Researcher profile

Paul Fearnhead

Paul Fearnhead contributes to research discovery and scholarly infrastructure.

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Published work

12 published item(s)

preprint2026arXiv

Tempered Guided Diffusion

Training-free conditional diffusion provides a flexible alternative to task-specific conditional model training, but existing samplers often allocate computation inefficiently: independent guided trajectories can vary widely in quality, and additional function evaluations along a single trajectory may not recover from poor early decisions. We propose Tempered Guided Diffusion (TGD), an annealed sequential Monte Carlo framework for training-free conditional sampling with diffusion priors. TGD targets tempered posterior distributions over the clean signal, using noisy diffusion states only as auxiliary variables for proposing reconstructions and propagating particles. Particles are reweighted by incremental likelihood ratios, resampled, and propagated across noise levels, concentrating computation on trajectories plausible under both the prior and observation. Under idealized exact-reconstruction assumptions, full TGD yields a consistent particle approximation to the posterior as the number of particles grows. For expensive reconstruction tasks, Accelerated TGD (A-TGD) retains early particle exploration but prunes to a single high-likelihood trajectory partway through sampling. Experiments on a controlled two-dimensional inverse problem and image inverse problems show improved posterior approximation and favorable wall-clock speed-quality tradeoffs over independent multi-trajectory baselines.

preprint2023arXiv

High-dimensional time series segmentation via factor-adjusted vector autoregressive modelling

Vector autoregressive (VAR) models are popularly adopted for modelling high-dimensional time series, and their piecewise extensions allow for structural changes in the data. In VAR modelling, the number of parameters grow quadratically with the dimensionality which necessitates the sparsity assumption in high dimensions. However, it is debatable whether such an assumption is adequate for handling datasets exhibiting strong serial and cross-sectional correlations. We propose a piecewise stationary time series model that simultaneously allows for strong correlations as well as structural changes, where pervasive serial and cross-sectional correlations are accounted for by a time-varying factor structure, and any remaining idiosyncratic dependence between the variables is handled by a piecewise stationary VAR model. We propose an accompanying two-stage data segmentation methodology which fully addresses the challenges arising from the latency of the component processes. Its consistency in estimating both the total number and the locations of the change points in the latent components, is established under conditions considerably more general than those in the existing literature. We demonstrate the competitive performance of the proposed methodology on simulated datasets and an application to US blue chip stocks data.

preprint2022arXiv

Consistency of a range of penalised cost approaches for detecting multiple changepoints

A common approach to detect multiple changepoints is to minimise a measure of data fit plus a penalty that is linear in the number of changepoints. This paper shows that the general finite sample behaviour of such a method can be related to its behaviour when analysing data with either none or one changepoint. This results in simpler conditions for verifying whether the method will consistently estimate the number and locations of the changepoints. We apply and demonstrate the usefulness of this result for a range of changepoint problems. Our new results include a weaker condition on the choice of penalty required to have consistency in a change-in-slope model; and the first results for the accuracy of recently-proposed methods for detecting spikes.

preprint2022arXiv

Continuously-Tempered PDMP Samplers

New sampling algorithms based on simulating continuous-time stochastic processes called piece-wise deterministic Markov processes (PDMPs) have shown considerable promise. However, these methods can struggle to sample from multi-modal or heavy-tailed distributions. We show how tempering ideas can improve the mixing of PDMPs in such cases. We introduce an extended distribution defined over the state of the posterior distribution and an inverse temperature, which interpolates between a tractable distribution when the inverse temperature is 0 and the posterior when the inverse temperature is 1. The marginal distribution of the inverse temperature is a mixture of a continuous distribution on [0,1) and a point mass at 1: which means that we obtain samples when the inverse temperature is 1, and these are draws from the posterior, but sampling algorithms will also explore distributions at lower temperatures which will improve mixing. We show how PDMPs, and particularly the Zig-Zag sampler, can be implemented to sample from such an extended distribution. The resulting algorithm is easy to implement and we show empirically that it can outperform existing PDMP-based samplers on challenging multimodal posteriors.

