This paper aims to provide differential privacy (DP) guarantees for Markov chain Monte Carlo (MCMC) algorithms. In a first part, we establish DP guarantees on samples output by MCMC algorithms as well as Monte Carlo estimators associated with these methods under assumptions on the convergence properties of the underlying Markov chain. In particular, our results highlight the critical condition of ensuring the target distribution is differentially private itself. In a second part, we specialise our analysis to the unadjusted Langevin algorithm and stochastic gradient Langevin dynamics and establish guarantees on their (R\'enyi) DP. To this end, we develop a novel methodology based on Girsanov's theorem combined with a perturbation trick to obtain bounds for an unbounded domain and in a non-convex setting. We establish: (i) uniform in $n$ privacy guarantees when the state of the chain after $n$ iterations is released, (ii) bounds on the privacy of the entire chain trajectory. These findings provide concrete guidelines for privacy-preserving MCMC.

We establish thresholds for the feasibility of random multi-graph alignment in two models. In the Gaussian model, we demonstrate an "all-or-nothing" phenomenon: above a critical threshold, exact alignment is achievable with high probability, while below it, even partial alignment is statistically impossible. In the sparse Erd\H{o}s-R\'enyi model, we rigorously identify a threshold below which no meaningful partial alignment is possible and conjecture that above this threshold, partial alignment can be achieved. To prove these results, we develop a general Bayesian estimation framework over metric spaces, which provides insight into a broader class of high-dimensional statistical problems.

Large language models (LLMs) have demonstrated remarkable in-context learning (ICL) abilities. However, existing theoretical analysis of ICL primarily exhibits two limitations: (a) Limited i.i.d. Setting. Most studies focus on supervised function learning tasks where prompts are constructed with i.i.d. input-label pairs. This i.i.d. assumption diverges significantly from real language learning scenarios where prompt tokens are interdependent. (b) Lack of Emergence Explanation. Most literature answers what ICL does from an implicit optimization perspective but falls short in elucidating how ICL emerges and the impact of pre-training phase on ICL. In our paper, to extend (a), we adopt a more practical paradigm, auto-regressive next-token prediction (AR-NTP), which closely aligns with the actual training of language models. Specifically, within AR-NTP, we emphasize prompt token-dependency, which involves predicting each subsequent token based on the preceding sequence. To address (b), we formalize a systematic pre-training and ICL framework, highlighting the layer-wise structure of sequences and topics, alongside a two-level expectation. In conclusion, we present data-dependent, topic-dependent and optimization-dependent PAC-Bayesian generalization bounds for pre-trained LLMs, investigating that ICL emerges from the generalization of sequences and topics. Our theory is supported by experiments on numerical linear dynamic systems, synthetic GINC and real-world language datasets.

Motivated by the great success of Bayesian additive regression trees (BART) on regression, we propose a nonparametric Bayesian approach for the function-on-scalar regression problem, termed as Functional BART (FBART). Utilizing spline-based function representation and tree-based domain partition model, FBART offers great flexibility in characterizing the complex and heterogeneous relationship between the response curve and scalar covariates. We devise a tailored Bayesian backfitting algorithm for estimating the parameters in the FBART model. Furthermore, we introduce an FBART model with shape constraints on the response curve, enhancing estimation and prediction performance when prior shape information of response curves is available. By incorporating a shape-constrained prior, we ensure that the posterior samples of the response curve satisfy the required shape constraints (e.g., monotonicity and/or convexity). Our proposed FBART model and its shape-constrained version are the new advances of BART models for functional data. Under certain regularity conditions, we derive the posterior convergence results for both FBART and its shape-constrained version. Finally, the superiority of the proposed methods over other competitive counterparts is validated through simulation experiments under various settings and analyses of two real datasets.

We develop an analysis of Thompson sampling for online learning under full feedback - also known as prediction with expert advice - where the learner's prior is defined over the space of an adversary's future actions, rather than the space of experts. We show regret decomposes into regret the learner expected a priori, plus a prior-robustness-type term we call excess regret. In the classical finite-expert setting, this recovers optimal rates. As an initial step towards practical online learning in settings with a potentially-uncountably-infinite number of experts, we show that Thompson sampling with a certain Gaussian process prior widely-used in the Bayesian optimization literature has a $\mathcal{O}(\beta\sqrt{T\log(1+\lambda)})$ rate against a $\beta$-bounded $\lambda$-Lipschitz adversary.

We study a ranking and selection (R&S) problem when all solutions share common parametric Bayesian input models updated with the data collected from multiple independent data-generating sources. Our objective is to identify the best system by designing a sequential sampling algorithm that collects input and simulation data given a budget. We adopt the most probable best (MPB) as the estimator of the optimum and show that its posterior probability of optimality converges to one at an exponential rate as the sampling budget increases. Assuming that the input parameters belong to a finite set, we characterize the $\epsilon$-optimal static sampling ratios for input and simulation data that maximize the convergence rate. Using these ratios as guidance, we propose the optimal sampling algorithm for R&S (OSAR) that achieves the $\epsilon$-optimal ratios almost surely in the limit. We further extend OSAR by adopting the kernel ridge regression to improve the simulation output mean prediction. This not only improves OSAR's finite-sample performance, but also lets us tackle the case where the input parameters lie in a continuous space with a strong consistency guarantee for finding the optimum. We numerically demonstrate that OSAR outperforms a state-of-the-art competitor.

