Daily Papers

Bayesian optimal experimental design is a sub-field of statistics focused on developing methods to make efficient use of experimental resources. Any potential design is evaluated in terms of a utility function, such as the (theoretically well-justified) expected information gain (EIG); unfortunately however, under most circumstances the EIG is intractable to evaluate. In this work we build off of successful variational approaches, which optimize a parameterized variational model with respect to bounds on the EIG. Past work focused on learning a new variational model from scratch for each new design considered. Here we present a novel neural architecture that allows experimenters to optimize a single variational model that can estimate the EIG for potentially infinitely many designs. To further improve computational efficiency, we also propose to train the variational model on a significantly cheaper-to-evaluate lower bound, and show empirically that the resulting model provides an excellent guide for more accurate, but expensive to evaluate bounds on the EIG. We demonstrate the effectiveness of our technique on generalized linear models, a class of statistical models that is widely used in the analysis of controlled experiments. Experiments show that our method is able to greatly improve accuracy over existing approximation strategies, and achieve these results with far better sample efficiency.

Real-time tsunami early warning relies on distributed sensor networks to infer seismic sources and seafloor motion. Optimizing these networks via Bayesian optimal experimental design (OED) is exceptionally challenging for systems governed by hyperbolic partial differential equations, which lack the spectral decay required by standard low-rank approximations. We present a scalable Bayesian OED framework for linear time-invariant systems. By reformulating the inverse problem in the data space, we transform OED into dense matrix subset selection. We propose a multi-GPU, Schur-complement-update-based, greedy algorithm that solves the OED problem using a pipelined approach that fully overlaps I/O with GPU computations. Our framework achieves near-perfect weak and strong scaling across hundreds of GPUs on Perlmutter and Frontier. Applied to the 2025 Gordon Bell Prize-winning digital twin for tsunami forecasting in the Cascadia Subduction Zone, we optimize a 175-sensor network, minimizing the uncertainty of a parameter field with over one billion degrees of freedom.

Bayesian Optimal Experimental Design (BOED) is a powerful tool to reduce the cost of running a sequence of experiments. When based on the Expected Information Gain (EIG), design optimization corresponds to the maximization of some intractable expected contrast between prior and posterior distributions. Scaling this maximization to high dimensional and complex settings has been an issue due to BOED inherent computational complexity. In this work, we introduce a pooled posterior distribution with cost-effective sampling properties and provide a tractable access to the EIG contrast maximization via a new EIG gradient expression. Diffusion-based samplers are used to compute the dynamics of the pooled posterior and ideas from bi-level optimization are leveraged to derive an efficient joint sampling-optimization loop. The resulting efficiency gain allows to extend BOED to the well-tested generative capabilities of diffusion models. By incorporating generative models into the BOED framework, we expand its scope and its use in scenarios that were previously impractical. Numerical experiments and comparison with state-of-the-art methods show the potential of the approach.

We introduce a gradient-free framework for Bayesian Optimal Experimental Design (BOED) in sequential settings, aimed at complex systems where gradient information is unavailable. Our method combines Ensemble Kalman Inversion (EKI) for design optimization with the Affine-Invariant Langevin Dynamics (ALDI) sampler for efficient posterior sampling-both of which are derivative-free and ensemble-based. To address the computational challenges posed by nested expectations in BOED, we propose variational Gaussian and parametrized Laplace approximations that provide tractable upper and lower bounds on the Expected Information Gain (EIG). These approximations enable scalable utility estimation in high-dimensional spaces and PDE-constrained inverse problems. We demonstrate the performance of our framework through numerical experiments ranging from linear Gaussian models to PDE-based inference tasks, highlighting the method's robustness, accuracy, and efficiency in information-driven experimental design.

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

Many critical applications, from autonomous scientific discovery to personalized medicine, demand systems that can both strategically acquire the most informative data and instantaneously perform inference based upon it. While amortized methods for Bayesian inference and experimental design offer part of the solution, neither approach is optimal in the most general and challenging task, where new data needs to be collected for instant inference. To tackle this issue, we introduce the Amortized Active Learning and Inference Engine (ALINE), a unified framework for amortized Bayesian inference and active data acquisition. ALINE leverages a transformer architecture trained via reinforcement learning with a reward based on self-estimated information gain provided by its own integrated inference component. This allows it to strategically query informative data points while simultaneously refining its predictions. Moreover, ALINE can selectively direct its querying strategy towards specific subsets of model parameters or designated predictive tasks, optimizing for posterior estimation, data prediction, or a mixture thereof. Empirical results on regression-based active learning, classical Bayesian experimental design benchmarks, and a psychometric model with selectively targeted parameters demonstrate that ALINE delivers both instant and accurate inference along with efficient selection of informative points.

This study addresses the challenge of estimating average treatment effects (ATEs) for advertising campaigns in online marketplaces where complete randomized experimentation is infeasible. We propose two key innovations: (1) a shrinkage estimator that optimally combines observational and experimental data without assuming smooth treatment effects across campaigns, and (2) a Bayesian adaptive experimental design framework that efficiently selects campaigns for randomized evaluation that minimizes cumulative risk. Our shrinkage estimator achieves lower risk compared to existing methods by balancing bias-variance tradeoffs, while our adaptive design significantly reduces the costs of campaign randomization. We establish theoretical guarantees including asymptotic normality and regret bounds. In an application to Amazon Ads data analyzing 2,583 campaigns, our approach achieves equivalent estimation precision while requiring only half of the randomized experiments needed by random sampling, the standard method widely used in practice today. The proposed method serves as a practical solution for marketplace platforms to efficiently measure advertising effectiveness while managing experimentation costs.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

We consider in this paper the problem of optimal experiment design where a decision maker can choose which points to sample to obtain an estimate hatβ of the hidden parameter β^{star} of an underlying linear model. The key challenge of this work lies in the heteroscedasticity assumption that we make, meaning that each covariate has a different and unknown variance. The goal of the decision maker is then to figure out on the fly the optimal way to allocate the total budget of T samples between covariates, as sampling several times a specific one will reduce the variance of the estimated model around it (but at the cost of a possible higher variance elsewhere). By trying to minimize the ell^2-loss E [lVerthatβ-β^{star}rVert^2] the decision maker is actually minimizing the trace of the covariance matrix of the problem, which corresponds then to online A-optimal design. Combining techniques from bandit and convex optimization we propose a new active sampling algorithm and we compare it with existing ones. We provide theoretical guarantees of this algorithm in different settings, including a O(T^{-2}) regret bound in the case where the covariates form a basis of the feature space, generalizing and improving existing results. Numerical experiments validate our theoretical findings.

Bayesian optimization is an approach to optimizing objective functions that take a long time (minutes or hours) to evaluate. It is best-suited for optimization over continuous domains of less than 20 dimensions, and tolerates stochastic noise in function evaluations. It builds a surrogate for the objective and quantifies the uncertainty in that surrogate using a Bayesian machine learning technique, Gaussian process regression, and then uses an acquisition function defined from this surrogate to decide where to sample. In this tutorial, we describe how Bayesian optimization works, including Gaussian process regression and three common acquisition functions: expected improvement, entropy search, and knowledge gradient. We then discuss more advanced techniques, including running multiple function evaluations in parallel, multi-fidelity and multi-information source optimization, expensive-to-evaluate constraints, random environmental conditions, multi-task Bayesian optimization, and the inclusion of derivative information. We conclude with a discussion of Bayesian optimization software and future research directions in the field. Within our tutorial material we provide a generalization of expected improvement to noisy evaluations, beyond the noise-free setting where it is more commonly applied. This generalization is justified by a formal decision-theoretic argument, standing in contrast to previous ad hoc modifications.

The optimization of expensive-to-evaluate black-box functions is prevalent in various scientific disciplines. Bayesian optimization is an automatic, general and sample-efficient method to solve these problems with minimal knowledge of the underlying function dynamics. However, the ability of Bayesian optimization to incorporate prior knowledge or beliefs about the function at hand in order to accelerate the optimization is limited, which reduces its appeal for knowledgeable practitioners with tight budgets. To allow domain experts to customize the optimization routine, we propose ColaBO, the first Bayesian-principled framework for incorporating prior beliefs beyond the typical kernel structure, such as the likely location of the optimizer or the optimal value. The generality of ColaBO makes it applicable across different Monte Carlo acquisition functions and types of user beliefs. We empirically demonstrate ColaBO's ability to substantially accelerate optimization when the prior information is accurate, and to retain approximately default performance when it is misleading.

Bayesian optimization provides sample-efficient global optimization for a broad range of applications, including automatic machine learning, engineering, physics, and experimental design. We introduce BoTorch, a modern programming framework for Bayesian optimization that combines Monte-Carlo (MC) acquisition functions, a novel sample average approximation optimization approach, auto-differentiation, and variance reduction techniques. BoTorch's modular design facilitates flexible specification and optimization of probabilistic models written in PyTorch, simplifying implementation of new acquisition functions. Our approach is backed by novel theoretical convergence results and made practical by a distinctive algorithmic foundation that leverages fast predictive distributions, hardware acceleration, and deterministic optimization. We also propose a novel "one-shot" formulation of the Knowledge Gradient, enabled by a combination of our theoretical and software contributions. In experiments, we demonstrate the improved sample efficiency of BoTorch relative to other popular libraries.

