arXiv subjects

Sara Wade

Publications and source records attributed to Sara Wade.

18 recordsLinked to original sources

arXiv2026

The generalized underlap coefficient with an application in clustering

Quantifying distributional separation across groups is fundamental in statistical learning and scientific discovery, yet most classical discrepancy measures are tailored to two-group comparisons. We generalize the underlap coefficient (UNL), a multi-group separation measure, to multivariate settings. We study its relationship with Bayes risk and mutual information, and further interpret the UNL as a measure of dependence between group labels and variables of interest. We propose an efficient importance sampling estimator of the UNL that can be combined with flexible density estimation methods. A key application is the assessment of partition-covariate dependence in clustering, where the UNL provides an interpretable measure of whether latent group structure can be explained by specific covariates. The methodology is illustrated on two real-world datasets.

stat.ME↗

arXiv2025

Understanding uncertainty in Bayesian cluster analysis

The Bayesian approach to clustering is often appreciated for its ability to provide uncertainty in the partition structure. However, summarizing the posterior distribution over the clustering structure can be challenging, due the discrete, unordered nature and massive dimension of the space. While recent advancements provide a single clustering estimate to represent the posterior, this ignores uncertainty and may even be unrepresentative in instances where the posterior is multimodal. To enhance our understanding of uncertainty, we propose a WASserstein Approximation for Bayesian clusterIng (WASABI), which summarizes the posterior samples with not one, but multiple clustering estimates, each corresponding to a different part of the partition space that receives substantial posterior mass. Specifically, we find such clustering estimates by approximating the posterior distribution in a Wasserstein distance sense, equipped with a suitable metric on the partition space. An interesting byproduct is that a locally optimal solution can be found using a k-medoids-like algorithm on the partition space to divide the posterior samples into groups, each represented by one of the clustering estimates. Using synthetic and real datasets, we show that WASABI helps to improve the understanding of uncertainty, particularly when clusters are not well separated or when the employed model is misspecified.

stat.CO↗

arXiv2025

Understanding the Trade-offs in Accuracy and Uncertainty Quantification: Architecture and Inference Choices in Bayesian Neural Networks

As modern neural networks get more complex, specifying a model with high predictive performance and sound uncertainty quantification becomes a more challenging task. Despite some promising theoretical results on the true posterior predictive distribution of Bayesian neural networks, the properties of even the most commonly used posterior approximations are often questioned. Computational burdens and intractable posteriors expose miscalibrated Bayesian neural networks to poor accuracy and unreliable uncertainty estimates. Approximate Bayesian inference aims to replace unknown and intractable posterior distributions with some simpler but feasible distributions. The dimensions of modern deep models, coupled with the lack of identifiability, make Markov chain Monte Carlo (MCMC) tremendously expensive and unable to fully explore the multimodal posterior. On the other hand, variational inference benefits from improved computational complexity but lacks the asymptotical guarantees of sampling-based inference and tends to concentrate around a single mode. The performance of both approaches heavily depends on architectural choices; this paper aims to shed some light on this by considering the computational costs, accuracy and uncertainty quantification in different scenarios including large width and out-of-sample data. To improve posterior exploration, different model averaging and ensembling techniques are studied, along with their benefits on predictive performance. In our experiments, variational inference overall provided better uncertainty quantification than MCMC; further, stacking and ensembles of variational approximations provided comparable accuracy to MCMC at a much-reduced cost.

cs.LG↗

arXiv2024

Variational Bayesian Bow tie Neural Networks with Shrinkage

Despite the dominant role of deep models in machine learning, limitations persist, including overconfident predictions, susceptibility to adversarial attacks, and underestimation of variability in predictions. The Bayesian paradigm provides a natural framework to overcome such issues and has become the gold standard for uncertainty estimation with deep models, also providing improved accuracy and a framework for tuning critical hyperparameters. However, exact Bayesian inference is challenging, typically involving variational algorithms that impose strong independence and distributional assumptions. Moreover, existing methods are sensitive to the architectural choice of the network. We address these issues by focusing on a stochastic relaxation of the standard feed-forward rectified neural network and using sparsity-promoting priors on the weights of the neural network for increased robustness to architectural design. Thanks to Polya-Gamma data augmentation tricks, which render a conditionally linear and Gaussian model, we derive a fast, approximate variational inference algorithm that avoids distributional assumptions and independence across layers. Suitable strategies to further improve scalability and account for multimodality are considered.

