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We present an exact Bayesian inference method for inferring posterior distributions encoded by probabilistic programs featuring possibly unbounded looping behaviors. Our method is built on an extended denotational semantics represented by probability generating functions, which resolves semantic intricacies induced by intertwining discrete probabilistic loops with conditioning (for encoding posterior observations). We implement our method in a tool called Prodigy; it augments existing computer algebra systems with the theory of generating functions for the (semi-)automatic inference and quantitative verification of conditioned probabilistic programs. Experimental results show that Prodigy can handle various infinite-state loopy programs and outperforms state-of-the-art exact inference tools over benchmarks of loop-free programs.

We introduce a physics-driven deep latent variable model (PDDLVM) to learn simultaneously parameter-to-solution (forward) and solution-to-parameter (inverse) maps of parametric partial differential equations (PDEs). Our formulation leverages conventional PDE discretization techniques, deep neural networks, probabilistic modelling, and variational inference to assemble a fully probabilistic coherent framework. In the posited probabilistic model, both the forward and inverse maps are approximated as Gaussian distributions with a mean and covariance parameterized by deep neural networks. The PDE residual is assumed to be an observed random vector of value zero, hence we model it as a random vector with a zero mean and a user-prescribed covariance. The model is trained by maximizing the probability, that is the evidence or marginal likelihood, of observing a residual of zero by maximizing the evidence lower bound (ELBO). Consequently, the proposed methodology does not require any independent PDE solves and is physics-informed at training time, allowing the real-time solution of PDE forward and inverse problems after training. The proposed framework can be easily extended to seamlessly integrate observed data to solve inverse problems and to build generative models. We demonstrate the efficiency and robustness of our method on finite element discretized parametric PDE problems such as linear and nonlinear Poisson problems, elastic shells with complex 3D geometries, and time-dependent nonlinear and inhomogeneous PDEs using a physics-informed neural network (PINN) discretization. We achieve up to three orders of magnitude speed-up after training compared to traditional finite element method (FEM), while outputting coherent uncertainty estimates.

Analysis of high-dimensional data, where the number of covariates is larger than the sample size, is a topic of current interest. In such settings, an important goal is to estimate the signal level $\tau^2$ and noise level $\sigma^2$, i.e., to quantify how much variation in the response variable can be explained by the covariates, versus how much of the variation is left unexplained. This thesis considers the estimation of these quantities in a semi-supervised setting, where for many observations only the vector of covariates $X$ is given with no responses $Y$. Our main research question is: how can one use the unlabeled data to better estimate $\tau^2$ and $\sigma^2$? We consider two frameworks: a linear regression model and a linear projection model in which linearity is not assumed. In the first framework, while linear regression is used, no sparsity assumptions on the coefficients are made. In the second framework, the linearity assumption is also relaxed and we aim to estimate the signal and noise levels defined by the linear projection. We first propose a naive estimator which is unbiased and consistent, under some assumptions, in both frameworks. We then show how the naive estimator can be improved by using zero-estimators, where a zero-estimator is a statistic arising from the unlabeled data, whose expected value is zero. In the first framework, we calculate the optimal zero-estimator improvement and discuss ways to approximate the optimal improvement. In the second framework, such optimality does no longer hold and we suggest two zero-estimators that improve the naive estimator although not necessarily optimally. Furthermore, we show that our approach reduces the variance for general initial estimators and we present an algorithm that potentially improves any initial estimator. Lastly, we consider four datasets and study the performance of our suggested methods.

Recently Chen and Poor initiated the study of learning mixtures of linear dynamical systems. While linear dynamical systems already have wide-ranging applications in modeling time-series data, using mixture models can lead to a better fit or even a richer understanding of underlying subpopulations represented in the data. In this work we give a new approach to learning mixtures of linear dynamical systems that is based on tensor decompositions. As a result, our algorithm succeeds without strong separation conditions on the components, and can be used to compete with the Bayes optimal clustering of the trajectories. Moreover our algorithm works in the challenging partially-observed setting. Our starting point is the simple but powerful observation that the classic Ho-Kalman algorithm is a close relative of modern tensor decomposition methods for learning latent variable models. This gives us a playbook for how to extend it to work with more complicated generative models.

