arXiv subjects

Nikolaos Demiris

Publications and source records attributed to Nikolaos Demiris.

13 recordsLinked to original sources

arXiv2026

Semi-Markov Models with Particle-Based Bayesian Inference for Epidemics

The COVID-19 pandemic has been characterised by multiple waves of transmission driven by interventions and emerging variants, challenging epidemic models that assume gradually evolving transmission dynamics. We propose a class of state-space models in which the transmission rate evolves through persistent regimes of random duration, governed by a semi-Markov process. This formulation yields an interpretable representation of sustained transmission phases and retains a parsimonious parameterisation. Particle-based Bayesian methods are well established for standard state-space models, but their use in semi-Markov settings has received comparatively limited attention. In epidemic applications, inference is further complicated by differential equation-driven latent dynamics and observation models defined through functionals of the latent process. We develop an inferential framework that accommodates these features, combining particle-based state updates with gradient-based parameter updates and enabling batch and sequential inference via particle and sequential Monte Carlo. We apply the proposed methodology to COVID-19 data from the United Kingdom and show that combining reported cases and deaths leads to more precise and stable inference compared to using deaths alone. These results illustrate the practical value of semi-Markov transmission models for epidemic analysis under complex observation schemes.

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arXiv2025

Network Meta Analysis of Mean Survival

Decisions based upon pairwise comparisons of multiple treatments are naturally performed in terms of the mean survival of the selected study arms or functions thereof. However, synthesis of treatment comparisons is usually performed on surrogates of the mean survival, such as hazard ratios or restricted mean survival times. Thus, network meta-analysis techniques may suffer from the limitations of these approaches, such as incorrect proportional hazards assumption or short-term follow-up periods. We propose a Bayesian framework for the network meta-analysis of the main outcome informing the decision, the mean survival of a treatment. Its derivation involves extrapolation of the observed survival curves. We use methods for stable extrapolation that integrate long term evidence based upon mortality projections. Extrapolations are performed using flexible poly-hazard parametric models and M-spline-based methods. We assess the computational and statistical efficiency of different techniques using a simulation study and apply the developed methods to two real data sets. The proposed method is formulated within a decision theoretic framework for cost-effectiveness analyses, where the `best' treatment is to be selected and incorporating the associated cost information is straightforward.

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arXiv2025

Exchangeable Gaussian Processes with application to epidemics

We develop a Bayesian non-parametric framework based on multi-task Gaussian processes, appropriate for temporal shrinkage. We focus on a particular class of dynamic hierarchical models to obtain evidence-based knowledge of infectious disease burden. These models induce a parsimonious way to capture cross-dependence between groups while retaining a natural interpretation based on an underlying mean process, itself expressed as a Gaussian process. We analyse distinct types of outbreak data from recent epidemics and find that the proposed models result in improved predictive ability against competing alternatives.

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arXiv2025

On a Reinforcement Learning Methodology for Epidemic Control, with application to COVID-19

This paper presents a real time, data driven decision support framework for epidemic control. We combine a compartmental epidemic model with sequential Bayesian inference and reinforcement learning (RL) controllers that adaptively choose intervention levels to balance disease burden, such as intensive care unit (ICU) load, against socio economic costs. We construct a context specific cost function using empirical experiments and expert feedback. We study two RL policies: an ICU threshold rule computed via Monte Carlo grid search, and a policy based on a posterior averaged Q learning agent. We validate the framework by fitting the epidemic model to publicly available ICU occupancy data from the COVID 19 pandemic in England and then generating counterfactual roll out scenarios under each RL controller, which allows us to compare the RL policies to the historical government strategy. Over a 300 day period and for a range of cost parameters, both controllers substantially reduce ICU burden relative to the observed interventions, illustrating how Bayesian sequential learning combined with RL can support the design of epidemic control policies.