preprint2022arXiv

cpop: Detecting changes in piecewise-linear signals

Changepoint detection is an important problem with applications across many application domains. There are many different types of changes that one may wish to detect, and a wide-range of algorithms and software for detecting them. However there are relatively few approaches for detecting changes-in-slope in the mean of a signal plus noise model. We describe the R package, cpop, available on the Comprehensive R Archive Network (CRAN). This package implements CPOP, a dynamic programming algorithm, to find the optimal set of changes that minimises an L_0 penalised cost, with the cost being a weighted residual sum of squares. The package has extended the CPOP algorithm so it can analyse data that is unevenly spaced, allow for heterogeneous noise variance, and allows for a grid of potential change locations to be different from the locations of the data points. There is also an implementation that uses the CROPS algorithm to detect all segmentations that are optimal as you vary the L_0 penalty for adding a change across a continuous range of values.

preprint2022arXiv

gfpop: an R Package for Univariate Graph-Constrained Change-Point Detection

In a world with data that change rapidly and abruptly, it is important to detect those changes accurately. In this paper we describe an R package implementing a generalized version of an algorithm recently proposed by Hocking et al. [2020] for penalized maximum likelihood inference of constrained multiple change-point models. This algorithm can be used to pinpoint the precise locations of abrupt changes in large data sequences. There are many application domains for such models, such as medicine, neuroscience or genomics. Often, practitioners have prior knowledge about the changes they are looking for. For example in genomic data, biologists sometimes expect peaks: up changes followed by down changes. Taking advantage of such prior information can substantially improve the accuracy with which we can detect and estimate changes. Hocking et al. [2020] described a graph framework to encode many examples of such prior information and a generic algorithm to infer the optimal model parameters, but implemented the algorithm for just a single scenario. We present the gfpop package that implements the algorithm in a generic manner in R/C++. gfpop works for a user-defined graph that can encode prior assumptions about the types of change that are possible and implements several loss functions (Gauss, Poisson, binomial, biweight and Huber). We then illustrate the use of gfpop on isotonic simulations and several applications in biology. For a number of graphs the algorithm runs in a matter of seconds or minutes for 10^5 data points.

preprint2022arXiv

Inference on Extended-Spectrum Beta-Lactamase Escherichia coli and Klebsiella pneumoniae data through SMC$^2$

We propose a novel stochastic model for the spread of antimicrobial-resistant bacteria in a population, together with an efficient algorithm for fitting such a model to sample data. We introduce an individual-based model for the epidemic, with the state of the model determining which individuals are colonised by the bacteria. The transmission rate of the epidemic takes into account both individuals' locations, individuals covariates, seasonality and environmental effects. The state of our model is only partially observed, with data consisting of test results from individuals from a sample of households taken roughly twice a week for 19 months. Fitting our model to data is challenging due to the large state space of our model. We develop an efficient SMC$^2$ algorithm to estimate parameters and compare models for the transmission rate. We implement this algorithm in a computationally efficient manner by using the scale invariance properties of the underlying epidemic model, which means we can define and fit our model for a population on the order of tens of thousands of individuals rather than millions. Our motivating application focuses on the dynamics of community-acquired Extended-Spectrum Beta-Lactamase-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae), using data collected as part of the Drivers of Resistance in Uganda and Malawi project. We infer the parameters of the model and learn key epidemic quantities such as the effective reproduction number, spatial distribution of prevalence, household cluster dynamics, and seasonality.

preprint2022arXiv

Poisson-FOCuS: An efficient online method for detecting count bursts with application to gamma ray burst detection

