arXiv subjects

Lorenzo Rimella

Publications and source records attributed to Lorenzo Rimella.

10 recordsLinked to original sources

arXiv2026

Scalable calibration of individual-based epidemic models through categorical approximations

Traditional compartmental models capture population-level dynamics but fail to characterize individual-level risk. The computational cost of exact likelihood evaluation for partially observed individual-based models, however, grows exponentially with the population size, necessitating approximate inference. Existing sampling-based methods usually require multiple simulations of the individuals in the population and rely on bespoke proposal distributions or summary statistics. We propose a deterministic approach to approximating the likelihood using categorical distributions. The approximate likelihood is amenable to automatic differentiation so that parameters can be estimated by maximization or posterior sampling using standard software libraries such as Stan or TensorFlow with little user effort. We prove the consistency of the maximum approximate likelihood estimator. We empirically test our approach on several classes of individual-based models for epidemiology: different sets of disease states, individual-specific transition rates, spatial interactions, under-reporting and misreporting. We demonstrate ground truth recovery and comparable marginal log-likelihood values at substantially reduced cost compared to competitor methods. Finally, we show the scalability and effectiveness of our approach with a real-world application on the 2001 UK Foot-and-Mouth outbreak, where the simplicity of the CAL allows us to include 162775 farms.

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arXiv2025

Approximating optimal SMC proposal distributions in individual-based epidemic models

Many epidemic models are naturally defined as individual-based models: where we track the state of each individual within a susceptible population. Inference for individual-based models is challenging due to the high-dimensional state-space of such models, which increases exponentially with population size. We consider sequential Monte Carlo algorithms for inference for individual-based epidemic models where we make direct observations of the state of a sample of individuals. Standard implementations, such as the bootstrap filter or the auxiliary particle filter are inefficient due to mismatch between the proposal distribution of the state and future observations. We develop new efficient proposal distributions that take account of future observations, leveraging the properties that (i) we can analytically calculate the optimal proposal distribution for a single individual given future observations and the future infection rate of that individual; and (ii) the dynamics of individuals are independent if we condition on their infection rates. Thus we construct estimates of the future infection rate for each individual, and then use an independent proposal for the state of each individual given this estimate. Empirical results show order of magnitude improvement in efficiency of the sequential Monte Carlo sampler for both SIS and SEIR models.

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arXiv2025

Hidden Markov Neural Networks

We define an evolving in-time Bayesian neural network called a Hidden Markov Neural Network, which addresses the crucial challenge in time-series forecasting and continual learning: striking a balance between adapting to new data and appropriately forgetting outdated information. This is achieved by modelling the weights of a neural network as the hidden states of a Hidden Markov model, with the observed process defined by the available data. A filtering algorithm is employed to learn a variational approximation of the evolving-in-time posterior distribution over the weights. By leveraging a sequential variant of Bayes by Backprop, enriched with a stronger regularization technique called variational DropConnect, Hidden Markov Neural Networks achieve robust regularization and scalable inference. Experiments on MNIST, dynamic classification tasks, and next-frame forecasting in videos demonstrate that Hidden Markov Neural Networks provide strong predictive performance while enabling effective uncertainty quantification.

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arXiv2025

Simulation Based Composite Likelihood

Inference for high-dimensional hidden Markov models is challenging due to the exponential-in-dimension computational cost of calculating the likelihood. To address this issue, we introduce an innovative composite likelihood approach called "Simulation Based Composite Likelihood" (SimBa-CL). With SimBa-CL, we approximate the likelihood by the product of its marginals, which we estimate using Monte Carlo sampling. In a similar vein to approximate Bayesian computation (ABC), SimBa-CL requires multiple simulations from the model, but, in contrast to ABC, it provides a likelihood approximation that guides the optimization of the parameters. Leveraging automatic differentiation libraries, it is simple to calculate gradients and Hessians to not only speed up optimization but also to build approximate confidence sets. We present extensive empirical results which validate our theory and demonstrate its advantage over SMC, and apply SimBa-CL to real-world Aphtovirus data.

