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Filippo Pagani

Publications and source records attributed to Filippo Pagani.

7 recordsLinked to original sources

A discomfort-informed adaptive Gibbs sampler for finite mixture models

Finite mixture models are frequently used to uncover latent structures in high-dimensional datasets (e.g.\ identifying clusters of patients in electronic health records). The inference of such structures can be performed in a Bayesian framework, and involves the use of sampling algorithms such as Gibbs samplers aimed at deriving posterior distribution of the probabilities of observations to belong to specific clusters. Unfortunately, traditional implementations of Gibbs samplers in this context often face critical challenges, such as inefficient use of computational resources and unnecessary updates for observations that are highly likely to remain in their current cluster. This paper introduces a new adaptive Gibbs sampler that improves the convergence efficiency over existing methods. In particular, our sampler is guided by a function that, at each iteration, uses the past of the chain to focus the updating on observations potentially misclassified in the current clustering, i.e.\ those with a low probability of belonging to their current component. Through simulation studies and two real data analyses, we empirically demonstrate that, in terms of convergence time, our method tends to perform more efficiently compared to state-of-the-art approaches.

stat.ME

Annealed variational mixtures for disease subtyping and biomarker discovery

Cluster analyses of high-dimensional data are often hampered by the presence of large numbers of variables that do not provide relevant information, as well as the perennial issue of choosing an appropriate number of clusters. These challenges are frequently encountered when analysing `omics datasets, such as in molecular precision medicine, where a key goal is to identify disease subtypes and the biomarkers that define them. Here we introduce an annealed variational Bayes algorithm for fitting high-dimensional mixture models while performing variable selection. Our algorithm is scalable and computationally efficient, and we provide an open source Python implementation, VBVarSel. In a range of simulated and real biomedical examples, we show that VBVarSel outperforms the current state of the art, and demonstrate its use for cancer subtyping and biomarker discovery.

stat.CO

FlexKnot and Gaussian Process for 21 cm global signal analysis and foreground separation

The cosmological 21 cm signal is one of the most promising avenues to study the Epoch of Reionization. One class of experiments aiming to detect this signal is global signal experiments measuring the sky-averaged 21 cm brightness temperature as a function of frequency. A crucial step in the interpretation and analysis of such measurements is separating foreground contributions from the remainder of the signal, requiring accurate models for both components. Current models for the signal (non-foreground) component, which may contain cosmological and systematic contributions, are incomplete and unable to capture the full signal. We propose two new methods for extracting this component from the data: Firstly, we employ a foreground-orthogonal Gaussian Process to extract the part of the signal that cannot be explained by the foregrounds. Secondly, we use a FlexKnot parameterization to model the full signal component in a free-form manner, not assuming any particular shape or functional form. This method uses Bayesian model selection to find the simplest signal that can explain the data. We test our methods on both, synthetic data and publicly available EDGES low-band data. We find that the Gaussian Process can clearly capture the foreground-orthogonal signal component of both data sets. The FlexKnot method correctly recovers the full shape of the input signal used in the synthetic data and yields a multi-modal distribution of different signal shapes that can explain the EDGES observations.

astro-ph.CO

Bayesian outcome-guided multi-view mixture models with applications in molecular precision medicine

Clustering is commonly performed as an initial analysis step for uncovering structure in 'omics datasets, e.g. to discover molecular subtypes of disease. The high-throughput, high-dimensional nature of these datasets means that they provide information on a diverse array of different biomolecular processes and pathways. Different groups of variables (e.g. genes or proteins) will be implicated in different biomolecular processes, and hence undertaking analyses that are limited to identifying just a single clustering partition of the whole dataset is therefore liable to conflate the multiple clustering structures that may arise from these distinct processes. To address this, we propose a multi-view Bayesian mixture model that identifies groups of variables (``views"), each of which defines a distinct clustering structure. We consider applications in stratified medicine, for which our principal goal is to identify clusters of patients that define distinct, clinically actionable disease subtypes. We adopt the semi-supervised, outcome-guided mixture modelling approach of Bayesian profile regression that makes use of a response variable in order to guide inference toward the clusterings that are most relevant in a stratified medicine context. We present the model, together with illustrative simulation examples, and examples from pan-cancer proteomics. We demonstrate how the approach can be used to perform integrative clustering, and consider an example in which different 'omics datasets are integrated in the context of breast cancer subtyping.

stat.ME

NuZZ: numerical Zig-Zag sampling for general models

Markov chain Monte Carlo (MCMC) is a key algorithm in computational statistics, and as datasets grow larger and models grow more complex, many popular MCMC algorithms become too computationally expensive to be practical. Recent progress has been made on this problem through development of MCMC algorithms based on Piecewise Deterministic Markov Processes (PDMPs), irreversible processes that can be engineered to converge at a rate which is independent of the size of data. While there has understandably been a surge of theoretical studies following these results, PDMPs have so far only been implemented for models where certain gradients can be bounded, which is not possible in many statistical contexts. Focusing on the Zig-Zag process, we present the Numerical Zig-Zag (NuZZ) algorithm, which is applicable to general statistical models without the need for bounds on the gradient of the log posterior. This allows us to perform numerical experiments on: (i) how the Zig-Zag dynamics behaves on some test problems with common challenging features; and (ii) how the error between the target and sampled distributions evolves as a function of computational effort for different MCMC algorithms including NuZZ. Moreover, due to the specifics of the NuZZ algorithms, we are able to give an explicit bound on the Wasserstein distance between the exact posterior and its numerically perturbed counterpart in terms of the user-specified numerical tolerances of NuZZ.

stat.ME

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

The first year of the COVID-19 pandemic put considerable strain on the national healthcare system in England. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, which was coupled to a model of the generalised epidemic. We named this model EpiBeds. Data from a partially complete patient-pathway line-list was used to provide initial estimates of the mean duration that individuals spend in the different hospital compartments. We then fitted EpiBeds using complete data on hospital occupancy and hospital deaths, enabling estimation of the proportion of individuals that follow different clinical pathways, and the reproduction number of the generalised epidemic. The construction of EpiBeds makes it straightforward to adapt to different patient pathways and settings beyond England. As part of the UK response to the pandemic, EpiBeds has provided weekly forecasts to the NHS for hospital bed occupancy and admissions in England, Wales, Scotland, and Northern Ireland.

q-bio.PE

An n-dimensional Rosenbrock Distribution for MCMC Testing

The Rosenbrock function is an ubiquitous benchmark problem for numerical optimisation, and variants have been proposed to test the performance of Markov Chain Monte Carlo algorithms. In this work we discuss the two-dimensional Rosenbrock density, its current $n$-dimensional extensions, and their advantages and limitations. We then propose a new extension to arbitrary dimensions called the Hybrid Rosenbrock distribution, which is composed of conditional normal kernels arranged in such a way that preserves the key features of the original kernel. Moreover, due to its structure, the Hybrid Rosenbrock distribution is analytically tractable and possesses several desirable properties, which make it an excellent test model for computational algorithms.

stat.CO