Bayesian optimization (BO) has established itself as a leading strategy for efficiently optimizing expensive-to-evaluate functions. Existing BO methods mostly rely on Gaussian process (GP) surrogate models and are not applicable to (doubly-stochastic) Gaussian Cox processes, where the observation process is modulated by a latent intensity function modeled as a GP. In this paper, we propose a novel maximum a posteriori inference of Gaussian Cox processes. It leverages the Laplace approximation and change of kernel technique to transform the problem into a new reproducing kernel Hilbert space, where it becomes more tractable computationally. It enables us to obtain both a functional posterior of the latent intensity function and the covariance of the posterior, thus extending existing works that often focus on specific link functions or estimating the posterior mean. Using the result, we propose a BO framework based on the Gaussian Cox process model and further develop a Nystr\"om approximation for efficient computation. Extensive evaluations on various synthetic and real-world datasets demonstrate significant improvement over state-of-the-art inference solutions for Gaussian Cox processes, as well as effective BO with a wide range of acquisition functions designed through the underlying Gaussian Cox process model.

We study preferential Bayesian optimization (BO) where reliable feedback is limited to pairwise comparison called duels. An important challenge in preferential BO, which uses the preferential Gaussian process (GP) model to represent flexible preference structure, is that the posterior distribution is a computationally intractable skew GP. The most widely used approach for preferential BO is Gaussian approximation, which ignores the skewness of the true posterior. Alternatively, Markov chain Monte Carlo (MCMC) based preferential BO is also proposed. In this work, we first verify the accuracy of Gaussian approximation, from which we reveal the critical problem that the predictive probability of duels can be inaccurate. This observation motivates us to improve the MCMC-based estimation for skew GP, for which we show the practical efficiency of Gibbs sampling and derive the low variance MC estimator. However, the computational time of MCMC can still be a bottleneck in practice. Towards building a more practical preferential BO, we develop a new method that achieves both high computational efficiency and low sample complexity, and then demonstrate its effectiveness through extensive numerical experiments.

Bayesian Optimization (BO) is a foundational strategy in the field of engineering design optimization for efficiently handling black-box functions with many constraints and expensive evaluations. This paper introduces a fast and accurate BO framework that leverages Pre-trained Transformers for Bayesian Optimization (PFN4sBO) to address constrained optimization problems in engineering. Unlike traditional BO methods that rely heavily on Gaussian Processes (GPs), our approach utilizes Prior-data Fitted Networks (PFNs), a type of pre-trained transformer, to infer constraints and optimal solutions without requiring any iterative retraining. We demonstrate the effectiveness of PFN-based BO through a comprehensive benchmark consisting of fifteen test problems, encompassing synthetic, structural, and engineering design challenges. Our findings reveal that PFN-based BO significantly outperforms Constrained Expected Improvement and Penalty-based GP methods by an order of magnitude in speed while also outperforming them in accuracy in identifying feasible, optimal solutions. This work showcases the potential of integrating machine learning with optimization techniques in solving complex engineering challenges, heralding a significant leap forward for optimization methodologies, opening up the path to using PFN-based BO to solve other challenging problems, such as enabling user-guided interactive BO, adaptive experiment design, or multi-objective design optimization. Additionally, we establish a benchmark for evaluating BO algorithms in engineering design, offering a robust platform for future research and development in the field. This benchmark framework for evaluating new BO algorithms in engineering design will be published at https://github.com/rosenyu304/BOEngineeringBenchmark.

The performance of many machine learning models depends on their hyper-parameter settings. Bayesian Optimization has become a successful tool for hyper-parameter optimization of machine learning algorithms, which aims to identify optimal hyper-parameters during an iterative sequential process. However, most of the Bayesian Optimization algorithms are designed to select models for effectiveness only and ignore the important issue of model training efficiency. Given that both model effectiveness and training time are important for real-world applications, models selected for effectiveness may not meet the strict training time requirements necessary to deploy in a production environment. In this work, we present a unified Bayesian Optimization framework for jointly optimizing models for both prediction effectiveness and training efficiency. We propose an objective that captures the tradeoff between these two metrics and demonstrate how we can jointly optimize them in a principled Bayesian Optimization framework. Experiments on model selection for recommendation tasks indicate models selected this way significantly improves model training efficiency while maintaining strong effectiveness as compared to state-of-the-art Bayesian Optimization algorithms.

Posterior sampling allows the exploitation of prior knowledge of the environment's transition dynamics to improve the sample efficiency of reinforcement learning. The prior is typically specified as a class of parametric distributions, a task that can be cumbersome in practice, often resulting in the choice of uninformative priors. In this work, we propose a novel posterior sampling approach in which the prior is given as a (partial) causal graph over the environment's variables. The latter is often more natural to design, such as listing known causal dependencies between biometric features in a medical treatment study. Specifically, we propose a hierarchical Bayesian procedure, called C-PSRL, simultaneously learning the full causal graph at the higher level and the parameters of the resulting factored dynamics at the lower level. For this procedure, we provide an analysis of its Bayesian regret, which explicitly connects the regret rate with the degree of prior knowledge. Our numerical evaluation conducted in illustrative domains confirms that C-PSRL strongly improves the efficiency of posterior sampling with an uninformative prior while performing close to posterior sampling with the full causal graph.

Bayesian optimisation is a popular, surrogate model-based approach for optimising expensive black-box functions. Given a surrogate model, the next location to expensively evaluate is chosen via maximisation of a cheap-to-query acquisition function. We present an epsilon-greedy procedure for Bayesian optimisation in batch settings in which the black-box function can be evaluated multiple times in parallel. Our epsilon-shotgun algorithm leverages the model's prediction, uncertainty, and the approximated rate of change of the landscape to determine the spread of batch solutions to be distributed around a putative location. The initial target location is selected either in an exploitative fashion on the mean prediction, or -- with probability epsilon -- from elsewhere in the design space. This results in locations that are more densely sampled in regions where the function is changing rapidly and in locations predicted to be good (i.e close to predicted optima), with more scattered samples in regions where the function is flatter and/or of poorer quality. We empirically evaluate the epsilon-shotgun methods on a range of synthetic functions and two real-world problems, finding that they perform at least as well as state-of-the-art batch methods and in many cases exceed their performance.

In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine learning model in order to decide whether to pause training and start a new model, or resume the training of a previously-considered model. We specifically tailor our method to machine learning problems by developing a novel positive-definite covariance kernel to capture a variety of training curves. Furthermore, we develop a Gaussian process prior that scales gracefully with additional temporal observations. Finally, we provide an information-theoretic framework to automate the decision process. Experiments on several common machine learning models show that our approach is extremely effective in practice.

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large combinatorial and unstructured spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose GameOpt, a novel game-theoretical approach to combinatorial BO. GameOpt establishes a cooperative game between the different optimization variables, and selects points that are game equilibria of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate- analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making GameOpt scalable to large combinatorial spaces. We demonstrate the application of GameOpt to the challenging protein design problem and validate its performance on four real-world protein datasets. Each protein can take up to 20^{X} possible configurations, where X is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.

Bayesian Optimization (BO) is typically used to optimize an unknown function f that is noisy and costly to evaluate, by exploiting an acquisition function that must be maximized at each optimization step. Even if provably asymptotically optimal BO algorithms are efficient at optimizing low-dimensional functions, scaling them to high-dimensional spaces remains an open problem, often tackled by assuming an additive structure for f. By doing so, BO algorithms typically introduce additional restrictive assumptions on the additive structure that reduce their applicability domain. This paper contains two main contributions: (i) we relax the restrictive assumptions on the additive structure of f without weakening the maximization guarantees of the acquisition function, and (ii) we address the over-exploration problem for decentralized BO algorithms. To these ends, we propose DuMBO, an asymptotically optimal decentralized BO algorithm that achieves very competitive performance against state-of-the-art BO algorithms, especially when the additive structure of f comprises high-dimensional factors.

Machine learning algorithms frequently require careful tuning of model hyperparameters, regularization terms, and optimization parameters. Unfortunately, this tuning is often a "black art" that requires expert experience, unwritten rules of thumb, or sometimes brute-force search. Much more appealing is the idea of developing automatic approaches which can optimize the performance of a given learning algorithm to the task at hand. In this work, we consider the automatic tuning problem within the framework of Bayesian optimization, in which a learning algorithm's generalization performance is modeled as a sample from a Gaussian process (GP). The tractable posterior distribution induced by the GP leads to efficient use of the information gathered by previous experiments, enabling optimal choices about what parameters to try next. Here we show how the effects of the Gaussian process prior and the associated inference procedure can have a large impact on the success or failure of Bayesian optimization. We show that thoughtful choices can lead to results that exceed expert-level performance in tuning machine learning algorithms. We also describe new algorithms that take into account the variable cost (duration) of learning experiments and that can leverage the presence of multiple cores for parallel experimentation. We show that these proposed algorithms improve on previous automatic procedures and can reach or surpass human expert-level optimization on a diverse set of contemporary algorithms including latent Dirichlet allocation, structured SVMs and convolutional neural networks.

