arXiv subjects

Michele Guindani

Publications and source records attributed to Michele Guindani.

At least 19 recordsLinked to original sources

arXiv2026

Bayesian Multi-Group Functional Factor Models with Parameter-Expanded Cumulative Shrinkage Priors

Functional data consist of trajectories observed over a continuous domain, such as time, space, or wavelength. Here we consider curves observed on different groups of subjects and propose a Bayesian multi-group functional factor analysis framework that jointly models the data via an explicit decomposition into group-specific mean functions and latent components that capture both common and distinct latent structures across the groups. We represent these functional components as linear combinations of a common set of B-spline bases, achieving a low-rank representation of the latent factors. We further impose a parameter-expanded cumulative shrinkage process prior on the factor loadings, which induces increasing shrinkage and automatically selects the number of active shared and group-specific factors. We evaluate the model's performance through simulation studies and show that the model accurately recovers the number of underlying factors and effectively distinguishes variations in functional observations driven by shared versus group-specific complex structures under various scenarios. For real data analysis, we apply the model to EEG data on alcoholic and healthy subjects and identify shared latent factors, that capture canonical characteristic components of the EEG curves, along with group-specific factors that reveal specific neural activity patterns.

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arXiv2025

Bayesian nonparametric modeling of multivariate count data with an unknown number of traits

Feature and trait allocation models are fundamental objects in Bayesian nonparametrics and play a prominent role in several applications. Existing approaches, however, typically assume full exchangeability of the data, which may be restrictive in settings characterized by heterogeneous but related groups. In this paper, we introduce a general and tractable class of Bayesian nonparametric priors for partially exchangeable trait allocation models, relying on completely random vectors. We provide a comprehensive theoretical analysis, including closed-form expressions for marginal and posterior distributions, and illustrate the tractability of our framework in the cases of binary and Poisson-distributed traits. A distinctive aspect of our approach is that the number of traits is a random quantity, thereby allowing us to model and estimate unobserved traits. Building on these results, we also develop a novel mixture model that infers the group partition structure from the data, effectively clustering trait allocations. This extension generalizes Bayesian nonparametric latent class models and avoids the systematic overclustering that arises when the number of traits is assumed to be fixed. We demonstrate the practical usefulness of our methodology through an application to the `Ndrangheta criminal network from the Operazione Infinito investigation, where our model provides insights into the organization of illicit activities.

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arXiv2025

Repulsive Mixture Model with Projection Determinantal Point Process

In many scientific domains, clustering aims to reveal interpretable latent structure that reflects relevant subpopulations or processes. Widely used Bayesian mixture models for model-based clustering often produce overlapping or redundant components because priors on cluster locations are specified independently, hindering interpretability. To mitigate this, repulsive priors have been proposed to encourage well-separated components, yet existing approaches face both computational and theoretical challenges. We introduce a fully tractable Bayesian repulsive mixture model by assigning a projection Determinantal Point Process (DPP) prior to the component locations. Projection DPPs induce strong repulsion and allow exact sampling, enabling parsimonious and interpretable posterior clustering. Leveraging their analytical tractability, we derive closed-form posterior and predictive distributions. These results, in turn, enable two efficient inference algorithms: a conditional Gibbs sampler and the first fully implementable marginal sampler for DPP-based mixtures. We also provide strong frequentist guarantees, including posterior consistency for density estimation, elimination of redundant components, and contraction of the mixing measure. Simulation studies confirm superior mixing and clustering performance compared to alternatives in misspecified settings. Finally, we demonstrate the utility of our method on event-related potential functional data, where it uncovers interpretable neuro-cognitive subgroups. Our results support the projection DPP mixtures as a theoretically sound and practically effective solution for Bayesian clustering.