Gamma-ray bursts are flashes of light from distant exploding stars. Cube satellites that monitor photons across different energy bands are used to detect these bursts. There is a need for computationally efficient algorithms, able to run using the limited computational resource onboard a cube satellite, that can detect when gamma-ray bursts occur. Current algorithms are based on monitoring photon counts across a grid of different sizes of time window. We propose a new algorithm, which extends the recently developed FOCuS algorithm for online change detection to Poisson data. Our algorithm is mathematically equivalent to searching over all possible window sizes, but at half the computational cost of the current grid-based methods. We demonstrate the additional power of our approach using simulations and data drawn from the Fermi gamma-ray burst catalogue.

preprint2020arXiv

Quasi-stationary Monte Carlo and the ScaLE Algorithm

This paper introduces a class of Monte Carlo algorithms which are based upon the simulation of a Markov process whose quasi-stationary distribution coincides with a distribution of interest. This differs fundamentally from, say, current Markov chain Monte Carlo methods which simulate a Markov chain whose stationary distribution is the target. We show how to approximate distributions of interest by carefully combining sequential Monte Carlo methods with methodology for the exact simulation of diffusions. The methodology introduced here is particularly promising in that it is applicable to the same class of problems as gradient based Markov chain Monte Carlo algorithms but entirely circumvents the need to conduct Metropolis-Hastings type accept/reject steps whilst retaining exactness: the paper gives theoretical guarantees ensuring the algorithm has the correct limiting target distribution. Furthermore, this methodology is highly amenable to big data problems. By employing a modification to existing na{\"ı}ve sub-sampling and control variate techniques it is possible to obtain an algorithm which is still exact but has sub-linear iterative cost as a function of data size.

preprint2020arXiv

Semi-automated simultaneous predictor selection for Regression-SARIMA models

Deciding which predictors to use plays an integral role in deriving statistical models in a wide range of applications. Motivated by the challenges of predicting events across a telecommunications network, we propose a semi-automated, joint model-fitting and predictor selection procedure for linear regression models. Our approach can model and account for serial correlation in the regression residuals, produces sparse and interpretable models and can be used to jointly select models for a group of related responses. This is achieved through fitting linear models under constraints on the number of non-zero coefficients using a generalisation of a recently developed Mixed Integer Quadratic Optimisation approach. The resultant models from our approach achieve better predictive performance on the motivating telecommunications data than methods currently used by industry.

preprint2010arXiv

An Adaptive Sequential Monte Carlo Sampler

Sequential Monte Carlo (SMC) methods are not only a popular tool in the analysis of state space models, but offer an alternative to MCMC in situations where Bayesian inference must proceed via simulation. This paper introduces a new SMC method that uses adaptive MCMC kernels for particle dynamics. The proposed algorithm features an online stochastic optimization procedure to select the best MCMC kernel and simultaneously learn optimal tuning parameters. Theoretical results are presented that justify the approach and give guidance on how it should be implemented. Empirical results, based on analysing data from mixture models, show that the new adaptive SMC algorithm (ASMC) can both choose the best MCMC kernel, and learn an appropriate scaling for it. ASMC with a choice between kernels outperformed the adaptive MCMC algorithm of Haario et al. (1998) in 5 out of the 6 cases considered.

preprint2010arXiv

On Estimating the Ability of NBA Players

This paper introduces a new model and methodology for estimating the ability of NBA players. The main idea is to directly measure how good a player is by comparing how their team performs when they are on the court as opposed to when they are off it. This is achieved in a such a way as to control for the changing abilities of the other players on court at different times during a match. The new method uses multiple seasons' data in a structured way to estimate player ability in an isolated season, measuring separately defensive and offensive merit as well as combining these to give an overall rating. The use of game statistics in predicting player ability will be considered. Results using data from the 2008/9 season suggest that LeBron James, who won the NBA MVP award, was the best overall player. The best defensive player was Lamar Odom and the best rookie was Russell Westbrook, neither of whom won an NBA award that season. The results further indicate that whilst the frequently-reported game statistics provide some information on offensive ability, they do not perform well in the prediction of defensive ability.