Dealing with missing data poses significant challenges in predictive analysis, often leading to biased conclusions when oversimplified assumptions about the missing data process are made. In cases where the data are missing not at random (MNAR), jointly modeling the data and missing data indicators is essential. Motivated by a real data application with partially missing multivariate outcomes related to leaf photosynthetic traits and several environmental covariates, we propose two methods under a selection model framework for handling data with missingness in the response variables suitable for recovering various missingness mechanisms. Both approaches use a multivariate extension of Bayesian additive regression trees (BART) to flexibly model the outcomes. The first approach simultaneously uses a probit regression model to jointly model the missingness. In scenarios where the relationship between the missingness and the data is more complex or non-linear, we propose a second approach using a probit BART model to characterize the missing data process, thereby employing two BART models simultaneously. Both models also effectively handle ignorable covariate missingness. The efficacy of both models compared to existing missing data approaches is demonstrated through extensive simulations, in both univariate and multivariate settings, and through the aforementioned application to the leaf photosynthetic trait data.

Federated Adversarial Learning (FAL) is a robust framework for resisting adversarial attacks on federated learning. Although some FAL studies have developed efficient algorithms, they primarily focus on convergence performance and overlook generalization. Generalization is crucial for evaluating algorithm performance on unseen data. However, generalization analysis is more challenging due to non-smooth adversarial loss functions. A common approach to addressing this issue is to leverage smoothness approximation. In this paper, we develop algorithm stability measures to evaluate the generalization performance of two popular FAL algorithms: \textit{Vanilla FAL (VFAL)} and {\it Slack FAL (SFAL)}, using three different smooth approximation methods: 1) \textit{Surrogate Smoothness Approximation (SSA)}, (2) \textit{Randomized Smoothness Approximation (RSA)}, and (3) \textit{Over-Parameterized Smoothness Approximation (OPSA)}. Based on our in-depth analysis, we answer the question of how to properly set the smoothness approximation method to mitigate generalization error in FAL. Moreover, we identify RSA as the most effective method for reducing generalization error. In highly data-heterogeneous scenarios, we also recommend employing SFAL to mitigate the deterioration of generalization performance caused by heterogeneity. Based on our theoretical results, we provide insights to help develop more efficient FAL algorithms, such as designing new metrics and dynamic aggregation rules to mitigate heterogeneity.

Prototype-based classification learning methods are known to be inherently interpretable. However, this paradigm suffers from major limitations compared to deep models, such as lower performance. This led to the development of the so-called deep Prototype-Based Networks (PBNs), also known as prototypical parts models. In this work, we analyze these models with respect to different properties, including interpretability. In particular, we focus on the Classification-by-Components (CBC) approach, which uses a probabilistic model to ensure interpretability and can be used as a shallow or deep architecture. We show that this model has several shortcomings, like creating contradicting explanations. Based on these findings, we propose an extension of CBC that solves these issues. Moreover, we prove that this extension has robustness guarantees and derive a loss that optimizes robustness. Additionally, our analysis shows that most (deep) PBNs are related to (deep) RBF classifiers, which implies that our robustness guarantees generalize to shallow RBF classifiers. The empirical evaluation demonstrates that our deep PBN yields state-of-the-art classification accuracy on different benchmarks while resolving the interpretability shortcomings of other approaches. Further, our shallow PBN variant outperforms other shallow PBNs while being inherently interpretable and exhibiting provable robustness guarantees.

The analysis of dynamical systems is a fundamental tool in the natural sciences and engineering. It is used to understand the evolution of systems as large as entire galaxies and as small as individual molecules. With predefined conditions on the evolution of dy-namical systems, the underlying differential equations have to fulfill specific constraints in time and space. This class of problems is known as boundary value problems. This thesis presents novel approaches to learn time-reversible deterministic and stochastic dynamics constrained by initial and final conditions. The dynamics are inferred by machine learning algorithms from observed data, which is in contrast to the traditional approach of solving differential equations by numerical integration. The work in this thesis examines a set of problems of increasing difficulty each of which is concerned with learning a different aspect of the dynamics. Initially, we consider learning deterministic dynamics from ground truth solutions which are constrained by deterministic boundary conditions. Secondly, we study a boundary value problem in discrete state spaces, where the forward dynamics follow a stochastic jump process and the boundary conditions are discrete probability distributions. In particular, the stochastic dynamics of a specific jump process, the Ehrenfest process, is considered and the reverse time dynamics are inferred with machine learning. Finally, we investigate the problem of inferring the dynamics of a continuous-time stochastic process between two probability distributions without any reference information. Here, we propose a novel criterion to learn time-reversible dynamics of two stochastic processes to solve the Schr\"odinger Bridge Problem.

Transfer learning aims to transfer knowledge or information from a source domain to a relevant target domain. In this paper, we understand transfer learning from the perspectives of knowledge transferability and trustworthiness. This involves two research questions: How is knowledge transferability quantitatively measured and enhanced across domains? Can we trust the transferred knowledge in the transfer learning process? To answer these questions, this paper provides a comprehensive review of trustworthy transfer learning from various aspects, including problem definitions, theoretical analysis, empirical algorithms, and real-world applications. Specifically, we summarize recent theories and algorithms for understanding knowledge transferability under (within-domain) IID and non-IID assumptions. In addition to knowledge transferability, we review the impact of trustworthiness on transfer learning, e.g., whether the transferred knowledge is adversarially robust or algorithmically fair, how to transfer the knowledge under privacy-preserving constraints, etc. Beyond discussing the current advancements, we highlight the open questions and future directions for understanding transfer learning in a reliable and trustworthy manner.