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arXiv2025

Discrete Autoregressive Switching Processes with Cumulative Shrinkage Priors for Graphical Modeling of Time Series Data

We propose a flexible Bayesian approach for sparse Gaussian graphical modeling of multivariate time series. We account for temporal correlation in the data by assuming that observations are characterized by an underlying and unobserved hidden discrete autoregressive process. We assume multivariate Gaussian emission distributions and capture spatial dependencies by modeling the state-specific precision matrices via graphical horseshoe priors. We characterize the mixing probabilities of the hidden process via a cumulative shrinkage prior that accommodates zero-inflated parameters for non-active components, and further incorporate a sparsity-inducing Dirichlet prior to estimate the effective number of states from the data. For posterior inference, we develop a sampling procedure that allows estimation of the number of discrete autoregressive lags and the number of states, and that cleverly avoids having to deal with the changing dimensions of the parameter space. We thoroughly investigate performance of our proposed methodology through several simulation studies. We further illustrate the use of our approach for the estimation of dynamic brain connectivity based on fMRI data collected on a subject performing a task-based experiment on latent learning

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arXiv2025

Decoding Neuronal Ensembles from Spatially-Referenced Calcium Traces: A Bayesian Semiparametric Approach

Understanding how neurons coordinate their activity is a fundamental question in neuroscience, with implications for learning, memory, and neurological disorders. Calcium imaging has emerged as a powerful method to observe large-scale neuronal activity in freely moving animals, providing time-resolved recordings of hundreds of neurons. However, fluorescence signals are noisy and only indirectly reflect underlying spikes of neuronal activity, complicating the extraction of reliable patterns of neuronal coordination. We introduce a fully Bayesian, semiparametric model that jointly infers spiking activity and identifies functionally coherent neuronal ensembles from calcium traces. Our approach models each neuron's spiking probability through a latent Gaussian process and encourages anatomically coherent clustering using a location-dependent stick-breaking prior. A spike-and-slab Dirichlet process captures heterogeneity in spike amplitudes while filtering out negligible events. We consider calcium imaging data from the hippocampal CA1 region of a mouse as it navigates a circular arena, a setting critical for understanding spatial memory and neuronal representation of environments. Our model uncovers spatially structured co-activation patterns among neurons and can be employed to reveal how ensemble structures vary with the animal's position.

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arXiv2025

Nonparametric Bayesian analysis for the Galton-Watson process

The Galton-Watson process is a model for population growth which assumes that individuals reproduce independently according to the same offspring distribution. Inference usually focuses on the offspring average as it allows to classify the process with respect to extinction. We propose a fully non-parametric approach for Bayesian inference on the GW model using a Dirichlet Process prior. The prior naturally generalizes the Dirichlet conjugate prior distribution, and it allows learning the support of the offspring distribution from the data as well as taking into account possible overdispersion of the data. The performance of the proposed approach is compared with both frequentist and Bayesian procedures via simulation. In particular, we show that the use of a DP prior yields good classification performance with both complete and incomplete data. A real-world data example concerning COVID-19 data from Sardinia illustrates the use of the approach in practice.

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arXiv2025

Quantifying Flow State Dynamics: A Prefrontal Cortex EEG-Based Model Validation Study. Unveiling the Prefrontal Cortex's Role in Flow State Experience: An Empirical EEG Analysis

This article aims to explore the optimization of mental performance through the analysis of metrics associated with the psychological state known as flow. Several clinical studies have shown a correlation between the mental state of flow (characterized by deep and relaxed concentration and high psychophysical efficiency) and brain activity measured through electroencephalography (EEG). This study confirms such a correlation, focusing in particular on the sports field, where the flow state tends to occur more frequently. To conduct the study, Sporthype developed proprietary software that integrates several predictive models, in particular the Flow State Index (FSI), implemented within the Holytics system. An analytical protocol was established, including mental exercises and data collection sessions using the portable EEG device Muse, accompanied by a questionnaire to gather athletes' subjective perceptions of their mental state. The results revealed a significant alignment between the EEG data and the subjective experiences reported in the questionnaires, confirming the feasibility of detecting the flow state through prefrontal cortex activity. Furthermore, the psychological exercises included in the study protocol showed a tangible positive effect in enhancing flow during athletic performance. Flow improves performance through a more harmonious synchronization between mind and body. Although golf was the main context of the experimentation, the mathematical models developed within Holytics were designed to be applicable to a wide range of sports. In addition to golf, preliminary tests have been conducted in other sports such as tennis, as well as in non-sport contexts, including gaming and mental training practices such as mindfulness, concentration, and visualization.