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arXiv2024

Disclosure risk assessment with Bayesian non-parametric hierarchical modelling

Micro and survey datasets often contain private information about individuals, like their health status, income or political preferences. Previous studies have shown that, even after data anonymization, a malicious intruder could still be able to identify individuals in the dataset by matching their variables to external information. Disclosure risk measures are statistical measures meant to quantify how big such a risk is for a specific dataset. One of the most common measures is the number of sample unique values that are also population-unique. \cite{Man12} have shown how mixed membership models can provide very accurate estimates of this measure. A limitation of that approach is that the number of extreme profiles has to be chosen by the modeller. In this article, we propose a non-parametric version of the model, based on the Hierarchical Dirichlet Process (HDP). The proposed approach does not require any tuning parameter or model selection step and provides accurate estimates of the disclosure risk measure, even with samples as small as 1$\%$ of the population size. Moreover, a data augmentation scheme to address the presence of structural zeros is presented. The proposed methodology is tested on a real dataset from the New York census.

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arXiv2024

A State-Space Perspective on Modelling and Inference for Online Skill Rating

We summarise popular methods used for skill rating in competitive sports, along with their inferential paradigms and introduce new approaches based on sequential Monte Carlo and discrete hidden Markov models. We advocate for a state-space model perspective, wherein players' skills are represented as time-varying, and match results serve as observed quantities. We explore the steps to construct the model and the three stages of inference: filtering, smoothing and parameter estimation. We examine the challenges of scaling up to numerous players and matches, highlighting the main approximations and reductions which facilitate statistical and computational efficiency. We additionally compare approaches in a realistic experimental pipeline that can be easily reproduced and extended with our open-source Python package, https://github.com/SamDuffield/abile.

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arXiv2023

Consistent and fast inference in compartmental models of epidemics using Poisson Approximate Likelihoods

Addressing the challenge of scaling-up epidemiological inference to complex and heterogeneous models, we introduce Poisson Approximate Likelihood (PAL) methods. In contrast to the popular ODE approach to compartmental modelling, in which a large population limit is used to motivate a deterministic model, PALs are derived from approximate filtering equations for finite-population, stochastic compartmental models, and the large population limit drives consistency of maximum PAL estimators. Our theoretical results appear to be the first likelihood-based parameter estimation consistency results which apply to a broad class of partially observed stochastic compartmental models and address the large population limit. PALs are simple to implement, involving only elementary arithmetic operations and no tuning parameters, and fast to evaluate, requiring no simulation from the model and having computational cost independent of population size. Through examples we demonstrate how PALs can be used to: fit an age-structured model of influenza, taking advantage of automatic differentiation in Stan; compare over-dispersion mechanisms in a model of rotavirus by embedding PALs within sequential Monte Carlo; and evaluate the role of unit-specific parameters in a meta-population model of measles.

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arXiv2022

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.

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arXiv2022

Exploiting locality in high-dimensional factorial hidden Markov models

We propose algorithms for approximate filtering and smoothing in high-dimensional Factorial hidden Markov models. The approximation involves discarding, in a principled way, likelihood factors according to a notion of locality in a factor graph associated with the emission distribution. This allows the exponential-in-dimension cost of exact filtering and smoothing to be avoided. We prove that the approximation accuracy, measured in a local total variation norm, is "dimension-free" in the sense that as the overall dimension of the model increases the error bounds we derive do not necessarily degrade. A key step in the analysis is to quantify the error introduced by localizing the likelihood function in a Bayes' rule update. The factorial structure of the likelihood function which we exploit arises naturally when data have known spatial or network structure. We demonstrate the new algorithms on synthetic examples and a London Underground passenger flow problem, where the factor graph is effectively given by the train network.

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arXiv2021

Inference in Stochastic Epidemic Models via Multinomial Approximations

We introduce a new method for inference in stochastic epidemic models which uses recursive multinomial approximations to integrate over unobserved variables and thus circumvent likelihood intractability. The method is applicable to a class of discrete-time, finite-population compartmental models with partial, randomly under-reported or missing count observations. In contrast to state-of-the-art alternatives such as Approximate Bayesian Computation techniques, no forward simulation of the model is required and there are no tuning parameters. Evaluating the approximate marginal likelihood of model parameters is achieved through a computationally simple filtering recursion. The accuracy of the approximation is demonstrated through analysis of real and simulated data using a model of the 1995 Ebola outbreak in the Democratic Republic of Congo. We show how the method can be embedded within a Sequential Monte Carlo approach to estimating the time-varying reproduction number of COVID-19 in Wuhan, China, recently published by Kucharski et al. 2020.

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