This paper studies the problem of performing a sequence of optimal interventions in a causal dynamical system where both the target variable of interest and the inputs evolve over time. This problem arises in a variety of domains e.g. system biology and operational research. Dynamic Causal Bayesian Optimization (DCBO) brings together ideas from sequential decision making, causal inference and Gaussian process (GP) emulation. DCBO is useful in scenarios where all causal effects in a graph are changing over time. At every time step DCBO identifies a local optimal intervention by integrating both observational and past interventional data collected from the system. We give theoretical results detailing how one can transfer interventional information across time steps and define a dynamic causal GP model which can be used to quantify uncertainty and find optimal interventions in practice. We demonstrate how DCBO identifies optimal interventions faster than competing approaches in multiple settings and applications.

We propose constrained causal Bayesian optimization (cCBO), an approach for finding interventions in a known causal graph that optimize a target variable under some constraints. cCBO first reduces the search space by exploiting the graph structure and, if available, an observational dataset; and then solves the restricted optimization problem by modelling target and constraint quantities using Gaussian processes and by sequentially selecting interventions via a constrained expected improvement acquisition function. We propose different surrogate models that enable to integrate observational and interventional data while capturing correlation among effects with increasing levels of sophistication. We evaluate cCBO on artificial and real-world causal graphs showing successful trade off between fast convergence and percentage of feasible interventions.

Recent work reported that simple Bayesian optimization (BO) methods perform well for high-dimensional real-world tasks, seemingly contradicting prior work and tribal knowledge. This paper investigates why. We identify underlying challenges that arise in high-dimensional BO and explain why recent methods succeed. Our empirical analysis shows that vanishing gradients caused by Gaussian process (GP) initialization schemes play a major role in the failures of high-dimensional Bayesian optimization (HDBO) and that methods that promote local search behaviors are better suited for the task. We find that maximum likelihood estimation (MLE) of GP length scales suffices for state-of-the-art performance. Based on this, we propose a simple variant of MLE called MSR that leverages these findings to achieve state-of-the-art performance on a comprehensive set of real-world applications. We present targeted experiments to illustrate and confirm our findings.

We propose an extension of Thompson sampling to optimization problems over function spaces where the objective is a known functional of an unknown operator's output. We assume that queries to the operator (such as running a high-fidelity simulator or physical experiment) are costly, while functional evaluations on the operator's output are inexpensive. Our algorithm employs a sample-then-optimize approach using neural operator surrogates. This strategy avoids explicit uncertainty quantification by treating trained neural operators as approximate samples from a Gaussian process (GP) posterior. We derive regret bounds and theoretical results connecting neural operators with GPs in infinite-dimensional settings. Experiments benchmark our method against other Bayesian optimization baselines on functional optimization tasks involving partial differential equations of physical systems, demonstrating better sample efficiency and significant performance gains.

Bayesian optimization (BO) is a sample-efficient, surrogate-based approach to black-box optimization (BBO), but its evaluation remains dominated by synthetic functions and hyperparameter optimization (HPO) tasks that are typically low-dimensional and single-objective. Engineering design poses a substantially different regime: problems are physics-based, often high-dimensional, constrained by requirements such as cost and manufacturability, and may involve multiple objectives or mixed variables. To close this benchmarking gap, we introduce BOCoDe, an open-source, PyTorch-native benchmark comprising 307 BBO problems, including 159 engineering design tasks and widely used synthetic and HPO benchmarks. Each problem includes cited provenance and machine-readable metadata that supports programmatic discovery, including by LLM-based agents, and all tasks are exposed through a unified API compatible with open-source BO libraries. We evaluate 31 BO and evolutionary algorithms across five problem classes spanning single- and multi-objective optimization, constrained and unconstrained settings, and mixed-variable search spaces. Analyses of problem structure show that engineering tasks uniquely span constrained and multi-objective settings that synthetic and HPO suites rarely cover, while embeddings from a tabular foundation model separate them most clearly from HPO tasks. Algorithm rankings also vary substantially across domains; in several problem classes, rankings obtained on standard benchmarks do not transfer to engineering tasks. BOCoDe establishes a reproducible and extensible foundation for developing and evaluating BO methods that better reflect the demands of engineering design. Code & data can be found at https://github.com/rosenyu304/BOCoDe

We propose a general-purpose approach for improving the ability of Large Language Models (LLMs) to intelligently and adaptively gather information from a user or other external source using the framework of sequential Bayesian experimental design (BED). This enables LLMs to act as effective multi-turn conversational agents and interactively interface with external environments. Our approach, which we call BED-LLM (Bayesian Experimental Design with Large Language Models), is based on iteratively choosing questions or queries that maximize the expected information gain (EIG) about the task of interest given the responses gathered previously. We show how this EIG can be formulated in a principled way using a probabilistic model derived from the LLM's belief distribution and provide detailed insights into key decisions in its construction. Further key to the success of BED-LLM are a number of specific innovations, such as a carefully designed estimator for the EIG, not solely relying on in-context updates for conditioning on previous responses, and a targeted strategy for proposing candidate queries. We find that BED-LLM achieves substantial gains in performance across a wide range of tests based on the 20-questions game and using the LLM to actively infer user preferences, compared to direct prompting of the LLM and other adaptive design strategies.

Bayesian optimization (BO) has contributed greatly to improving model performance by suggesting promising hyperparameter configurations iteratively based on observations from multiple training trials. However, only partial knowledge (i.e., the measured performances of trained models and their hyperparameter configurations) from previous trials is transferred. On the other hand, Self-Distillation (SD) only transfers partial knowledge learned by the task model itself. To fully leverage the various knowledge gained from all training trials, we propose the BOSS framework, which combines BO and SD. BOSS suggests promising hyperparameter configurations through BO and carefully selects pre-trained models from previous trials for SD, which are otherwise abandoned in the conventional BO process. BOSS achieves significantly better performance than both BO and SD in a wide range of tasks including general image classification, learning with noisy labels, semi-supervised learning, and medical image analysis tasks.

Bayesian optimisation (BO) uses probabilistic surrogate models - usually Gaussian processes (GPs) - for the optimisation of expensive black-box functions. At each BO iteration, the GP hyperparameters are fit to previously-evaluated data by maximising the marginal likelihood. However, this fails to account for uncertainty in the hyperparameters themselves, leading to overconfident model predictions. This uncertainty can be accounted for by taking the Bayesian approach of marginalising out the model hyperparameters. We investigate whether a fully-Bayesian treatment of the Gaussian process hyperparameters in BO (FBBO) leads to improved optimisation performance. Since an analytic approach is intractable, we compare FBBO using three approximate inference schemes to the maximum likelihood approach, using the Expected Improvement (EI) and Upper Confidence Bound (UCB) acquisition functions paired with ARD and isotropic Matern kernels, across 15 well-known benchmark problems for 4 observational noise settings. FBBO using EI with an ARD kernel leads to the best performance in the noise-free setting, with much less difference between combinations of BO components when the noise is increased. FBBO leads to over-exploration with UCB, but is not detrimental with EI. Therefore, we recommend that FBBO using EI with an ARD kernel as the default choice for BO.

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

Bayesian optimisation is a popular approach for optimising expensive black-box functions. The next location to be evaluated is selected via maximising an acquisition function that balances exploitation and exploration. Gaussian processes, the surrogate models of choice in Bayesian optimisation, are often used with a constant prior mean function equal to the arithmetic mean of the observed function values. We show that the rate of convergence can depend sensitively on the choice of mean function. We empirically investigate 8 mean functions (constant functions equal to the arithmetic mean, minimum, median and maximum of the observed function evaluations, linear, quadratic polynomials, random forests and RBF networks), using 10 synthetic test problems and two real-world problems, and using the Expected Improvement and Upper Confidence Bound acquisition functions. We find that for design dimensions ge5 using a constant mean function equal to the worst observed quality value is consistently the best choice on the synthetic problems considered. We argue that this worst-observed-quality function promotes exploitation leading to more rapid convergence. However, for the real-world tasks the more complex mean functions capable of modelling the fitness landscape may be effective, although there is no clearly optimum choice.

Most bandit algorithms assume that the reward variances or their upper bounds are known, and that they are the same for all arms. This naturally leads to suboptimal performance and higher regret due to variance overestimation. On the other hand, underestimated reward variances may lead to linear regret due to committing early to a suboptimal arm. This motivated prior works on variance-adaptive frequentist algorithms, which have strong instance-dependent regret bounds but cannot incorporate prior knowledge on reward variances. We lay foundations for the Bayesian setting, which incorporates prior knowledge. This results in lower regret in practice, due to using the prior in the algorithm design, and also improved regret guarantees. Specifically, we study Gaussian bandits with {unknown heterogeneous reward variances}, and develop a Thompson sampling algorithm with prior-dependent Bayes regret bounds. We achieve lower regret with lower reward variances and more informative priors on them, which is precisely why we pay only for what is uncertain. This is the first result of its kind. Finally, we corroborate our theory with extensive experiments, which show the superiority of our variance-adaptive Bayesian algorithm over prior frequentist approaches. We also show that our approach is robust to model misspecification and can be applied with estimated priors.