stat.ML↗

arXiv2024

Covariate-dependent hierarchical Dirichlet processes

Bayesian hierarchical modeling is a natural framework to effectively integrate data and borrow information across groups. In this paper, we address problems related to density estimation and identifying clusters across related groups, by proposing a hierarchical Bayesian approach that incorporates additional covariate information. To achieve flexibility, our approach builds on ideas from Bayesian nonparametrics, combining the hierarchical Dirichlet process with dependent Dirichlet processes. The proposed model is widely applicable, accommodating multiple and mixed covariate types through appropriate kernel functions as well as different output types through suitable component-specific likelihoods. This extends our ability to discern the relationship between covariates and clusters, while also effectively borrowing information and quantifying differences across groups. By employing a data augmentation trick, we are able to tackle the intractable normalized weights and construct a Markov chain Monte Carlo algorithm for posterior inference. The proposed method is illustrated on simulated data and two real data sets on single-cell RNA sequencing (scRNA-seq) and calcium imaging. For scRNA-seq data, we show that the incorporation of cell dynamics facilitates the discovery of additional cell subgroups. On calcium imaging data, our method identifies interpretable clusters of time frames with similar neural activity, aligning with the observed behavior of the animal.

stat.ME↗

arXiv2023

Shared Differential Clustering across Single-cell RNA Sequencing Datasets with the Hierarchical Dirichlet Process

Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data collection. In this work, we construct an integrated Bayesian model that simultaneously addresses normalization, imputation and batch effects and also nonparametrically clusters cells into groups across multiple datasets. A Gibbs sampler based on a finite-dimensional approximation of the HDP is developed for posterior inference.

q-bio.GN↗

arXiv2023

Fast Deep Mixtures of Gaussian Process Experts

Mixtures of experts have become an indispensable tool for flexible modelling in a supervised learning context, allowing not only the mean function but the entire density of the output to change with the inputs. Sparse Gaussian processes (GP) have shown promise as a leading candidate for the experts in such models, and in this article, we propose to design the gating network for selecting the experts from such mixtures of sparse GPs using a deep neural network (DNN). Furthermore, a fast one pass algorithm called Cluster-Classify-Regress (CCR) is leveraged to approximate the maximum a posteriori (MAP) estimator extremely quickly. This powerful combination of model and algorithm together delivers a novel method which is flexible, robust, and extremely efficient. In particular, the method is able to outperform competing methods in terms of accuracy and uncertainty quantification. The cost is competitive on low-dimensional and small data sets, but is significantly lower for higher-dimensional and big data sets. Iteratively maximizing the distribution of experts given allocations and allocations given experts does not provide significant improvement, which indicates that the algorithm achieves a good approximation to the local MAP estimator very fast. This insight can be useful also in the context of other mixture of experts models.

cs.LG↗

arXiv2023

Bayesian dependent mixture models: A predictive comparison and survey

For exchangeable data, mixture models are an extremely useful tool for density estimation due to their attractive balance between smoothness and flexibility. When additional covariate information is present, mixture models can be extended for flexible regression by modeling the mixture parameters, namely the weights and atoms, as functions of the covariates. These types of models are interpretable and highly flexible, allowing non only the mean but the whole density of the response to change with the covariates, which is also known as density regression. This article reviews Bayesian covariate-dependent mixture models and highlights which data types can be accommodated by the different models along with the methodological and applied areas where they have been used. In addition to being highly flexible, these models are also numerous; we focus on nonparametric constructions and broadly organize them into three categories: 1) joint models of the responses and covariates, 2) conditional models with single-weights and covariate-dependent atoms, and 3) conditional models with covariate-dependent weights. The diversity and variety of the available models in the literature raises the question of how to choose among them for the application at hand. We attempt to shed light on this question through a careful analysis of the predictive equations for the conditional mean and density function as well as predictive comparisons in three simulated data examples.