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arXiv2025

A Bayesian Approach for Inference on Mixed Graphical Models

Mixed data refers to a type of data in which variables can be of multiple types, such as continuous, discrete, or categorical. This data is routinely collected in various fields, including healthcare and social sciences. A common goal in the analysis of such data is to identify dependence relationships between variables, for an understanding of their associations. In this paper, we propose a Bayesian pairwise graphical model that estimates conditional independencies between any type of data. We implement a flexible modeling construction, that includes zero-inflated count data and can also handle missing data. We show that the model maintains both global and local Markov properties. We employ a spike-and-slab prior for the estimation of the graph and implement an MCMC algorithm for posterior inference based on conditional likelihoods. We assess performances on four simulation scenarios with distinct dependence structures, that also include cases with data missing at random, and compare results with existing methods. Finally, we present an analysis of real data from adolescents diagnosed with an eating disorder. Estimated graphs show differences in the associations estimated at intake and discharge, suggesting possible effects of the treatment on cognitive and behavioral measures in the adolescents.

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arXiv2025

BISON: Bi-clustering of spatial omics data with feature selection

The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context. Understanding gene functions and interactions in different spatial domains is crucial, as it can enhance our comprehension of biological mechanisms, such as cancer-immune interactions and cell differentiation in various regions. It is necessary to cluster tissue regions into distinct spatial domains and identify discriminating genes that elucidate the clustering result, referred to as spatial domain-specific discriminating genes (DGs). Existing methods for identifying these genes typically rely on a two-stage approach, which can lead to the phenomenon known as \textit{double-dipping}. To address the challenge, we propose a unified Bayesian latent block model that simultaneously detects a list of DGs contributing to spatial domain identification while clustering these DGs and spatial locations. The efficacy of our proposed method is validated through a series of simulation experiments, and its capability to identify DGs is demonstrated through applications to benchmark SRT datasets.

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arXiv2024

Bayesian Controlled FDR Variable Selection via Parameter-Expanded Latent Knockoffs

In many research fields, researchers aim to identify significant associations between a set of explanatory variables and a response while controlling the FDR. The Knockoff filter has been recently proposed in the frequentist paradigm to introduce controlled noise in a model by cleverly constructing copies of the predictors as auxiliary variables. We develop a fully Bayesian generalization of the classical model-X knockoff filter for normally distributed covariates. In our approach, we consider a joint model for the covariates and the response, where the conditional independence structure of the covariates is captured through a Gaussian graphical model and used to define a latent knockoff layer through a parameter-expanded representation of the response model. Estimating the covariate graph informs the knockoff construction and improves inference on the covariate effects. We use a modified spike-and-slab prior on the regression coefficients, avoiding the increase of the model dimension typical of the classical knockoff filter. We also address extensions to non-Gaussian responses. Our model performs variable selection using an upper bound on the posterior probability of non-inclusion. We show that the induced latent knockoff layer defines valid Gaussian model-X knockoffs under the proposed construction and that the resulting procedure controls the Bayesian FDR at an arbitrary level, in finite samples, if the distribution of the covariates is fully known; under an estimated graphical structure, it satisfies an asymptotic FDR guarantee. We use simulated data to demonstrate that our proposal increases the stability of the selection with respect to classical knockoff methods. With respect to Bayesian variable selection methods, our selection procedure achieves comparable or better performances, while maintaining control over the FDR. We conclude with an application to real data.

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arXiv2024

Clustering Computer Mouse Tracking Data with Informed Hierarchical Shrinkage Partition Priors

Mouse-tracking data, which record computer mouse trajectories while participants perform an experimental task, provide valuable insights into subjects' underlying cognitive processes. Neuroscientists are interested in clustering the subjects' responses during computer mouse-tracking tasks to reveal patterns of individual decision-making behaviors and identify population subgroups with similar neurobehavioral responses. These data can be combined with neuro-imaging data to provide additional information for personalized interventions. In this article, we develop a novel hierarchical shrinkage partition (HSP) prior for clustering summary statistics derived from the trajectories of mouse-tracking data. The HSP model defines a subjects' cluster as a set of subjects that gives rise to more similar (rather than identical) nested partitions of the conditions. The proposed model can incorporate prior information about the partitioning of either subjects or conditions to facilitate clustering, and it allows for deviations of the nested partitions within each subject group. These features distinguish the HSP model from other bi-clustering methods that typically create identical nested partitions of conditions within a subject group. Furthermore, it differs from existing nested clustering methods, which define clusters based on common parameters in the sampling model and identify subject groups by different distributions. We illustrate the unique features of the HSP model on a mouse tracking dataset from a pilot study and in simulation studies. Our results show the ability and effectiveness of the proposed exploratory framework in clustering and revealing possible different behavioral patterns across subject groups.