Bayesian optimization has attracted huge attention from diverse research areas in science and engineering, since it is capable of efficiently finding a global optimum of an expensive-to-evaluate black-box function. In general, a probabilistic regression model is widely used as a surrogate function to model an explicit distribution over function evaluations given an input to estimate and a training dataset. Beyond the probabilistic regression-based methods, density ratio estimation-based Bayesian optimization has been suggested in order to estimate a density ratio of the groups relatively close and relatively far to a global optimum. Developing this line of research further, supervised classifiers are employed to estimate a class probability for the two groups instead of a density ratio. However, the supervised classifiers used in this strategy are prone to be overconfident for known knowledge on global solution candidates. Supposing that we have access to unlabeled points, e.g., predefined fixed-size pools, we propose density ratio estimation-based Bayesian optimization with semi-supervised learning to solve this challenge. Finally, we show the empirical results of our methods and several baseline methods in two distinct scenarios with unlabeled point sampling and a fixed-size pool, and analyze the validity of our methods in diverse experiments.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

Many applications involve estimating the mean of multiple binomial outcomes as a common problem -- assessing intergenerational mobility of census tracts, estimating prevalence of infectious diseases across countries, and measuring click-through rates for different demographic groups. The most standard approach is to report the plain average of each outcome. Despite simplicity, the estimates are noisy when the sample sizes or mean parameters are small. In contrast, the Empirical Bayes (EB) methods are able to boost the average accuracy by borrowing information across tasks. Nevertheless, the EB methods require a Bayesian model where the parameters are sampled from a prior distribution which, unlike the commonly-studied Gaussian case, is unidentified due to discreteness of binomial measurements. Even if the prior distribution is known, the computation is difficult when the sample sizes are heterogeneous as there is no simple joint conjugate prior for the sample size and mean parameter. In this paper, we consider the compound decision framework which treats the sample size and mean parameters as fixed quantities. We develop an approximate Stein's Unbiased Risk Estimator (SURE) for the average mean squared error given any class of estimators. For a class of machine learning-assisted linear shrinkage estimators, we establish asymptotic optimality, regret bounds, and valid inference. Unlike existing work, we work with the binomials directly without resorting to Gaussian approximations. This allows us to work with small sample sizes and/or mean parameters in both one-sample and two-sample settings. We demonstrate our approach using three datasets on firm discrimination, education outcomes, and innovation rates.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

We study adaptive querying for learning user-dependent quantities of interest, such as responses to held-out items and psychometric indicators, within tight question budgets. Classical Bayesian design and computerized adaptive testing typically rely on restrictive parametric assumptions or expensive posterior approximations, limiting their use in heterogeneous, high-dimensional, and cold-start settings. We introduce a persona-induced latent variable model that represents a user's state through membership in a finite dictionary of AI personas, each offering response distributions produced by a large language model. This yields expressive priors with closed-form posterior updates and efficient finite-mixture predictions, enabling scalable Bayesian design for sequential item selection. Experiments on synthetic data and WorldValuesBench demonstrate that persona-based posteriors deliver accurate probabilistic predictions and an interpretable adaptive elicitation pipeline.

We investigate an active pure-exploration setting, that includes best-arm identification, in the context of linear stochastic bandits. While asymptotically optimal algorithms exist for standard multi-arm bandits, the existence of such algorithms for the best-arm identification in linear bandits has been elusive despite several attempts to address it. First, we provide a thorough comparison and new insight over different notions of optimality in the linear case, including G-optimality, transductive optimality from optimal experimental design and asymptotic optimality. Second, we design the first asymptotically optimal algorithm for fixed-confidence pure exploration in linear bandits. As a consequence, our algorithm naturally bypasses the pitfall caused by a simple but difficult instance, that most prior algorithms had to be engineered to deal with explicitly. Finally, we avoid the need to fully solve an optimal design problem by providing an approach that entails an efficient implementation.

In the stochastic multi-armed bandit problem, a randomized probability matching policy called Thompson sampling (TS) has shown excellent performance in various reward models. In addition to the empirical performance, TS has been shown to achieve asymptotic problem-dependent lower bounds in several models. However, its optimality has been mainly addressed under light-tailed or one-parameter models that belong to exponential families. In this paper, we consider the optimality of TS for the Pareto model that has a heavy tail and is parameterized by two unknown parameters. Specifically, we discuss the optimality of TS with probability matching priors that include the Jeffreys prior and the reference priors. We first prove that TS with certain probability matching priors can achieve the optimal regret bound. Then, we show the suboptimality of TS with other priors, including the Jeffreys and the reference priors. Nevertheless, we find that TS with the Jeffreys and reference priors can achieve the asymptotic lower bound if one uses a truncation procedure. These results suggest carefully choosing noninformative priors to avoid suboptimality and show the effectiveness of truncation procedures in TS-based policies.

We consider the problem of finding an input to a stochastic black box function such that the scalar output of the black box function is as close as possible to a target value in the sense of the expected squared error. While the optimization of stochastic black boxes is classic in (robust) Bayesian optimization, the current approaches based on Gaussian processes predominantly focus either on i) maximization/minimization rather than target value optimization or ii) on the expectation, but not the variance of the output, ignoring output variations due to stochasticity in uncontrollable environmental variables. In this work, we fill this gap and derive acquisition functions for common criteria such as the expected improvement, the probability of improvement, and the lower confidence bound, assuming that aleatoric effects are Gaussian with known variance. Our experiments illustrate that this setting is compatible with certain extensions of Gaussian processes, and show that the thus derived acquisition functions can outperform classical Bayesian optimization even if the latter assumptions are violated. An industrial use case in billet forging is presented.

Bayesian Optimization (BO) is widely and successfully adopted for solving optimization problems having an expensive-to-evaluate, black-box, and non-convex objective function. However, the vanilla BO algorithm is not able to exploit possible symmetries characterizing the target problem. An intuitive case is given by optimal location problems, whose decision variables refer to a finite set of points within a continuous space, with the order of points not affecting the value of the objective function. We refer to this setting as optimization over layouts to distinguish from optimization over point-clouds where, instead, the order of points counts. As an instance of optimization over layouts we consider a real-life industrial-relevant application, that is the optimization of the layout of an offshore wind farm: given identical wind turbines, switching any pair of them has not any effect on the annual energy production. Based on Optimal Transport theory, we propose a Permutation-Invariant BO approach, namely PIBO, proved to provide better wind farm layouts when compared to the vanilla BO approach while cutting computation time roughly in half.

Bayesian optimization is a highly efficient approach to optimizing objective functions which are expensive to query. These objectives are typically represented by Gaussian process (GP) surrogate models which are easy to optimize and support exact inference. While standard GP surrogates have been well-established in Bayesian optimization, Bayesian neural networks (BNNs) have recently become practical function approximators, with many benefits over standard GPs such as the ability to naturally handle non-stationarity and learn representations for high-dimensional data. In this paper, we study BNNs as alternatives to standard GP surrogates for optimization. We consider a variety of approximate inference procedures for finite-width BNNs, including high-quality Hamiltonian Monte Carlo, low-cost stochastic MCMC, and heuristics such as deep ensembles. We also consider infinite-width BNNs and partially stochastic models such as deep kernel learning. We evaluate this collection of surrogate models on diverse problems with varying dimensionality, number of objectives, non-stationarity, and discrete and continuous inputs. We find: (i) the ranking of methods is highly problem dependent, suggesting the need for tailored inductive biases; (ii) HMC is the most successful approximate inference procedure for fully stochastic BNNs; (iii) full stochasticity may be unnecessary as deep kernel learning is relatively competitive; (iv) infinite-width BNNs are particularly promising, especially in high dimensions.

Bayesian neural learning feature a rigorous approach to estimation and uncertainty quantification via the posterior distribution of weights that represent knowledge of the neural network. This not only provides point estimates of optimal set of weights but also the ability to quantify uncertainty in decision making using the posterior distribution. Markov chain Monte Carlo (MCMC) techniques are typically used to obtain sample-based estimates of the posterior distribution. However, these techniques face challenges in convergence and scalability, particularly in settings with large datasets and network architectures. This paper address these challenges in two ways. First, parallel tempering is used used to explore multiple modes of the posterior distribution and implemented in multi-core computing architecture. Second, we make within-chain sampling schemes more efficient by using Langevin gradient information in forming Metropolis-Hastings proposal distributions. We demonstrate the techniques using time series prediction and pattern classification applications. The results show that the method not only improves the computational time, but provides better prediction or decision making capabilities when compared to related methods.

Bayesian optimization (BO) is a powerful approach for optimizing complex and expensive-to-evaluate black-box functions. Its importance is underscored in many applications, notably including hyperparameter tuning, but its efficacy depends on efficiently balancing exploration and exploitation. While there has been substantial progress in BO methods, striking this balance remains a delicate process. In this light, we present LLAMBO, a novel approach that integrates the capabilities of Large Language Models (LLM) within BO. At a high level, we frame the BO problem in natural language, enabling LLMs to iteratively propose and evaluate promising solutions conditioned on historical evaluations. More specifically, we explore how combining contextual understanding, few-shot learning proficiency, and domain knowledge of LLMs can improve model-based BO. Our findings illustrate that LLAMBO is effective at zero-shot warmstarting, and enhances surrogate modeling and candidate sampling, especially in the early stages of search when observations are sparse. Our approach is performed in context and does not require LLM finetuning. Additionally, it is modular by design, allowing individual components to be integrated into existing BO frameworks, or function cohesively as an end-to-end method. We empirically validate LLAMBO's efficacy on the problem of hyperparameter tuning, highlighting strong empirical performance across a range of diverse benchmarks, proprietary, and synthetic tasks.