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arXiv2025

On robust Bayesian causal inference

This paper develops a Bayesian framework for robust causal inference from longitudinal observational data. Many contemporary methods rely on structural assumptions, such as factor models, to adjust for unobserved confounding, but they can lead to biased causal estimands when mis-specified. We focus on directly estimating time--unit--specific causal effects and use generalised Bayesian inference to quantify model mis-specification and adjust for it, while retaining interpretable posterior inference. We select the learning rate~$\omega$ based on a proper scoring rule that jointly evaluates point and interval accuracy of the causal estimand, thus providing a coherent, decision-theoretic foundation for tuning~$\omega$. Simulation studies and applications to real data demonstrate improved calibration, sharpness, and robustness in estimating causal effects.

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arXiv2024

Stable Survival Extrapolation via Transfer Learning

The mean survival is the key ingredient of the decision process in several applications, notably in health economic evaluations. It is defined as the area under the complete survival curve, thus necessitating extrapolation of the observed data. This may be achieved in a more stable manner by borrowing long term evidence from registry and demographic data. Such borrowing can be seen as an implicit bias-variance trade-off in unseen data. In this article we employ a Bayesian mortality model and transfer its projections in order to construct the baseline population that acts as an anchor of the survival model. We then propose extrapolation methods based on flexible parametric polyhazard models which can naturally accommodate diverse shapes, including non-proportional hazards and crossing survival curves, while typically maintaining a natural interpretation. We estimate the mean survival and related estimands in three cases, namely breast cancer, cardiac arrhythmia and advanced melanoma. Specifically, we evaluate the survival disadvantage of triple-negative breast cancer cases, the efficacy of combining immunotherapy with mRNA cancer therapeutics for melanoma treatment and the suitability of implantable cardioverter defibrilators for cardiac arrhythmia. The latter is conducted in a competing risks context illustrating how working on the cause-specific hazard alone minimizes potential instability. The results suggest that the proposed approach offers a flexible, interpretable and robust approach when survival extrapolation is required.

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arXiv2023

Bayesian Evidence Synthesis for Modeling SARS-CoV-2 Transmission

The acute phase of the Covid-19 pandemic has made apparent the need for decision support based upon accurate epidemic modeling. This process is substantially hampered by under-reporting of cases and related data incompleteness issues. In this article we adopt the Bayesian paradigm and synthesize publicly available data via a discrete-time stochastic epidemic modeling framework. The models allow for estimating the total number of infections while accounting for the endemic phase of the pandemic. We assess the prediction of the infection rate utilizing mobility information, notably the principal components of the mobility data. We evaluate variational Bayes in this context and find that Hamiltonian Monte Carlo offers a robust inference alternative for such models. We elaborate upon vector analysis of the epidemic dynamics, thus enriching the traditional tools used for decision making. In particular, we show how certain 2-dimensional plots on the phase plane may yield intuitive information regarding the speed and the type of transmission dynamics. We investigate the potential of a two-stage analysis as a consequence of cutting feedback, for inference on certain functionals of the model parameters. Finally, we show that a point mass on critical parameters is overly restrictive and investigate informative priors as a suitable alternative.

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arXiv2023

Multiphasic stochastic epidemic models

At the onset of the Covid-19 pandemic, a number of non-pharmaceutical interventions have been implemented in order to reduce transmission, thus leading to multiple phases of transmission. The disease reproduction number $R_t$, a way of quantifying transmissibility, has been a key part in assessing the impact of such interventions. We discuss the distinct types of transmission models used and how they are linked. We consider a hierarchical stochastic epidemic model with piece-wise constant $R_t$, appropriate for modelling the distinct phases of the epidemic and quantifying the true disease magnitude. The location and scale of $R_t$ changes are inferred directly from data while the number of transmissibility phases is allowed to vary. We determine the model complexity via appropriate Poisson point process and Dirichlet process-type modelling components. The models are evaluated using synthetic data sets and the methods are applied to freely available data from California and New York states as well as the United Kingdom and Greece. We estimate the true infected cases and the corresponding $R_t$, among other quantities, and independently validate the proposed approach using a large seroprevalence study.

