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The proximal Galerkin finite element method is a high-order, nonlinear numerical method that preserves the geometric and algebraic structure of bound constraints in infinite-dimensional function spaces. This paper introduces the proximal Galerkin method and applies it to solve free-boundary problems, enforce discrete maximum principles, and develop scalable, mesh-independent algorithms for optimal design. The paper begins with a derivation of the latent variable proximal point (LVPP) method: an unconditionally stable alternative to the interior point method. LVPP is an infinite-dimensional optimization algorithm that may be viewed as having an adaptive (Bayesian) barrier function that is updated with a new informative prior at each (outer loop) optimization iteration. One of the main benefits of this algorithm is witnessed when analyzing the classical obstacle problem. Therein, we find that the original variational inequality can be replaced by a sequence of semilinear partial differential equations (PDEs) that are readily discretized and solved with, e.g., high-order finite elements. Throughout this work, we arrive at several unexpected contributions that may be of independent interest. These include (1) a semilinear PDE we refer to as the entropic Poisson equation; (2) an algebraic/geometric connection between high-order positivity-preserving discretizations and infinite-dimensional Lie groups; and (3) a gradient-based, bound-preserving algorithm for two-field density-based topology optimization. The complete latent variable proximal Galerkin methodology combines ideas from nonlinear programming, functional analysis, tropical algebra, and differential geometry and can potentially lead to new synergies among these areas as well as within variational and numerical analysis.

Gaussian graphical models are nowadays commonly applied to the comparison of groups sharing the same variables, by jointy learning their independence structures. We consider the case where there are exactly two dependent groups and the association structure is represented by a family of coloured Gaussian graphical models suited to deal with paired data problems. To learn the two dependent graphs, together with their across-graph association structure, we implement a fused graphical lasso penalty. We carry out a comprehensive analysis of this approach, with special attention to the role played by some relevant submodel classes. In this way, we provide a broad set of tools for the application of Gaussian graphical models to paired data problems. These include results useful for the specification of penalty values in order to obtain a path of lasso solutions and an ADMM algorithm that solves the fused graphical lasso optimization problem. Finally, we present an application of our method to cancer genomics where it is of interest to compare cancer cells with a control sample from histologically normal tissues adjacent to the tumor. All the methods described in this article are implemented in the $\texttt{R}$ package $\texttt{pdglasso}$ availabe at: //github.com/savranciati/pdglasso.

According to ICH Q8 guidelines, the biopharmaceutical manufacturer submits a design space (DS) definition as part of the regulatory approval application, in which case process parameter (PP) deviations within this space are not considered a change and do not trigger a regulatory post approval procedure. A DS can be described by non-linear PP ranges, i.e., the range of one PP conditioned on specific values of another. However, independent PP ranges (linear combinations) are often preferred in biopharmaceutical manufacturing due to their operation simplicity. While some statistical software supports the calculation of a DS comprised of linear combinations, such methods are generally based on discretizing the parameter space - an approach that scales poorly as the number of PPs increases. Here, we introduce a novel method for finding linear PP combinations using a numeric optimizer to calculate the largest design space within the parameter space that results in critical quality attribute (CQA) boundaries within acceptance criteria, predicted by a regression model. A precomputed approximation of tolerance intervals is used in inequality constraints to facilitate fast evaluations of this boundary using a single matrix multiplication. Correctness of the method was validated against different ground truths with known design spaces. Compared to stateof-the-art, grid-based approaches, the optimizer-based procedure is more accurate, generally yields a larger DS and enables the calculation in higher dimensions. Furthermore, a proposed weighting scheme can be used to favor certain PPs over others and therefore enabling a more dynamic approach to DS definition and exploration. The increased PP ranges of the larger DS provide greater operational flexibility for biopharmaceutical manufacturers.

We present an extended validation of semi-analytical, semi-empirical covariance matrices for the two-point correlation function (2PCF) on simulated catalogs representative of Luminous Red Galaxies (LRG) data collected during the initial two months of operations of the Stage-IV ground-based Dark Energy Spectroscopic Instrument (DESI). We run the pipeline on multiple effective Zel'dovich (EZ) mock galaxy catalogs with the corresponding cuts applied and compare the results with the mock sample covariance to assess the accuracy and its fluctuations. We propose an extension of the previously developed formalism for catalogs processed with standard reconstruction algorithms. We consider methods for comparing covariance matrices in detail, highlighting their interpretation and statistical properties caused by sample variance, in particular, nontrivial expectation values of certain metrics even when the external covariance estimate is perfect. With improved mocks and validation techniques, we confirm a good agreement between our predictions and sample covariance. This allows one to generate covariance matrices for comparable datasets without the need to create numerous mock galaxy catalogs with matching clustering, only requiring 2PCF measurements from the data itself. The code used in this paper is publicly available at //github.com/oliverphilcox/RascalC.