We review our recent work in the area of autonomous materials research, highlighting the coupling of machine learning methods and models and more problem-aware modeling. We review the general Bayesian framework for closed-loop design employed by many autonomous materials platforms. We then provide examples of our work on such platforms. We finally review our approaches to extend current statistical and ML models to better reflect problem-specific structure including the use of physics-based models and incorporation of operational considerations into the decision-making procedure.

Black box optimisation of an unknown function from expensive and noisy evaluations is a ubiquitous problem in machine learning, academic research and industrial production. An abstraction of the problem can be formulated as a kernel based bandit problem (also known as Bayesian optimisation), where a learner aims at optimising a kernelized function through sequential noisy observations. The existing work predominantly assumes feedback is immediately available; an assumption which fails in many real world situations, including recommendation systems, clinical trials and hyperparameter tuning. We consider a kernel bandit problem under stochastically delayed feedback, and propose an algorithm with mathcal{O}(Gamma_k(T)T+E[tau]) regret, where T is the number of time steps, Gamma_k(T) is the maximum information gain of the kernel with T observations, and tau is the delay random variable. This represents a significant improvement over the state of the art regret bound of mathcal{O}(Gamma_k(T)T+E[tau]Gamma_k(T)) reported in Verma et al. (2022). In particular, for very non-smooth kernels, the information gain grows almost linearly in time, trivializing the existing results. We also validate our theoretical results with simulations.

The relationship between material properties and independent variables such as temperature, external field or time, is usually represented by a curve or surface in a multi-dimensional space. Determining such a curve or surface requires a series of experiments or calculations which are often time and cost consuming. A general strategy uses an appropriate utility function to sample the space to recommend the next optimal experiment or calculation within an active learning loop. However, knowing what the optimal sampling strategy to use to minimize the number of experiments is an outstanding problem. We compare a number of strategies based on directed exploration on several materials problems of varying complexity using a Kriging based model. These include one dimensional curves such as the fatigue life curve for 304L stainless steel and the Liquidus line of the Fe-C phase diagram, surfaces such as the Hartmann 3 function in 3D space and the fitted intermolecular potential for Ar-SH, and a four dimensional data set of experimental measurements for BaTiO3 based ceramics. We also consider the effects of experimental noise on the Hartmann 3 function. We find that directed exploration guided by maximum variance provides better performance overall, converging faster across several data sets. However, for certain problems, the trade-off methods incorporating exploitation can perform at least as well, if not better than maximum variance. Thus, we discuss how the choice of the utility function depends on the distribution of the data, the model performance and uncertainties, additive noise as well as the budget.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

Reinforcement learning (RL) has shown remarkable success across a wide range of complex tasks. However, RL outcomes can be highly stochastic, and both expected performance and variability often depend on hyperparameter (HP) configurations. We propose efficient and risk-averse heteroscedastic Bayesian Optimization (ERAHBO), a Bayesian optimization method that models both the mean and variance of learning outcomes as functions of the HP configurations. ERAHBO aims to identify HP configurations that achieve high average return while reducing variability across training runs, and it improves the sample efficiency of the HP optimization via adaptive re-sampling rather than a fixed budget per HP. Empirical evaluations across diverse RL algorithms and environments demonstrate that ERAHBO generally outperforms both risk-neutral and risk-averse baselines, delivering improved sample efficiency for risk-averse returns.

Bayesian Optimisation (BO) refers to a class of methods for global optimisation of a function f which is only accessible via point evaluations. It is typically used in settings where f is expensive to evaluate. A common use case for BO in machine learning is model selection, where it is not possible to analytically model the generalisation performance of a statistical model, and we resort to noisy and expensive training and validation procedures to choose the best model. Conventional BO methods have focused on Euclidean and categorical domains, which, in the context of model selection, only permits tuning scalar hyper-parameters of machine learning algorithms. However, with the surge of interest in deep learning, there is an increasing demand to tune neural network architectures. In this work, we develop NASBOT, a Gaussian process based BO framework for neural architecture search. To accomplish this, we develop a distance metric in the space of neural network architectures which can be computed efficiently via an optimal transport program. This distance might be of independent interest to the deep learning community as it may find applications outside of BO. We demonstrate that NASBOT outperforms other alternatives for architecture search in several cross validation based model selection tasks on multi-layer perceptrons and convolutional neural networks.

We investigate stochastic combinatorial multi-armed bandit with semi-bandit feedback (CMAB). In CMAB, the question of the existence of an efficient policy with an optimal asymptotic regret (up to a factor poly-logarithmic with the action size) is still open for many families of distributions, including mutually independent outcomes, and more generally the multivariate sub-Gaussian family. We propose to answer the above question for these two families by analyzing variants of the Combinatorial Thompson Sampling policy (CTS). For mutually independent outcomes in [0,1], we propose a tight analysis of CTS using Beta priors. We then look at the more general setting of multivariate sub-Gaussian outcomes and propose a tight analysis of CTS using Gaussian priors. This last result gives us an alternative to the Efficient Sampling for Combinatorial Bandit policy (ESCB), which, although optimal, is not computationally efficient.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Resided at the intersection of multi-fidelity optimization (MFO) and Bayesian optimization (BO), MF BO has found a niche in solving expensive engineering design optimization problems, thanks to its advantages in incorporating physical and mathematical understandings of the problems, saving resources, addressing exploitation-exploration trade-off, considering uncertainty, and processing parallel computing. The increasing number of works dedicated to MF BO suggests the need for a comprehensive review of this advanced optimization technique. In this paper, we survey recent developments of two essential ingredients of MF BO: Gaussian process (GP) based MF surrogates and acquisition functions. We first categorize the existing MF modeling methods and MFO strategies to locate MF BO in a large family of surrogate-based optimization and MFO algorithms. We then exploit the common properties shared between the methods from each ingredient of MF BO to describe important GP-based MF surrogate models and review various acquisition functions. By doing so, we expect to provide a structured understanding of MF BO. Finally, we attempt to reveal important aspects that require further research for applications of MF BO in solving intricate yet important design optimization problems, including constrained optimization, high-dimensional optimization, optimization under uncertainty, and multi-objective optimization.

To minimize the average of a set of log-convex functions, the stochastic Newton method iteratively updates its estimate using subsampled versions of the full objective's gradient and Hessian. We contextualize this optimization problem as sequential Bayesian inference on a latent state-space model with a discriminatively-specified observation process. Applying Bayesian filtering then yields a novel optimization algorithm that considers the entire history of gradients and Hessians when forming an update. We establish matrix-based conditions under which the effect of older observations diminishes over time, in a manner analogous to Polyak's heavy ball momentum. We illustrate various aspects of our approach with an example and review other relevant innovations for the stochastic Newton method.

Autonomous scientific discovery systems increasingly use large language models (LLMs) to propose new hypotheses, but many such systems condition primarily on experimental memory: archives of high-scoring candidates or heuristic summaries of recent trials. We argue that discovery agents should instead maintain explicit, uncertainty-aware beliefs about hypothesis quality. We introduce BayesEvolve, a belief-guided discovery framework that converts experimental evidence into a predictive belief state and uses this belief to guide future experimentation. As a controlled testbed for belief-guided discovery, we evaluate BayesEvolve on shifted BBOB-style black-box optimization tasks, leaving program and laboratory discovery domains to future work. BayesEvolve improves sample efficiency over memory- and archive-guided LLM baselines under a fixed evaluation budget. We further show that the belief state is predictive on held-out candidate pools, that controlled decision-rule ablations favor belief-guided selection with an annealed uncertainty bonus, and that BayesEvolve exhibits productive late-stage concentration rather than unfocused exploration.

Designing learnable information-theoretic objectives for robot exploration remains challenging. Such objectives aim to guide exploration toward data that reduces uncertainty in model parameters, yet it is often unclear what information the collected data can actually reveal. Although reinforcement learning (RL) can optimize a given objective, constructing objectives that reflect parametric learnability is difficult in high-dimensional robotic systems. Many parameter directions are weakly observable or unidentifiable, and even when identifiable directions are selected, omitted directions can still influence exploration and distort information measures. To address this challenge, we propose Quasi-Optimal Experimental Design (Q{\footnotesize OED}), an adaptive information objective grounded in optimal experimental design. Q{\footnotesize OED} (i) performs eigenspace analysis of the Fisher information matrix to identify an observable subspace and select identifiable parameter directions, and (ii) modifies the exploration objective to emphasize these directions while suppressing nuisance effects from non-critical parameters. Under bounded nuisance influence and limited coupling between critical and nuisance directions, Q{\footnotesize OED} provides a constant-factor approximation to the ideal information objective that explores all parameters. We evaluate Q{\footnotesize OED} on simulated and real-world navigation and manipulation tasks, where identifiable-direction selection and nuisance suppression yield performance improvements of 35.23{\percent} and 21.98{\percent}, respectively. When integrated as an exploration objective in model-based policy optimization, Q{\footnotesize OED} further improves policy performance over established RL baselines.

