The optimization of atomic structures plays a pivotal role in understanding and designing materials with desired properties. However, conventional methods often struggle with the formidable task of navigating the vast potential energy surface, especially in high-dimensional spaces with numerous local minima. Recent advancements in machine learning-driven surrogate models offer a promising avenue for alleviating this computational burden. In this study, we propose a novel approach that combines the strengths of universal machine learning potentials with a Bayesian approach of the GOFEE/BEACON framework. By leveraging the comprehensive chemical knowledge encoded in pretrained universal machine learning potentials as a prior estimate of energy and forces, we enable the Gaussian process to focus solely on capturing the intricate nuances of the potential energy surface. We demonstrate the efficacy of our approach through comparative analyses across diverse systems, including periodic bulk materials, surface structures, and a cluster.

In this paper, we investigate the use of probabilistic graphical models, specifically stochastic blockmodels, for the purpose of hierarchical entity clustering on knowledge graphs. These models, seldom used in the Semantic Web community, decompose a graph into a set of probability distributions. The parameters of these distributions are then inferred allowing for their subsequent sampling to generate a random graph. In a non-parametric setting, this allows for the induction of hierarchical clusterings without prior constraints on the hierarchy's structure. Specifically, this is achieved by the integration of the Nested Chinese Restaurant Process and the Stick Breaking Process into the generative model. In this regard, we propose a model leveraging such integration and derive a collapsed Gibbs sampling scheme for its inference. To aid in understanding, we describe the steps in this derivation and provide an implementation for the sampler. We evaluate our model on synthetic and real-world datasets and quantitatively compare against benchmark models. We further evaluate our results qualitatively and find that our model is capable of inducing coherent cluster hierarchies in small scale settings. The work presented in this paper provides the first step for the further application of stochastic blockmodels for knowledge graphs on a larger scale. We conclude the paper with potential avenues for future work on more scalable inference schemes.

Generative Bayesian Computation (GBC) methods are developed to provide an efficient computational solution for maximum expected utility (MEU). We propose a density-free generative method based on quantiles that naturally calculates expected utility as a marginal of quantiles. Our approach uses a deep quantile neural estimator to directly estimate distributional utilities. Generative methods assume only the ability to simulate from the model and parameters and as such are likelihood-free. A large training dataset is generated from parameters and output together with a base distribution. Our method a number of computational advantages primarily being density-free with an efficient estimator of expected utility. A link with the dual theory of expected utility and risk taking is also discussed. To illustrate our methodology, we solve an optimal portfolio allocation problem with Bayesian learning and a power utility (a.k.a. fractional Kelly criterion). Finally, we conclude with directions for future research.

This is the second manuscript in a two-part series that uses diagnostic testing to understand the connection between prevalence (i.e. number of elements in a class), uncertainty quantification (UQ), and classification theory. Part I considered the context of supervised machine learning (ML) and established a duality between prevalence and the concept of relative conditional probability. The key idea of that analysis was to train a family of discriminative classifiers by minimizing a sum of prevalence-weighted empirical risk functions. The resulting outputs can be interpreted as relative probability level-sets, which thereby yield uncertainty estimates in the class labels. This procedure also demonstrated that certain discriminative and generative ML models are equivalent. Part II considers the extent to which these results can be extended to tasks in unsupervised learning through recourse to ideas in linear algebra. We first observe that the distribution of an impure population, for which the class of a corresponding sample is unknown, can be parameterized in terms of a prevalence. This motivates us to introduce the concept of linearly independent populations, which have different but unknown prevalence values. Using this, we identify an isomorphism between classifiers defined in terms of impure and pure populations. In certain cases, this also leads to a nonlinear system of equations whose solution yields the prevalence values of the linearly independent populations, fully realizing unsupervised learning as a generalization of supervised learning. We illustrate our methods in the context of synthetic data and a research-use-only SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA).

Chain-of-Thought (CoT) prompting and its variants have gained popularity as effective methods for solving multi-step reasoning problems using pretrained large language models (LLMs). In this work, we analyze CoT prompting from a statistical estimation perspective, providing a comprehensive characterization of its sample complexity. To this end, we introduce a multi-step latent variable model that encapsulates the reasoning process, where the latent variable encodes the task information. Under this framework, we demonstrate that when the pretraining dataset is sufficiently large, the estimator formed by CoT prompting is equivalent to a Bayesian estimator. This estimator effectively solves the multi-step reasoning problem by aggregating a posterior distribution inferred from the demonstration examples in the prompt. Moreover, we prove that the statistical error of the CoT estimator can be decomposed into two main components: (i) a prompting error, which arises from inferring the true task using CoT prompts, and (ii) the statistical error of the pretrained LLM. We establish that, under appropriate assumptions, the prompting error decays exponentially to zero as the number of demonstrations increases. Additionally, we explicitly characterize the approximation and generalization errors of the pretrained LLM. Notably, we construct a transformer model that approximates the target distribution of the multi-step reasoning problem with an error that decreases exponentially in the number of transformer blocks. Our analysis extends to other variants of CoT, including Self-Consistent CoT, Tree-of-Thought, and Selection-Inference, offering a broad perspective on the efficacy of these methods. We also provide numerical experiments to validate the theoretical findings.