Modern challenges of robustness, fairness, and decision-making in machine learning have led to the formulation of multi-distribution learning (MDL) frameworks in which a predictor is optimized across multiple distributions. We study the calibration properties of MDL to better understand how the predictor performs uniformly across the multiple distributions. Through classical results on decomposing proper scoring losses, we first derive the Bayes optimal rule for MDL, demonstrating that it maximizes the generalized entropy of the associated loss function. Our analysis reveals that while this approach ensures minimal worst-case loss, it can lead to non-uniform calibration errors across the multiple distributions and there is an inherent calibration-refinement trade-off, even at Bayes optimality. Our results highlight a critical limitation: despite the promise of MDL, one must use caution when designing predictors tailored to multiple distributions so as to minimize disparity.

Since the debut of DPO, it has been shown that aligning a target LLM with human preferences via the KL-constrained RLHF loss is mathematically equivalent to a special kind of reward modeling task. Concretely, the task requires: 1) using the target LLM to parameterize the reward model, and 2) tuning the reward model so that it has a 1:1 linear relationship with the true reward. However, we identify a significant issue: the DPO loss might have multiple minimizers, of which only one satisfies the required linearity condition. The problem arises from a well-known issue of the underlying Bradley-Terry preference model: it does not always have a unique maximum likelihood estimator (MLE). Consequently,the minimizer of the RLHF loss might be unattainable because it is merely one among many minimizers of the DPO loss. As a better alternative, we propose an energy-based model (EBM) that always has a unique MLE, inherently satisfying the linearity requirement. To approximate the MLE in practice, we propose a contrastive loss named Energy Preference Alignment (EPA), wherein each positive sample is contrasted against one or more strong negatives as well as many free weak negatives. Theoretical properties of our EBM enable the approximation error of EPA to almost surely vanish when a sufficient number of negatives are used. Empirically, we demonstrate that EPA consistently delivers better performance on open benchmarks compared to DPO, thereby showing the superiority of our EBM.

Conditional independence (CI) testing is a fundamental task in modern statistics and machine learning. The conditional randomization test (CRT) was recently introduced to test whether two random variables, $X$ and $Y$, are conditionally independent given a potentially high-dimensional set of random variables, $Z$. The CRT operates exceptionally well under the assumption that the conditional distribution $X|Z$ is known. However, since this distribution is typically unknown in practice, accurately approximating it becomes crucial. In this paper, we propose using conditional diffusion models (CDMs) to learn the distribution of $X|Z$. Theoretically and empirically, it is shown that CDMs closely approximate the true conditional distribution. Furthermore, CDMs offer a more accurate approximation of $X|Z$ compared to GANs, potentially leading to a CRT that performs better than those based on GANs. To accommodate complex dependency structures, we utilize a computationally efficient classifier-based conditional mutual information (CMI) estimator as our test statistic. The proposed testing procedure performs effectively without requiring assumptions about specific distribution forms or feature dependencies, and is capable of handling mixed-type conditioning sets that include both continuous and discrete variables. Theoretical analysis shows that our proposed test achieves a valid control of the type I error. A series of experiments on synthetic data demonstrates that our new test effectively controls both type-I and type-II errors, even in high dimensional scenarios.

Here, nodes from the two-cluster Stochastic Block Model (SBM) are coupled with feature vectors, which are derived from a Gaussian Mixture Model (GMM) that corresponds to their respective node labels. With only a subset of the CSBM node labels accessible for training, our primary objective becomes the accurate classification of the remaining nodes. Venturing into the transductive learning landscape, we, for the first time, pinpoint the information-theoretical threshold for the exact recovery of all test nodes in CSBM. Concurrently, we design an optimal spectral estimator inspired by Principal Component Analysis (PCA) with the training labels and essential data from both the adjacency matrix and feature vectors. We also evaluate the efficacy of graph ridge regression and Graph Convolutional Networks (GCN) on this synthetic dataset. Our findings underscore that graph ridge regression and GCN possess the ability to achieve the information threshold of exact recovery in a manner akin to the optimal estimator when using the optimal weighted self-loops. This highlights the potential role of feature learning in augmenting the proficiency of GCN, especially in the realm of semi-supervised learning.

Reliability analysis is a sub-field of uncertainty quantification that assesses the probability of a system performing as intended under various uncertainties. Traditionally, this analysis relies on deterministic models, where experiments are repeatable, i.e., they produce consistent outputs for a given set of inputs. However, real-world systems often exhibit stochastic behavior, leading to non-repeatable outcomes. These so-called stochastic simulators produce different outputs each time the model is run, even with fixed inputs. This paper formally introduces reliability analysis for stochastic models and addresses it by using suitable surrogate models to lower its typically high computational cost. Specifically, we focus on the recently introduced generalized lambda models and stochastic polynomial chaos expansions. These emulators are designed to learn the inherent randomness of the simulator's response and enable efficient uncertainty quantification at a much lower cost than traditional Monte Carlo simulation. We validate our methodology through three case studies. First, using an analytical function with a closed-form solution, we demonstrate that the emulators converge to the correct solution. Second, we present results obtained from the surrogates using a toy example of a simply supported beam. Finally, we apply the emulators to perform reliability analysis on a realistic wind turbine case study, where only a dataset of simulation results is available.