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arXiv2023

Sample size determination via learning-type curves

This paper is concerned with sample size determination methodology for prediction models. We propose combining the individual calculations via a learning-type curve. We suggest two distinct ways of doing so, a deterministic skeleton of a learning curve and a Gaussian process centred upon its deterministic counterpart. We employ several learning algorithms for modelling the primary endpoint and distinct measures for trial efficacy. We find that the performance may vary with the sample size, but borrowing information across sample size universally improves the performance of such calculations. The Gaussian process-based learning curve appears more robust and statistically efficient, while computational efficiency is comparable. We suggest that anchoring against historical evidence when extrapolating sample sizes should be adopted when such data are available. The methods are illustrated on binary and survival endpoints.

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arXiv2022

Bayesian analysis of diffusion-driven multi-type epidemic models with application to COVID-19

We consider a flexible Bayesian evidence synthesis approach to model the age-specific transmission dynamics of COVID-19 based on daily mortality counts. The temporal evolution of transmission rates in populations containing multiple types of individuals is reconstructed via an appropriate dimension-reduction formulation driven by independent diffusion processes. A suitably tailored compartmental model is used to learn the latent counts of infection, accounting for fluctuations in transmission influenced by public health interventions and changes in human behaviour. The model is fitted to freely available COVID-19 data sources from the UK, Greece, and Austria and validated using a large-scale prevalence survey in England. In particular, we demonstrate how model expansion can facilitate evidence reconciliation at a latent level. The code implementing this work is made freely available via the Bernadette R package.

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arXiv2022

A modelling framework for the analysis of the SARS-CoV2 transmission dynamics

Despite the progress in medical data collection the actual burden of SARS-CoV-2 remains unknown due to under-ascertainment of cases. This was apparent in the acute phase of the pandemic and the use of reported deaths has been pointed out as a more reliable source of information, likely less prone to under-reporting. Since daily deaths occur from past infections weighted by their probability of death, one may infer the total number of infections accounting for their age distribution, using the data on reported deaths. We adopt this framework and assume that the dynamics generating the total number of infections can be described by a continuous time transmission model expressed through a system of non-linear ordinary differential equations where the transmission rate is modelled as a diffusion process allowing to reveal both the effect of control strategies and the changes in individuals behavior. We develop this flexible Bayesian tool in Stan and study 3 pairs of European countries, estimating the time-varying reproduction number($R_t$) as well as the true cumulative number of infected individuals. As we estimate the true number of infections we offer a more accurate estimate of $R_t$. We also provide an estimate of the daily reporting ratio and discuss the effects of changes in mobility and testing on the inferred quantities.

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arXiv2021

Inference and model determination for Temperature-Driven non-linear Ecological Models

This paper is concerned with a contemporary Bayesian approach to the effect of temperature on developmental rates. We develop statistical methods using recent computational tools to model four commonly used ecological non-linear mathematical curves that describe arthropods' developmental rates. Such models address the effect of temperature fluctuations on the developmental rate of arthropods. In addition to the widely used Gaussian distributional assumption, we also explore Inverse Gamma--based alternatives, which naturally accommodate adaptive variance fluctuation with temperature. Moreover, to overcome the associated parameter indeterminacy in the case of no development, we suggest the Zero Inflated Inverse Gamma model. The ecological models are compared graphically via posterior predictive plots and quantitatively via Marginal likelihood estimates and Information criteria values. Inference is performed using the Stan software and we investigate the statistical and computational efficiency of its Hamiltonian Monte Carlo and Variational Inference methods. We explore model uncertainty and use Bayesian Model Averaging framework for robust estimation of the key ecological parameters

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arXiv2019

Contemporary statistical inference for infectious disease models using Stan

This paper is concerned with the application of recent statistical advances to inference of infectious disease dynamics. We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and Variational Inference as implemented in the freely available Stan software. We apply the two methods to real data from outbreaks as well as routinely collected observations. Our results suggest that both inference methods are computationally feasible in this context, and show a trade-off between statistical efficiency versus computational speed. The latter appears particularly relevant for real-time applications.

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