Distribution data refers to a data set where each sample is represented as a probability distribution, a subject area receiving burgeoning interest in the field of statistics. Although several studies have developed distribution-to-distribution regression models for univariate variables, the multivariate scenario remains under-explored due to technical complexities. In this study, we introduce models for regression from one Gaussian distribution to another, utilizing the Wasserstein metric. These models are constructed using the geometry of the Wasserstein space, which enables the transformation of Gaussian distributions into components of a linear matrix space. Owing to their linear regression frameworks, our models are intuitively understandable, and their implementation is simplified because of the optimal transport problem's analytical solution between Gaussian distributions. We also explore a generalization of our models to encompass non-Gaussian scenarios. We establish the convergence rates of in-sample prediction errors for the empirical risk minimizations in our models. In comparative simulation experiments, our models demonstrate superior performance over a simpler alternative method that transforms Gaussian distributions into matrices. We present an application of our methodology using weather data for illustration purposes.

The number of modes in a probability density function is representative of the model's complexity and can also be viewed as the number of existing subpopulations. Despite its relevance, little research has been devoted to its estimation. Focusing on the univariate setting, we propose a novel approach targeting prediction accuracy inspired by some overlooked aspects of the problem. We argue for the need for structure in the solutions, the subjective and uncertain nature of modes, and the convenience of a holistic view blending global and local density properties. Our method builds upon a combination of flexible kernel estimators and parsimonious compositional splines. Feature exploration, model selection and mode testing are implemented in the Bayesian inference paradigm, providing soft solutions and allowing to incorporate expert judgement in the process. The usefulness of our proposal is illustrated through a case study in sports analytics, showcasing multiple companion visualisation tools. A thorough simulation study demonstrates that traditional modality-driven approaches paradoxically struggle to provide accurate results. In this context, our method emerges as a top-tier alternative offering innovative solutions for analysts.

Cell type deconvolution is a computational method that estimates the proportions of different cell types within bulk transcriptomics data by leveraging information from reference single-cell RNA sequencing data. Despite its origin as a simple linear regression model, this approach faces challenges due to technical and biological variability and biases between the bulk and single-cell datasets. While several new methods have been developed, most only provide point estimates of cell type proportions, neglecting the uncertainty inherent in these estimates. Consequently, false positives can arise when comparing changes in cell type proportions across multiple individuals. In this paper, we introduce MEAD, a comprehensive statistical framework for efficient cell type deconvolution. Our approach constructs asymptotically valid confidence intervals for individual cell type proportions, as well as for quantifying changes in cell type proportions across multiple individuals. Our analysis accounts for factors such as biological variability in gene expressions, gene-gene dependence, cross-platform biases, and sequencing errors, without relying on parametric assumptions about the data distributions. Moreover, we establish necessary and sufficient conditions for identifying cell type proportions in the presence of platform-specific biases across sequencing technologies.

A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.

Deep supervised learning has achieved great success in the last decade. However, its deficiencies of dependence on manual labels and vulnerability to attacks have driven people to explore a better solution. As an alternative, self-supervised learning attracts many researchers for its soaring performance on representation learning in the last several years. Self-supervised representation learning leverages input data itself as supervision and benefits almost all types of downstream tasks. In this survey, we take a look into new self-supervised learning methods for representation in computer vision, natural language processing, and graph learning. We comprehensively review the existing empirical methods and summarize them into three main categories according to their objectives: generative, contrastive, and generative-contrastive (adversarial). We further investigate related theoretical analysis work to provide deeper thoughts on how self-supervised learning works. Finally, we briefly discuss open problems and future directions for self-supervised learning. An outline slide for the survey is provided.

Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.