We analyze the Bayesian regret of the Gaussian process posterior sampling reinforcement learning (GP-PSRL) algorithm. Posterior sampling is a heuristic for decision-making under uncertainty that has been used to develop successful algorithms for a variety of continuous control problems. However, theoretical work on GP-PSRL is limited. All known regret bounds either have a sub-optimal growth rate, require strong smoothness assumptions, or fail to properly account for the fact that the set of possible system states is unbounded. Through a recursive application of the Borell-Tsirelson-Ibragimov-Sudakov inequality, we show that, with high probability, the states actually visited by the algorithm are contained within a ball of near-constant radius. We then use the chaining method to control the regret suffered by GP-PSRL under weak smoothness conditions. Our main result is a Bayesian regret bound of the order mathcal{O}(Hγ_TT), where H is the horizon, T is the number of time steps and γ_T is the expected information gain. With this result, we resolve the limitations with prior theoretical work on PSRL, and provide the theoretical foundation and tools for analyzing PSRL in complex settings.

The human intrinsic desire to pursue knowledge, also known as curiosity, is considered essential in the process of skill acquisition. With the aid of artificial curiosity, we could equip current techniques for control, such as Reinforcement Learning, with more natural exploration capabilities. A promising approach in this respect has consisted of using Bayesian surprise on model parameters, i.e. a metric for the difference between prior and posterior beliefs, to favour exploration. In this contribution, we propose to apply Bayesian surprise in a latent space representing the agent's current understanding of the dynamics of the system, drastically reducing the computational costs. We extensively evaluate our method by measuring the agent's performance in terms of environment exploration, for continuous tasks, and looking at the game scores achieved, for video games. Our model is computationally cheap and compares positively with current state-of-the-art methods on several problems. We also investigate the effects caused by stochasticity in the environment, which is often a failure case for curiosity-driven agents. In this regime, the results suggest that our approach is resilient to stochastic transitions.

We introduce and study the problem of detecting whether an agent is updating their prior beliefs given new evidence in an optimal way that is Bayesian, or whether they are biased towards their own prior. In our model, biased agents form posterior beliefs that are a convex combination of their prior and the Bayesian posterior, where the more biased an agent is, the closer their posterior is to the prior. Since we often cannot observe the agent's beliefs directly, we take an approach inspired by information design. Specifically, we measure an agent's bias by designing a signaling scheme and observing the actions they take in response to different signals, assuming that they are maximizing their own expected utility; our goal is to detect bias with a minimum number of signals. Our main results include a characterization of scenarios where a single signal suffices and a computationally efficient algorithm to compute optimal signaling schemes.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Amid mounting concern about the reliability and credibility of machine learning research, we present a principled framework for making robust and generalizable claims: the multiverse analysis. Our framework builds upon the multiverse analysis (Steegen et al., 2016) introduced in response to psychology's own reproducibility crisis. To efficiently explore high-dimensional and often continuous ML search spaces, we model the multiverse with a Gaussian Process surrogate and apply Bayesian experimental design. Our framework is designed to facilitate drawing robust scientific conclusions about model performance, and thus our approach focuses on exploration rather than conventional optimization. In the first of two case studies, we investigate disputed claims about the relative merit of adaptive optimizers. Second, we synthesize conflicting research on the effect of learning rate on the large batch training generalization gap. For the machine learning community, the multiverse analysis is a simple and effective technique for identifying robust claims, for increasing transparency, and a step toward improved reproducibility.

We investigate the extent to which offline demonstration data can improve online learning. It is natural to expect some improvement, but the question is how, and by how much? We show that the degree of improvement must depend on the quality of the demonstration data. To generate portable insights, we focus on Thompson sampling (TS) applied to a multi-armed bandit as a prototypical online learning algorithm and model. The demonstration data is generated by an expert with a given competence level, a notion we introduce. We propose an informed TS algorithm that utilizes the demonstration data in a coherent way through Bayes' rule and derive a prior-dependent Bayesian regret bound. This offers insight into how pretraining can greatly improve online performance and how the degree of improvement increases with the expert's competence level. We also develop a practical, approximate informed TS algorithm through Bayesian bootstrapping and show substantial empirical regret reduction through experiments.

Some classical uncertainty quantification problems require the estimation of multiple expectations. Estimating all of them accurately is crucial and can have a major impact on the analysis to perform, and standard existing Monte Carlo methods can be costly to do so. We propose here a new procedure based on importance sampling and control variates for estimating more efficiently multiple expectations with the same sample. We first show that there exists a family of optimal estimators combining both importance sampling and control variates, which however cannot be used in practice because they require the knowledge of the values of the expectations to estimate. Motivated by the form of these optimal estimators and some interesting properties, we therefore propose an adaptive algorithm. The general idea is to adaptively update the parameters of the estimators for approaching the optimal ones. We suggest then a quantitative stopping criterion that exploits the trade-off between approaching these optimal parameters and having a sufficient budget left. This left budget is then used to draw a new independent sample from the final sampling distribution, allowing to get unbiased estimators of the expectations. We show how to apply our procedure to sensitivity analysis, by estimating Sobol' indices and quantifying the impact of the input distributions. Finally, realistic test cases show the practical interest of the proposed algorithm, and its significant improvement over estimating the expectations separately.

Motivated by the need to efficiently identify multiple candidates in high trial-and-error cost tasks such as drug discovery, we propose a near-optimal algorithm to identify all ε-best arms (i.e., those at most ε worse than the optimum). Specifically, we introduce LinFACT, an algorithm designed to optimize the identification of all ε-best arms in linear bandits. We establish a novel information-theoretic lower bound on the sample complexity of this problem and demonstrate that LinFACT achieves instance optimality by matching this lower bound up to a logarithmic factor. A key ingredient of our proof is to integrate the lower bound directly into the scaling process for upper bound derivation, determining the termination round and thus the sample complexity. We also extend our analysis to settings with model misspecification and generalized linear models. Numerical experiments, including synthetic and real drug discovery data, demonstrate that LinFACT identifies more promising candidates with reduced sample complexity, offering significant computational efficiency and accelerating early-stage exploratory experiments.

Eight percent of global carbon dioxide emissions can be attributed to the production of cement, the main component of concrete, which is also the dominant source of CO2 emissions in the construction of data centers. The discovery of lower-carbon concrete formulae is therefore of high significance for sustainability. However, experimenting with new concrete formulae is time consuming and labor intensive, as one usually has to wait to record the concrete's 28-day compressive strength, a quantity whose measurement can by its definition not be accelerated. This provides an opportunity for experimental design methodology like Bayesian Optimization (BO) to accelerate the search for strong and sustainable concrete formulae. Herein, we 1) propose modeling steps that make concrete strength amenable to be predicted accurately by a Gaussian process model with relatively few measurements, 2) formulate the search for sustainable concrete as a multi-objective optimization problem, and 3) leverage the proposed model to carry out multi-objective BO with real-world strength measurements of the algorithmically proposed mixes. Our experimental results show improved trade-offs between the mixtures' global warming potential (GWP) and their associated compressive strengths, compared to mixes based on current industry practices. Our methods are open-sourced at github.com/facebookresearch/SustainableConcrete.

We consider the problem of global optimization with noisy zeroth order oracles - a well-motivated problem useful for various applications ranging from hyper-parameter tuning for deep learning to new material design. Existing work relies on Gaussian processes or other non-parametric family, which suffers from the curse of dimensionality. In this paper, we propose a new algorithm GO-UCB that leverages a parametric family of functions (e.g., neural networks) instead. Under a realizable assumption and a few other mild geometric conditions, we show that GO-UCB achieves a cumulative regret of O(T) where T is the time horizon. At the core of GO-UCB is a carefully designed uncertainty set over parameters based on gradients that allows optimistic exploration. Synthetic and real-world experiments illustrate GO-UCB works better than Bayesian optimization approaches in high dimensional cases, even if the model is misspecified.

Performance of machine learning algorithms depends critically on identifying a good set of hyperparameters. While recent approaches use Bayesian optimization to adaptively select configurations, we focus on speeding up random search through adaptive resource allocation and early-stopping. We formulate hyperparameter optimization as a pure-exploration non-stochastic infinite-armed bandit problem where a predefined resource like iterations, data samples, or features is allocated to randomly sampled configurations. We introduce a novel algorithm, Hyperband, for this framework and analyze its theoretical properties, providing several desirable guarantees. Furthermore, we compare Hyperband with popular Bayesian optimization methods on a suite of hyperparameter optimization problems. We observe that Hyperband can provide over an order-of-magnitude speedup over our competitor set on a variety of deep-learning and kernel-based learning problems.