We study the open question of how players learn to play a social optimum pure-strategy Nash equilibrium (PSNE) through repeated interactions in general-sum coordination games. A social optimum of a game is the stable Pareto-optimal state that provides a maximum return in the sum of all players' payoffs (social welfare) and always exists. We consider finite repeated games where each player only has access to its own utility (or payoff) function but is able to exchange information with other players. We develop a novel regret matching (RM) based algorithm for computing an efficient PSNE solution that could approach a desired Pareto-optimal outcome yielding the highest social welfare among all the attainable equilibria in the long run. Our proposed learning procedure follows the regret minimization framework but extends it in three major ways: (1) agents use global, instead of local, utility for calculating regrets, (2) each agent maintains a small and diminishing exploration probability in order to explore various PSNEs, and (3) agents stay with the actions that achieve the best global utility thus far, regardless of regrets. We prove that these three extensions enable the algorithm to select the stable social optimum equilibrium instead of converging to an arbitrary or cyclic equilibrium as in the conventional RM approach. We demonstrate the effectiveness of our approach through a set of applications in multi-agent distributed control, including a large-scale resource allocation game and a hard combinatorial task assignment problem for which no efficient (polynomial) solution exists.

In the context of the high-dimensional Gaussian linear regression for ordered variables, we study the variable selection procedure via the minimization of the penalized least-squares criterion. We focus on model selection where the penalty function depends on an unknown multiplicative constant commonly calibrated for prediction. We propose a new proper calibration of this hyperparameter to simultaneously control predictive risk and false discovery rate. We obtain non-asymptotic theoretical bounds on the False Discovery Rate with respect to the hyperparameter and we provide an algorithm to calibrate it. It is based on completely observable quantities in view of applications. Our algorithm is validated by an extensive simulation study and is compared with some existing variable selection procedures. Finally, we propose a study to generalize our approach in complete variable selection.

In high dimensional variable selection problems, statisticians often seek to design multiple testing procedures that control the False Discovery Rate (FDR), while concurrently identifying a greater number of relevant variables. Model-X methods, such as Knockoffs and conditional randomization tests, achieve the primary goal of finite-sample FDR control, assuming a known distribution of covariates. However, whether these methods can also achieve the secondary goal of maximizing discoveries remains uncertain. In fact, designing procedures to discover more relevant variables with finite-sample FDR control is a largely open question, even within the arguably simplest linear models. In this paper, we develop near-optimal multiple testing procedures for high dimensional Bayesian linear models with isotropic covariates. We introduce Model-X procedures that provably control the frequentist FDR from finite samples, even when the model is misspecified, and conjecturally achieve near-optimal power when the data follow the Bayesian linear model. Our proposed procedure, PoEdCe, incorporates three key ingredients: Posterior Expectation, distilled Conditional randomization test (dCRT), and the Benjamini-Hochberg procedure with e-values (eBH). The optimality conjecture of PoEdCe is based on a heuristic calculation of its asymptotic true positive proportion (TPP) and false discovery proportion (FDP), which is supported by methods from statistical physics as well as extensive numerical simulations. Our result establishes the Bayesian linear model as a benchmark for comparing the power of various multiple testing procedures.

Valid statistical inference is challenging when the sample is subject to unknown selection bias. Data integration can be used to correct for selection bias when we have a parallel probability sample from the same population with some common measurements. How to model and estimate the selection probability or the propensity score (PS) of a non-probability sample using an independent probability sample is the challenging part of the data integration. We approach this difficult problem by employing multiple candidate models for PS combined with empirical likelihood. By incorporating multiple propensity score models into the internal bias calibration constraint in the empirical likelihood setup, the selection bias can be eliminated so long as the multiple candidate models contain a true PS model. The bias calibration constraint under the multiple PS models is called multiple bias calibration. Multiple PS models can include both missing-at-random and missing-not-at-random models. Asymptotic properties are discussed, and some limited simulation studies are presented to compare the proposed method with some existing competitors. Plasmode simulation studies using the Culture \& Community in a Time of Crisis dataset demonstrate the practical usage and advantages of the proposed method.

Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to disentangle independent factors from observations. However, in real scenarios, factors with semantics are not necessarily independent. Instead, there might be an underlying causal structure which renders these factors dependent. We thus propose a new VAE based framework named CausalVAE, which includes a Causal Layer to transform independent exogenous factors into causal endogenous ones that correspond to causally related concepts in data. We further analyze the model identifiabitily, showing that the proposed model learned from observations recovers the true one up to a certain degree. Experiments are conducted on various datasets, including synthetic and real word benchmark CelebA. Results show that the causal representations learned by CausalVAE are semantically interpretable, and their causal relationship as a Directed Acyclic Graph (DAG) is identified with good accuracy. Furthermore, we demonstrate that the proposed CausalVAE model is able to generate counterfactual data through "do-operation" to the causal factors.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.