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arXiv2024

Bayesian Bivariate Conway-Maxwell-Poisson Regression Model for Correlated Count Data in Sports

Count data play a crucial role in sports analytics, providing valuable insights into various aspects of the game. Models that accurately capture the characteristics of count data are essential for making reliable inferences. In this paper, we propose the use of the Conway-Maxwell-Poisson (CMP) model for analyzing count data in sports. The CMP model offers flexibility in modeling data with different levels of dispersion. Here we consider a bivariate CMP model that models the potential correlation between home and away scores by incorporating a random effect specification. We illustrate the advantages of the CMP model through simulations. We then analyze data from baseball and soccer games before, during, and after the COVID-19 pandemic. The performance of our proposed CMP model matches or outperforms standard Poisson and Negative Binomial models, providing a good fit and an accurate estimation of the observed effects in count data with any level of dispersion. The results highlight the robustness and flexibility of the CMP model in analyzing count data in sports, making it a suitable default choice for modeling a diverse range of count data types in sports, where the data dispersion may vary.

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arXiv2024

Semi-parametric local variable selection under misspecification

Local variable selection aims to test for the effect of covariates on an outcome within specific regions. We outline a challenge that arises in the presence of non-linear effects and model misspecification. Specifically, for common semi-parametric methods even slight model misspecification can result in a high false positive rate, in a manner that is highly sensitive to the chosen basis functions. We propose a methodology based on orthogonal cut splines that avoids false positive inflation for any choice of knots, and achieves consistent local variable selection. Our approach offers simplicity, handles both continuous and categorical covariates, and provides theory for high-dimensional covariates and model misspecification. We discuss settings with either independent or dependent data. Our proposal allows including adjustment covariates that do not undergo selection, enhancing the model's flexibility. Our examples describe salary gaps associated with various discrimination factors at different ages, and the effects of covariates on functional data measuring brain activation at different times.

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arXiv2024

Local Level Dynamic Random Partition Models for Changepoint Detection

Motivated by an increasing demand for models that can effectively describe features of complex multivariate time series, e.g. from sensor data in biomechanics, motion analysis, and sports science, we introduce a novel state-space modeling framework where the state equation encodes the evolution of latent partitions of the data over time. Building on the principles of dynamic linear models, our approach develops a random partition model capable of linking data partitions to previous ones over time, using a straightforward Markov structure that accounts for temporal persistence and facilitates changepoint detection. The selection of changepoints involves multiple dependent decisions, and we address this time-dependence by adopting a non-marginal false discovery rate control. This leads to a simple decision rule that ensures more stringent control of the false discovery rate compared to approaches that do not consider dependence. The method is efficiently implemented using a Gibbs sampling algorithm, leading to a straightforward approach compared to existing methods for dependent random partition models. Additionally, we show how the proposed method can be adapted to handle multiview clustering scenarios. Simulation studies and the analysis of a human gesture phase dataset collected through various sensing technologies show the effectiveness of the method in dynamically clustering multivariate time series and detecting changepoints.