Matrix completion focuses on recovering missing or incomplete information in matrices. This problem arises in various applications, including image processing and network analysis. Previous research proposed Poisson matrix completion for count data with noise that follows a Poisson distribution, which assumes that the mean and variance are equal. Since overdispersed count data, whose variance is greater than the mean, is more likely to occur in realistic settings, we assume that the noise follows the negative binomial (NB) distribution, which can be more general than the Poisson distribution. In this paper, we introduce NB matrix completion by proposing a nuclear-norm regularized model that can be solved by proximal gradient descent. In our experiments, we demonstrate that the NB model outperforms Poisson matrix completion in various noise and missing data settings on real data.

Text classification, a classic task in natural language processing (NLP), involves assigning predefined categories to textual data and is crucial for applications ranging from sentiment analysis to spam detection. This thesis advances text classification by harnessing the intrinsic knowledge of Pretrained Language Models (PLMs) to address three challenging scenarios: distractor selection for multiple-choice cloze questions, improving robustness for prompt-based zero-shot text classification, and demonstration selection for retrieval-based in-context learning. Firstly, we focus on selecting distractors for multiple-choice cloze questions, ensuring that they are misleading yet incorrect. We assess the relationship between human experts' annotations (accept/reject) and various features, including context-free features (e.g., word frequency) and context-sensitive features (e.g., conditional probabilities of fillin-the-blank words). We utilize pretrained embeddings and follow annotation instructions for context-free feature design, and we find that using contextualized word representations from PLMs as features drastically improves performance over traditional feature-based models, even rivaling human performance (Chapter 3).

In this paper we introduce the so-called Generalized Naive Bayes structure as an extension of the Naive Bayes structure. We give a new greedy algorithm that finds a good fitting Generalized Naive Bayes (GNB) probability distribution. We prove that this fits the data at least as well as the probability distribution determined by the classical Naive Bayes (NB). Then, under a not very restrictive condition, we give a second algorithm for which we can prove that it finds the optimal GNB probability distribution, i.e. best fitting structure in the sense of KL divergence. Both algorithms are constructed to maximize the information content and aim to minimize redundancy. Based on these algorithms, new methods for feature selection are introduced. We discuss the similarities and differences to other related algorithms in terms of structure, methodology, and complexity. Experimental results show, that the algorithms introduced outperform the related algorithms in many cases.

We consider a Bayesian budgeted multi-armed bandit problem, in which each arm consumes a different amount of resources when selected and there is a budget constraint on the total amount of resources that can be used. Budgeted Thompson Sampling (BTS) offers a very effective heuristic to this problem, but its arm-selection rule does not take into account the remaining budget information. We adopt \textit{Information Relaxation Sampling} framework that generalizes Thompson Sampling for classical $K$-armed bandit problems, and propose a series of algorithms that are randomized like BTS but more carefully optimize their decisions with respect to the budget constraint. In a one-to-one correspondence with these algorithms, a series of performance benchmarks that improve the conventional benchmark are also suggested. Our theoretical analysis and simulation results show that our algorithms (and our benchmarks) make incremental improvements over BTS (respectively, the conventional benchmark) across various settings including a real-world example.

In this paper we introduce a kernel-based measure for detecting differences between two conditional distributions. Using the `kernel trick' and nearest-neighbor graphs, we propose a consistent estimate of this measure which can be computed in nearly linear time (for a fixed number of nearest neighbors). Moreover, when the two conditional distributions are the same, the estimate has a Gaussian limit and its asymptotic variance has a simple form that can be easily estimated from the data. The resulting test attains precise asymptotic level and is universally consistent for detecting differences between two conditional distributions. We also provide a resampling based test using our estimate that applies to the conditional goodness-of-fit problem, which controls Type I error in finite samples and is asymptotically consistent with only a finite number of resamples. A method to de-randomize the resampling test is also presented. The proposed methods can be readily applied to a broad range of problems, ranging from classical nonparametric statistics to modern machine learning. Specifically, we explore three applications: testing model calibration, regression curve evaluation, and validation of emulator models in simulation-based inference. We illustrate the superior performance of our method for these tasks, both in simulations as well as on real data. In particular, we apply our method to (1) assess the calibration of neural network models trained on the CIFAR-10 dataset, (2) compare regression functions for wind power generation across two different turbines, and (3) validate emulator models on benchmark examples with intractable posteriors and for generating synthetic `redshift' associated with galaxy images.