stat.ME↗

arXiv2022

Leveraging variational autoencoders for multiple data imputation

Missing data persists as a major barrier to data analysis across numerous applications. Recently, deep generative models have been used for imputation of missing data, motivated by their ability to capture highly non-linear and complex relationships in the data. In this work, we investigate the ability of deep models, namely variational autoencoders (VAEs), to account for uncertainty in missing data through multiple imputation strategies. We find that VAEs provide poor empirical coverage of missing data, with underestimation and overconfident imputations, particularly for more extreme missing data values. To overcome this, we employ $β$-VAEs, which viewed from a generalized Bayes framework, provide robustness to model misspecification. Assigning a good value of $β$ is critical for uncertainty calibration and we demonstrate how this can be achieved using cross-validation. In downstream tasks, we show how multiple imputation with $β$-VAEs can avoid false discoveries that arise as artefacts of imputation.

stat.ML↗

arXiv2022

Mixtures of Gaussian Process Experts with SMC$^2$

Gaussian processes are a key component of many flexible statistical and machine learning models. However, they exhibit cubic computational complexity and high memory constraints due to the need of inverting and storing a full covariance matrix. To circumvent this, mixtures of Gaussian process experts have been considered where data points are assigned to independent experts, reducing the complexity by allowing inference based on smaller, local covariance matrices. Moreover, mixtures of Gaussian process experts substantially enrich the model's flexibility, allowing for behaviors such as non-stationarity, heteroscedasticity, and discontinuities. In this work, we construct a novel inference approach based on nested sequential Monte Carlo samplers to simultaneously infer both the gating network and Gaussian process expert parameters. This greatly improves inference compared to importance sampling, particularly in settings when a stationary Gaussian process is inappropriate, while still being thoroughly parallelizable.

stat.ML↗

arXiv2022

Bayesian nonparametric scalar-on-image regression via Potts-Gibbs random partition models

Scalar-on-image regression aims to investigate changes in a scalar response of interest based on high-dimensional imaging data. We propose a novel Bayesian nonparametric scalar-on-image regression model that utilises the spatial coordinates of the voxels to group voxels with similar effects on the response to have a common coefficient. We employ the Potts-Gibbs random partition model as the prior for the random partition in which the partition process is spatially dependent, thereby encouraging groups representing spatially contiguous regions. In addition, Bayesian shrinkage priors are utilised to identify the covariates and regions that are most relevant for the prediction. The proposed model is illustrated using the simulated data sets.

stat.ME↗

arXiv2021

Machine learning in the social and health sciences

The uptake of machine learning (ML) approaches in the social and health sciences has been rather slow, and research using ML for social and health research questions remains fragmented. This may be due to the separate development of research in the computational/data versus social and health sciences as well as a lack of accessible overviews and adequate training in ML techniques for non data science researchers. This paper provides a meta-mapping of research questions in the social and health sciences to appropriate ML approaches, by incorporating the necessary requirements to statistical analysis in these disciplines. We map the established classification into description, prediction, and causal inference to common research goals, such as estimating prevalence of adverse health or social outcomes, predicting the risk of an event, and identifying risk factors or causes of adverse outcomes. This meta-mapping aims at overcoming disciplinary barriers and starting a fluid dialogue between researchers from the social and health sciences and methodologically trained researchers. Such mapping may also help to fully exploit the benefits of ML while considering domain-specific aspects relevant to the social and health sciences, and hopefully contribute to the acceleration of the uptake of ML applications to advance both basic and applied social and health sciences research.

cs.LG↗

arXiv2021

On MCMC for variationally sparse Gaussian processes: A pseudo-marginal approach

Gaussian processes (GPs) are frequently used in machine learning and statistics to construct powerful models. However, when employing GPs in practice, important considerations must be made, regarding the high computational burden, approximation of the posterior, choice of the covariance function and inference of its hyperparmeters. To address these issues, Hensman et al. (2015) combine variationally sparse GPs with Markov chain Monte Carlo (MCMC) to derive a scalable, flexible and general framework for GP models. Nevertheless, the resulting approach requires intractable likelihood evaluations for many observation models. To bypass this problem, we propose a pseudo-marginal (PM) scheme that offers asymptotically exact inference as well as computational gains through doubly stochastic estimators for the intractable likelihood and large datasets. In complex models, the advantages of the PM scheme are particularly evident, and we demonstrate this on a two-level GP regression model with a nonparametric covariance function to capture non-stationarity.