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arXiv2024

Bayesian temporal biclustering with applications to multi-subject neuroscience studies

We consider the problem of analyzing multivariate time series collected on multiple subjects, with the goal of identifying groups of subjects exhibiting similar trends in their recorded measurements over time as well as time-varying groups of associated measurements. To this end, we propose a Bayesian model for temporal biclustering featuring nested partitions, where a time-invariant partition of subjects induces a time-varying partition of measurements. Our approach allows for data-driven determination of the number of subject and measurement clusters as well as estimation of the number and location of changepoints in measurement partitions. To efficiently perform model fitting and posterior estimation with Markov Chain Monte Carlo, we derive a blocked update of measurements' cluster-assignment sequences. We illustrate the performance of our model in two applications to functional magnetic resonance imaging data and to an electroencephalogram dataset. The results indicate that the proposed model can combine information from potentially many subjects to discover a set of interpretable, dynamic patterns. Experiments on simulated data compare the estimation performance of the proposed model against ground-truth values and other statistical methods, showing that it performs well at identifying ground-truth subject and measurement clusters even when no subject or time dependence is present.

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arXiv2024

Flexible aggregation of compositional predictors with shared effects for microbiome association analysis

Ongoing advancements in microbiome profiling have provided unprecedented insights into the molecular dynamics of microbial communities, sparking a surge of interest in uncovering the microbiome's critical role in human health. Identifying microbial features linked to clinical outcomes, however, remains challenging due to the high-dimensional, sparse, and compositional nature of microbiome data. Additionally, many microbial taxa, although classified as distinct, may share functional roles, complicating traditional variable selection methods. To overcome these obstacles, we introduce Bayesian Regression with Agglomerated Compositional Effects (BRACE), a novel approach using a spike-and-cluster prior combining Bernoulli activity indicators, an Ewens exchangeable partition prior on the finite active set, and a projection-based constrained Gaussian prior on cluster effects to perform data-adaptive clustering and variable selection. The methodological innovation of our work lies in how we combine the Ewens partition prior with a projection-based constrained Gaussian on the cluster atoms to enforce the sum-to-zero constraint. BRACE groups microbial taxa with similar effects on the outcome, yielding more interpretable models while enabling effective dimension reduction. Through comprehensive simulations and a real-world application examining the influence of oral microbiome composition on insulin resistance, we demonstrate BRACE's superior performance over existing methods, particularly in identifying key features with shared effects on outcomes.

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arXiv2024

Bayesian Time-Varying Tensor Vector Autoregressive Models for Dynamic Effective Connectivity

In contemporary neuroscience, a key area of interest is dynamic effective connectivity, which is crucial for understanding the dynamic interactions and causal relationships between different brain regions. Dynamic effective connectivity can provide insights into how brain network interactions are altered in neurological disorders such as dyslexia. Time-varying vector autoregressive (TV-VAR) models have been employed to draw inferences for this purpose. However, their significant computational requirements pose challenges, since the number of parameters to be estimated increases quadratically with the number of time series. In this paper, we propose a computationally efficient Bayesian time-varying VAR approach. For dealing with large-dimensional time series, the proposed framework employs a tensor decomposition for the VAR coefficient matrices at different lags. Dynamically varying connectivity patterns are captured by assuming that at any given time only a subset of components in the tensor decomposition is active. Latent binary time series select the active components at each time via an innovative and parsimonious Ising model in the time-domain. Furthermore, we propose parsity-inducing priors to achieve global-local shrinkage of the VAR coefficients, determine automatically the rank of the tensor decomposition and guide the selection of the lags of the auto-regression. We show the performances of our model formulation via simulation studies and data from a real fMRI study involving a book reading experiment.

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arXiv2023

Multiple hypothesis screening using mixtures of non-local distributions with applications to genomic studies

The analysis of large-scale datasets, especially in biomedical contexts, frequently involves a principled screening of multiple hypotheses. The celebrated two-group model jointly models the distribution of the test statistics with mixtures of two competing densities, the null and the alternative distributions. We investigate the use of weighted densities and, in particular, non-local densities as working alternative distributions, to enforce separation from the null and thus refine the screening procedure. We show how these weighted alternatives improve various operating characteristics, such as the Bayesian False Discovery rate, of the resulting tests for a fixed mixture proportion with respect to a local, unweighted likelihood approach. Parametric and nonparametric model specifications are proposed, along with efficient samplers for posterior inference. By means of a simulation study, we exhibit how our model compares with both well-established and state-of-the-art alternatives in terms of various operating characteristics. Finally, to illustrate the versatility of our method, we conduct three differential expression analyses with publicly-available datasets from genomic studies of heterogeneous nature.

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