To make effective decisions, it is important to have a thorough understanding of the causal relationships among actions, environments, and outcomes. This review aims to surface three crucial aspects of decision-making through a causal lens: 1) the discovery of causal relationships through causal structure learning, 2) understanding the impacts of these relationships through causal effect learning, and 3) applying the knowledge gained from the first two aspects to support decision making via causal policy learning. Moreover, we identify challenges that hinder the broader utilization of causal decision-making and discuss recent advances in overcoming these challenges. Finally, we provide future research directions to address these challenges and to further enhance the implementation of causal decision-making in practice, with real-world applications illustrated based on the proposed causal decision-making. We aim to offer a comprehensive methodology and practical implementation framework by consolidating various methods in this area into a Python-based collection. URL: https://causaldm.github.io/Causal-Decision-Making.

Machine learning (ML) has been playing important roles in drug discovery in the past years by providing (pre-)screening tools for prioritising chemical compounds to pass through wet lab experiments. One of the main ML tasks in drug discovery is to build quantitative structure-activity relationship (QSAR) models, associating the molecular structure of chemical compounds with an activity or property. These properties -- including absorption, distribution, metabolism, excretion and toxicity (ADMET) -- are essential to model compound behaviour, activity and interactions in the organism. Although several methods exist, the majority of them do not provide an appropriate model's personalisation, yielding to bias and lack of generalisation to new data since the chemical space usually shifts from application to application. This fact leads to low predictive performance when completely new data is being tested by the model. The area of Automated Machine Learning (AutoML) emerged aiming to solve this issue, outputting tailored ML algorithms to the data at hand. Although an important task, AutoML has not been practically used to assist cheminformatics and computational chemistry researchers often, with just a few works related to the field. To address these challenges, this work introduces Auto-ADMET, an interpretable evolutionary-based AutoML method for chemical ADMET property prediction. Auto-ADMET employs a Grammar-based Genetic Programming (GGP) method with a Bayesian Network Model to achieve comparable or better predictive performance against three alternative methods -- standard GGP method, pkCSM and XGBOOST model -- on 12 benchmark chemical ADMET property prediction datasets. The use of a Bayesian Network model on Auto-ADMET's evolutionary process assisted in both shaping the search procedure and interpreting the causes of its AutoML performance.

Network tomography is a crucial problem in network monitoring, where the observable path performance metric values are used to infer the unobserved ones, making it essential for tasks such as route selection, fault diagnosis, and traffic control. However, most existing methods either assume complete knowledge of network topology and metric formulas-an unrealistic expectation in many real-world scenarios with limited observability-or rely entirely on black-box end-to-end models. To tackle this, in this paper, we argue that a good network tomography requires synergizing the knowledge from both data and appropriate inductive bias from (partial) prior knowledge. To see this, we propose Deep Network Tomography (DeepNT), a novel framework that leverages a path-centric graph neural network to predict path performance metrics without relying on predefined hand-crafted metrics, assumptions, or the real network topology. The path-centric graph neural network learns the path embedding by inferring and aggregating the embeddings of the sequence of nodes that compose this path. Training path-centric graph neural networks requires learning the neural netowrk parameters and network topology under discrete constraints induced by the observed path performance metrics, which motivates us to design a learning objective that imposes connectivity and sparsity constraints on topology and path performance triangle inequality on path performance. Extensive experiments on real-world and synthetic datasets demonstrate the superiority of DeepNT in predicting performance metrics and inferring graph topology compared to state-of-the-art methods.

Linear representation hypothesis posits that high-level concepts are encoded as linear directions in the representation spaces of LLMs. Park et al. (2024) formalize this notion by unifying multiple interpretations of linear representation, such as 1-dimensional subspace representation and interventions, using a causal inner product. However, their framework relies on single-token counterfactual pairs and cannot handle ambiguous contrasting pairs, limiting its applicability to complex or context-dependent concepts. We introduce a new notion of binary concepts as unit vectors in a canonical representation space, and utilize LLMs' (neural) activation differences along with maximum likelihood estimation (MLE) to compute concept directions (i.e., steering vectors). Our method, Sum of Activation-base Normalized Difference (SAND), formalizes the use of activation differences modeled as samples from a von Mises-Fisher (vMF) distribution, providing a principled approach to derive concept directions. We extend the applicability of Park et al. (2024) by eliminating the dependency on unembedding representations and single-token pairs. Through experiments with LLaMA models across diverse concepts and benchmarks, we demonstrate that our lightweight approach offers greater flexibility, superior performance in activation engineering tasks like monitoring and manipulation.