

arXiv2021

bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R

We present an R package bssm for Bayesian non-linear/non-Gaussian state space modelling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package accommodates also discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package implements also a direct pseudo-marginal MCMC and a delayed acceptance pseudo-marginal MCMC using intermediate approximations. The package offers an easy-to-use interface to define models with linear-Gaussian state dynamics with non-Gaussian observation models, and has an Rcpp interface for specifying custom non-linear and diffusion models.

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arXiv2021

Unbiased inference for discretely observed hidden Markov model diffusions

We develop a Bayesian inference method for diffusions observed discretely and with noise, which is free of discretisation bias. Unlike existing unbiased inference methods, our method does not rely on exact simulation techniques. Instead, our method uses standard time-discretised approximations of diffusions, such as the Euler--Maruyama scheme. Our approach is based on particle marginal Metropolis--Hastings, a particle filter, randomised multilevel Monte Carlo, and importance sampling type correction of approximate Markov chain Monte Carlo. The resulting estimator leads to inference without a bias from the time-discretisation as the number of Markov chain iterations increases. We give convergence results and recommend allocations for algorithm inputs. Our method admits a straightforward parallelisation, and can be computationally efficient. The user-friendly approach is illustrated on three examples, where the underlying diffusion is an Ornstein--Uhlenbeck process, a geometric Brownian motion, and a 2d non-reversible Langevin equation.

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arXiv2020

Conditional particle filters with diffuse initial distributions

Conditional particle filters (CPFs) are powerful smoothing algorithms for general nonlinear/non-Gaussian hidden Markov models. However, CPFs can be inefficient or difficult to apply with diffuse initial distributions, which are common in statistical applications. We propose a simple but generally applicable auxiliary variable method, which can be used together with the CPF in order to perform efficient inference with diffuse initial distributions. The method only requires simulatable Markov transitions that are reversible with respect to the initial distribution, which can be improper. We focus in particular on random-walk type transitions which are reversible with respect to a uniform initial distribution (on some domain), and autoregressive kernels for Gaussian initial distributions. We propose to use on-line adaptations within the methods. In the case of random-walk transition, our adaptations use the estimated covariance and acceptance rate adaptation, and we detail their theoretical validity. We tested our methods with a linear-Gaussian random-walk model, a stochastic volatility model, and a stochastic epidemic compartment model with time-varying transmission rate. The experimental findings demonstrate that our method works reliably with little user specification, and can be substantially better mixing than a direct particle Gibbs algorithm that treats initial states as parameters.

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arXiv2020

Importance sampling correction versus standard averages of reversible MCMCs in terms of the asymptotic variance

We establish an ordering criterion for the asymptotic variances of two consistent Markov chain Monte Carlo (MCMC) estimators: an importance sampling (IS) estimator, based on an approximate reversible chain and subsequent IS weighting, and a standard MCMC estimator, based on an exact reversible chain. Essentially, we relax the criterion of the Peskun type covariance ordering by considering two different invariant probabilities, and obtain, in place of a strict ordering of asymptotic variances, a bound of the asymptotic variance of IS by that of the direct MCMC. Simple examples show that IS can have arbitrarily better or worse asymptotic variance than Metropolis-Hastings and delayed-acceptance (DA) MCMC. Our ordering implies that IS is guaranteed to be competitive up to a factor depending on the supremum of the (marginal) IS weight. We elaborate upon the criterion in case of unbiased estimators as part of an auxiliary variable framework. We show how the criterion implies asymptotic variance guarantees for IS in terms of pseudo-marginal (PM) and DA corrections, essentially if the ratio of exact and approximate likelihoods is bounded. We also show that convergence of the IS chain can be less affected by unbounded high-variance unbiased estimators than PM and DA chains.

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arXiv2020

Importance sampling type estimators based on approximate marginal MCMC

We consider importance sampling (IS) type weighted estimators based on Markov chain Monte Carlo (MCMC) targeting an approximate marginal of the target distribution. In the context of Bayesian latent variable models, the MCMC typically operates on the hyperparameters, and the subsequent weighting may be based on IS or sequential Monte Carlo (SMC), but allows for multilevel techniques as well. The IS approach provides a natural alternative to delayed acceptance (DA) pseudo-marginal/particle MCMC, and has many advantages over DA, including a straightforward parallelisation and additional flexibility in MCMC implementation. We detail minimal conditions which ensure strong consistency of the suggested estimators, and provide central limit theorems with expressions for asymptotic variances. We demonstrate how our method can make use of SMC in the state space models context, using Laplace approximations and time-discretised diffusions. Our experimental results are promising and show that the IS type approach can provide substantial gains relative to an analogous DA scheme, and is often competitive even without parallelisation.

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arXiv2019

Coupled conditional backward sampling particle filter

The conditional particle filter (CPF) is a promising algorithm for general hidden Markov model smoothing. Empirical evidence suggests that the variant of CPF with backward sampling (CBPF) performs well even with long time series. Previous theoretical results have not been able to demonstrate the improvement brought by backward sampling, whereas we provide rates showing that CBPF can remain effective with a fixed number of particles independent of the time horizon. Our result is based on analysis of a new coupling of two CBPFs, the coupled conditional backward sampling particle filter (CCBPF). We show that CCBPF has good stability properties in the sense that with fixed number of particles, the coupling time in terms of iterations increases only linearly with respect to the time horizon under a general (strong mixing) condition. The CCBPF is useful not only as a theoretical tool, but also as a practical method that allows for unbiased estimation of smoothing expectations, following the recent developments by Jacob et al. (to appear). Unbiased estimation has many advantages, such as enabling the construction of asymptotically exact confidence intervals and straightforward parallelisation.

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arXiv2019

On the use of approximate Bayesian computation Markov chain Monte Carlo with inflated tolerance and post-correction

Approximate Bayesian computation allows for inference of complicated probabilistic models with intractable likelihoods using model simulations. The Markov chain Monte Carlo implementation of approximate Bayesian computation is often sensitive to the tolerance parameter: low tolerance leads to poor mixing and large tolerance entails excess bias. We consider an approach using a relatively large tolerance for the Markov chain Monte Carlo sampler to ensure its sufficient mixing, and post-processing the output leading to estimators for a range of finer tolerances. We introduce an approximate confidence interval for the related post-corrected estimators, and propose an adaptive approximate Bayesian computation Markov chain Monte Carlo, which finds a `balanced' tolerance level automatically, based on acceptance rate optimisation. Our experiments show that post-processing based estimators can perform better than direct Markov chain targetting a fine tolerance, that our confidence intervals are reliable, and that our adaptive algorithm leads to reliable inference with little user specification.

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