Optimizing high-dimensional and complex black-box functions is crucial in numerous scientific applications. While Bayesian optimization (BO) is a powerful method for sample-efficient optimization, it struggles with the curse of dimensionality and scaling to thousands of evaluations. Recently, leveraging generative models to solve black-box optimization problems has emerged as a promising framework. However, those methods often underperform compared to BO methods due to limited expressivity and difficulty of uncertainty estimation in high-dimensional spaces. To overcome these issues, we introduce DiBO, a novel framework for solving high-dimensional black-box optimization problems. Our method iterates two stages. First, we train a diffusion model to capture the data distribution and deep ensembles to predict function values with uncertainty quantification. Second, we cast the candidate selection as a posterior inference problem to balance exploration and exploitation in high-dimensional spaces. Concretely, we fine-tune diffusion models to amortize posterior inference. Extensive experiments demonstrate that our method outperforms state-of-the-art baselines across synthetic and real-world tasks. Our code is publicly available https://github.com/umkiyoung/DiBO{here}.

Polymeric nano- and micro-scale particles have critical roles in tackling critical healthcare and energy challenges with their miniature characteristics. However, tailoring their synthesis process to meet specific design targets has traditionally depended on domain expertise and costly trial-and-errors. Recently, modeling strategies, particularly Bayesian optimization (BO), have been proposed to aid materials discovery for maximized/minimized properties. Coming from practical demands, this study for the first time integrates constrained and composite Bayesian optimization (CCBO) to perform efficient target value optimization under black-box feasibility constraints and limited data for laboratory experimentation. Using a synthetic problem that simulates electrospraying, a model nanomanufacturing process, CCBO strategically avoided infeasible conditions and efficiently optimized particle production towards predefined size targets, surpassing standard BO pipelines and providing decisions comparable to human experts. Further laboratory experiments validated CCBO capability to guide the rational synthesis of poly(lactic-co-glycolic acid) (PLGA) particles with diameters of 300 nm and 3.0 mum via electrospraying. With minimal initial data and unknown experiment constraints, CCBO reached the design targets within 4 iterations. Overall, the CCBO approach presents a versatile and holistic optimization paradigm for next-generation target-driven particle synthesis empowered by artificial intelligence (AI).

Bayesian neural networks (BNNs) augment deep networks with uncertainty quantification by Bayesian treatment of the network weights. However, such models face the challenge of Bayesian inference in a high-dimensional and usually over-parameterized space. This paper investigates a new line of Bayesian deep learning by performing Bayesian inference on network structure. Instead of building structure from scratch inefficiently, we draw inspirations from neural architecture search to represent the network structure. We then develop an efficient stochastic variational inference approach which unifies the learning of both network structure and weights. Empirically, our method exhibits competitive predictive performance while preserving the benefits of Bayesian principles across challenging scenarios. We also provide convincing experimental justification for our modeling choice.

Diffusion models recently proved to be remarkable priors for Bayesian inverse problems. However, training these models typically requires access to large amounts of clean data, which could prove difficult in some settings. In this work, we present a novel method based on the expectation-maximization algorithm for training diffusion models from incomplete and noisy observations only. Unlike previous works, our method leads to proper diffusion models, which is crucial for downstream tasks. As part of our method, we propose and motivate an improved posterior sampling scheme for unconditional diffusion models. We present empirical evidence supporting the effectiveness of our method.

We consider the problem of learning a target function corresponding to a single hidden layer neural network, with a quadratic activation function after the first layer, and random weights. We consider the asymptotic limit where the input dimension and the network width are proportionally large. Recent work [Cui & al '23] established that linear regression provides Bayes-optimal test error to learn such a function when the number of available samples is only linear in the dimension. That work stressed the open challenge of theoretically analyzing the optimal test error in the more interesting regime where the number of samples is quadratic in the dimension. In this paper, we solve this challenge for quadratic activations and derive a closed-form expression for the Bayes-optimal test error. We also provide an algorithm, that we call GAMP-RIE, which combines approximate message passing with rotationally invariant matrix denoising, and that asymptotically achieves the optimal performance. Technically, our result is enabled by establishing a link with recent works on optimal denoising of extensive-rank matrices and on the ellipsoid fitting problem. We further show empirically that, in the absence of noise, randomly-initialized gradient descent seems to sample the space of weights, leading to zero training loss, and averaging over initialization leads to a test error equal to the Bayes-optimal one.

The Evidence Lower Bound (ELBO) is a quantity that plays a key role in variational inference. It can also be used as a criterion in model selection. However, though extremely popular in practice in the variational Bayes community, there has never been a general theoretic justification for selecting based on the ELBO. In this paper, we show that the ELBO maximization strategy has strong theoretical guarantees, and is robust to model misspecification while most works rely on the assumption that one model is correctly specified. We illustrate our theoretical results by an application to the selection of the number of principal components in probabilistic PCA.

We propose the Bayes-UCBVI algorithm for reinforcement learning in tabular, stage-dependent, episodic Markov decision process: a natural extension of the Bayes-UCB algorithm by Kaufmann et al. (2012) for multi-armed bandits. Our method uses the quantile of a Q-value function posterior as upper confidence bound on the optimal Q-value function. For Bayes-UCBVI, we prove a regret bound of order O(H^3SAT) where H is the length of one episode, S is the number of states, A the number of actions, T the number of episodes, that matches the lower-bound of Ω(H^3SAT) up to poly-log terms in H,S,A,T for a large enough T. To the best of our knowledge, this is the first algorithm that obtains an optimal dependence on the horizon H (and S) without the need for an involved Bernstein-like bonus or noise. Crucial to our analysis is a new fine-grained anti-concentration bound for a weighted Dirichlet sum that can be of independent interest. We then explain how Bayes-UCBVI can be easily extended beyond the tabular setting, exhibiting a strong link between our algorithm and Bayesian bootstrap (Rubin, 1981).

Building local surrogates to accelerate stationary point searches on potential energy surfaces spans decades of effort. Done correctly, surrogates can reduce the number of expensive electronic structure evaluations by roughly an order of magnitude while preserving the accuracy of the underlying theory, with the gain depending on oracle cost, search distance, and the availability of analytical forces. We present a unified Bayesian optimization view of minimization, single-point saddle searches, and double-ended path searches: all three share one six-step surrogate loop and differ only in the inner optimization target and the acquisition criterion. The framework uses Gaussian process regression with derivative observations, inverse-distance kernels, and active learning, and we develop optional extensions for production use, including farthest-point sampling with the Earth Mover's Distance, MAP regularization, an adaptive trust radius, and random Fourier features for scaling. Accompanying pedagogical Rust code demonstrates that all three applications use the same Bayesian optimization loop, bridging the gap between theoretical formulation and practical execution.

Reinforcement Learning algorithms that learn from human feedback (RLHF) need to be efficient in terms of statistical complexity, computational complexity, and query complexity. In this work, we consider the RLHF setting where the feedback is given in the format of preferences over pairs of trajectories. In the linear MDP model, using randomization in algorithm design, we present an algorithm that is sample efficient (i.e., has near-optimal worst-case regret bounds) and has polynomial running time (i.e., computational complexity is polynomial with respect to relevant parameters). Our algorithm further minimizes the query complexity through a novel randomized active learning procedure. In particular, our algorithm demonstrates a near-optimal tradeoff between the regret bound and the query complexity. To extend the results to more general nonlinear function approximation, we design a model-based randomized algorithm inspired by the idea of Thompson sampling. Our algorithm minimizes Bayesian regret bound and query complexity, again achieving a near-optimal tradeoff between these two quantities. Computation-wise, similar to the prior Thompson sampling algorithms under the regular RL setting, the main computation primitives of our algorithm are Bayesian supervised learning oracles which have been heavily investigated on the empirical side when applying Thompson sampling algorithms to RL benchmark problems.

Understanding causality should be a core requirement of any attempt to build real impact through AI. Due to the inherent unobservability of counterfactuals, large randomised trials (RCTs) are the standard for causal inference. But large experiments are generically expensive, and randomisation carries its own costs, e.g. when suboptimal decisions are trialed. Recent work has proposed more sample-efficient alternatives to RCTs, but these are not adaptable to the downstream application for which the causal effect is sought. In this work, we develop a task-specific approach to experimental design and derive sampling strategies customised to particular downstream applications. Across a range of important tasks, real-world datasets, and sample sizes, our method outperforms other benchmarks, e.g. requiring an order-of-magnitude less data to match RCT performance on targeted marketing tasks.

Recently, partial Bayesian neural networks (pBNNs), which only consider a subset of the parameters to be stochastic, were shown to perform competitively with full Bayesian neural networks. However, pBNNs are often multi-modal in the latent-variable space and thus challenging to approximate with parametric models. To address this problem, we propose an efficient sampling-based training strategy, wherein the training of a pBNN is formulated as simulating a Feynman--Kac model. We then describe variations of sequential Monte Carlo samplers that allow us to simultaneously estimate the parameters and the latent posterior distribution of this model at a tractable computational cost. We show on various synthetic and real-world datasets that our proposed training scheme outperforms the state of the art in terms of predictive performance.