stat.CO↗

arXiv2021

Colombian Women's Life Patterns: A Multivariate Density Regression Approach

Women in Colombia face difficulties related to the patriarchal traits of their societies and well-known conflict afflicting the country since 1948. In this critical context, our aim is to study the relationship between baseline socio-demographic factors and variables associated to fertility, partnership patterns, and work activity. To best exploit the explanatory structure, we propose a Bayesian multivariate density regression model, which can accommodate mixed responses with censored, constrained, and binary traits. The flexible nature of the models allows for nonlinear regression functions and non-standard features in the errors, such as asymmetry or multi-modality. The model has interpretable covariate-dependent weights constructed through normalization, allowing for combinations of categorical and continuous covariates. Computational difficulties for inference are overcome through an adaptive truncation algorithm combining adaptive Metropolis-Hastings and sequential Monte Carlo to create a sequence of automatically truncated posterior mixtures. For our study on Colombian women's life patterns, a variety of quantities are visualised and described, and in particular, our findings highlight the detrimental impact of family violence on women's choices and behaviors.

stat.AP↗

arXiv2019

Enriched Mixtures of Gaussian Process Experts

Mixtures of experts probabilistically divide the input space into regions, where the assumptions of each expert, or conditional model, need only hold locally. Combined with Gaussian process (GP) experts, this results in a powerful and highly flexible model. We focus on alternative mixtures of GP experts, which model the joint distribution of the inputs and targets explicitly. We highlight issues of this approach in multi-dimensional input spaces, namely, poor scalability and the need for an unnecessarily large number of experts, degrading the predictive performance and increasing uncertainty. We construct a novel model to address these issues through a nested partitioning scheme that automatically infers the number of components at both levels. Multiple response types are accommodated through a generalised GP framework, while multiple input types are included through a factorised exponential family structure. We show the effectiveness of our approach in estimating a parsimonious probabilistic description of both synthetic data of increasing dimension and an Alzheimer's challenge dataset.

stat.ML↗

arXiv2019

Posterior Inference for Sparse Hierarchical Non-stationary Models

Gaussian processes are valuable tools for non-parametric modelling, where typically an assumption of stationarity is employed. While removing this assumption can improve prediction, fitting such models is challenging. In this work, hierarchical models are constructed based on Gaussian Markov random fields with stochastic spatially varying parameters. Importantly, this allows for non-stationarity while also addressing the computational burden through a sparse banded representation of the precision matrix. In this setting, efficient Markov chain Monte Carlo (MCMC) sampling is challenging due to the strong coupling a posteriori of the parameters and hyperparameters. We develop and compare three adaptive MCMC schemes and make use of banded matrix operations for faster inference. Furthermore, a novel extension to multi-dimensional settings is proposed through an additive structure that retains the flexibility and scalability of the model, while also inheriting interpretability from the additive approach. A thorough assessment of the efficiency and accuracy of the methods in nonstationary settings is presented for both simulated experiments and a computer emulation problem.

stat.CO↗

arXiv2019

Bayesian cluster analysis: Point estimation and credible balls

Clustering is widely studied in statistics and machine learning, with applications in a variety of fields. As opposed to classical algorithms which return a single clustering solution, Bayesian nonparametric models provide a posterior over the entire space of partitions, allowing one to assess statistical properties, such as uncertainty on the number of clusters. However, an important problem is how to summarize the posterior; the huge dimension of partition space and difficulties in visualizing it add to this problem. In a Bayesian analysis, the posterior of a real-valued parameter of interest is often summarized by reporting a point estimate such as the posterior mean along with 95% credible intervals to characterize uncertainty. In this paper, we extend these ideas to develop appropriate point estimates and credible sets to summarize the posterior of clustering structure based on decision and information theoretic techniques.

stat.ME↗

arXiv2018

Pseudo-marginal Bayesian inference for supervised Gaussian process latent variable models

We introduce a Bayesian framework for inference with a supervised version of the Gaussian process latent variable model. The framework overcomes the high correlations between latent variables and hyperparameters by using an unbiased pseudo estimate for the marginal likelihood that approximately integrates over the latent variables. This is used to construct a Markov Chain to explore the posterior of the hyperparameters. We demonstrate the procedure on simulated and real examples, showing its ability to capture uncertainty and multimodality of the hyperparameters and improved uncertainty quantification in predictions when compared with variational inference.

stat.ML↗