Offline reinforcement learning enables agents to leverage large pre-collected datasets of environment transitions to learn control policies, circumventing the need for potentially expensive or unsafe online data collection. Significant progress has been made recently in offline model-based reinforcement learning, approaches which leverage a learned dynamics model. This typically involves constructing a probabilistic model, and using the model uncertainty to penalize rewards where there is insufficient data, solving for a pessimistic MDP that lower bounds the true MDP. Existing methods, however, exhibit a breakdown between theory and practice, whereby pessimistic return ought to be bounded by the total variation distance of the model from the true dynamics, but is instead implemented through a penalty based on estimated model uncertainty. This has spawned a variety of uncertainty heuristics, with little to no comparison between differing approaches. In this paper, we compare these heuristics, and design novel protocols to investigate their interaction with other hyperparameters, such as the number of models, or imaginary rollout horizon. Using these insights, we show that selecting these key hyperparameters using Bayesian Optimization produces superior configurations that are vastly different to those currently used in existing hand-tuned state-of-the-art methods, and result in drastically stronger performance.

How can we perform efficient inference and learning in directed probabilistic models, in the presence of continuous latent variables with intractable posterior distributions, and large datasets? We introduce a stochastic variational inference and learning algorithm that scales to large datasets and, under some mild differentiability conditions, even works in the intractable case. Our contributions are two-fold. First, we show that a reparameterization of the variational lower bound yields a lower bound estimator that can be straightforwardly optimized using standard stochastic gradient methods. Second, we show that for i.i.d. datasets with continuous latent variables per datapoint, posterior inference can be made especially efficient by fitting an approximate inference model (also called a recognition model) to the intractable posterior using the proposed lower bound estimator. Theoretical advantages are reflected in experimental results.

We advance the study of incentivized bandit exploration, in which arm choices are viewed as recommendations and are required to be Bayesian incentive compatible. Recent work has shown under certain independence assumptions that after collecting enough initial samples, the popular Thompson sampling algorithm becomes incentive compatible. We give an analog of this result for linear bandits, where the independence of the prior is replaced by a natural convexity condition. This opens up the possibility of efficient and regret-optimal incentivized exploration in high-dimensional action spaces. In the semibandit model, we also improve the sample complexity for the pre-Thompson sampling phase of initial data collection.

Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety, and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by extrapolation from the available evidence at the time. This includes collected trial data and relevant external data. However, relevant external data are typically available as averages only, for example from trials on alternative treatments reported in the literature. Here we report on such an example from a drug development for wet age-related macular degeneration. This disease is the leading cause of severe vision loss in the elderly. While current treatment options are efficacious, they are also a substantial burden for the patient. Hence, new treatments are under development which need to be compared against existing treatments. The general statistical problem this leads to is meta-analysis, which addresses the question of how we can combine datasets collected under different conditions. Bayesian methods have long been used to achieve partial pooling. Here we consider the challenge when the model of interest is complex (hierarchical and nonlinear) and one dataset is given as raw data while the second dataset is given as averages only. In such a situation, common meta-analytic methods can only be applied when the model is sufficiently simple for analytic approaches. When the model is too complex, for example nonlinear, an analytic approach is not possible. We provide a Bayesian solution by using simulation to approximately reconstruct the likelihood of the external summary and allowing the parameters in the model to vary under the different conditions. We first evaluate our approach using fake-data simulations and then report results for the drug development program that motivated this research.

In this report, we survey Bayesian Optimization methods focussed on the Multi-Armed Bandit Problem. We take the help of the paper "Portfolio Allocation for Bayesian Optimization". We report a small literature survey on the acquisition functions and the types of portfolio strategies used in papers discussing Bayesian Optimization. We also replicate the experiments and report our findings and compare them to the results in the paper. Code link: https://colab.research.google.com/drive/1GZ14klEDoe3dcBeZKo5l8qqrKf_GmBDn?usp=sharing#scrollTo=XgIBau3O45_V.

Bayesian filtering approximates the true underlying behavior of a time-varying system by inverting an explicit generative model to convert noisy measurements into state estimates. This process typically requires either storage, inversion, and multiplication of large matrices or Monte Carlo estimation, neither of which are practical in high-dimensional state spaces such as the weight spaces of artificial neural networks. Here, we frame the standard Bayesian filtering problem as optimization over a time-varying objective. Instead of maintaining matrices for the filtering equations or simulating particles, we specify an optimizer that defines the Bayesian filter implicitly. In the linear-Gaussian setting, we show that every Kalman filter has an equivalent formulation using K steps of gradient descent. In the nonlinear setting, our experiments demonstrate that our framework results in filters that are effective, robust, and scalable to high-dimensional systems, comparing well against the standard toolbox of Bayesian filtering solutions. We suggest that it is easier to fine-tune an optimizer than it is to specify the correct filtering equations, making our framework an attractive option for high-dimensional filtering problems.

In this work, we initiate the idea of using denoising diffusion models to learn priors for online decision making problems. Our special focus is on the meta-learning for bandit framework, with the goal of learning a strategy that performs well across bandit tasks of a same class. To this end, we train a diffusion model that learns the underlying task distribution and combine Thompson sampling with the learned prior to deal with new tasks at test time. Our posterior sampling algorithm is designed to carefully balance between the learned prior and the noisy observations that come from the learner's interaction with the environment. To capture realistic bandit scenarios, we also propose a novel diffusion model training procedure that trains even from incomplete and/or noisy data, which could be of independent interest. Finally, our extensive experimental evaluations clearly demonstrate the potential of the proposed approach.

Bayesian predictive inference provides a principled framework for uncertainty quantification, data efficiency, and robust generalization. However, exact inference is often intractable, and scalable approximations may remain computationally expensive or require restrictive modeling assumptions that degrade predictive performance. Prior-Data Fitted and in-context models have recently emerged as an amortized alternative by learning to map datasets directly to predictive distributions, but existing approaches are tightly coupled to the support of the training prior and lack explicit mechanisms for adapting to new priors at test time, resulting in limited robustness under distribution shift. We introduce a multi-task in-context learning framework for amortized hierarchical Bayesian predictive inference that explicitly represents prior information as a prefix of in-context datasets. A transformer trained on sequences of prior and target tasks learns to adapt its predictions across families of priors. On a suite of evaluations with increasing difficulty, including out-of-meta-distribution priors and priors with high-dimensional latent structures, our method matches oracle Bayesian predictors while being orders of magnitude faster. We further demonstrate its practical relevance on a real-world spatiotemporal temperature prediction benchmark. Code is available at https://github.com/martianmartina/multi-task-bayesian-icl/.

In this review, we present econometric and statistical methods for analyzing randomized experiments. For basic experiments we stress randomization-based inference as opposed to sampling-based inference. In randomization-based inference, uncertainty in estimates arises naturally from the random assignment of the treatments, rather than from hypothesized sampling from a large population. We show how this perspective relates to regression analyses for randomized experiments. We discuss the analyses of stratified, paired, and clustered randomized experiments, and we stress the general efficiency gains from stratification. We also discuss complications in randomized experiments such as non-compliance. In the presence of non-compliance we contrast intention-to-treat analyses with instrumental variables analyses allowing for general treatment effect heterogeneity. We consider in detail estimation and inference for heterogeneous treatment effects in settings with (possibly many) covariates. These methods allow researchers to explore heterogeneity by identifying subpopulations with different treatment effects while maintaining the ability to construct valid confidence intervals. We also discuss optimal assignment to treatment based on covariates in such settings. Finally, we discuss estimation and inference in experiments in settings with interactions between units, both in general network settings and in settings where the population is partitioned into groups with all interactions contained within these groups.

Meta-Bayesian optimisation (meta-BO) aims to improve the sample efficiency of Bayesian optimisation by leveraging data from related tasks. While previous methods successfully meta-learn either a surrogate model or an acquisition function independently, joint training of both components remains an open challenge. This paper proposes the first end-to-end differentiable meta-BO framework that generalises neural processes to learn acquisition functions via transformer architectures. We enable this end-to-end framework with reinforcement learning (RL) to tackle the lack of labelled acquisition data. Early on, we notice that training transformer-based neural processes from scratch with RL is challenging due to insufficient supervision, especially when rewards are sparse. We formalise this claim with a combinatorial analysis showing that the widely used notion of regret as a reward signal exhibits a logarithmic sparsity pattern in trajectory lengths. To tackle this problem, we augment the RL objective with an auxiliary task that guides part of the architecture to learn a valid probabilistic model as an inductive bias. We demonstrate that our method achieves state-of-the-art regret results against various baselines in experiments on standard hyperparameter optimisation tasks and also outperforms others in the real-world problems of mixed-integer programming tuning, antibody design, and logic synthesis for electronic design automation.

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a 2.4times greater reduction in validation BPB, an 18.2% relative decrease in binding energy, and more than 60% relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.

Hyperparameter tuning of deep learning models can lead to order-of-magnitude performance gains for the same amount of compute. Despite this, systematic tuning is uncommon, particularly for large models, which are expensive to evaluate and tend to have many hyperparameters, necessitating difficult judgment calls about tradeoffs, budgets, and search bounds. To address these issues and propose a practical method for robustly tuning large models, we present Cost-Aware Pareto Region Bayesian Search (CARBS), a Bayesian optimization algorithm that performs local search around the performance-cost Pareto frontier. CARBS does well even in unbounded search spaces with many hyperparameters, learns scaling relationships so that it can tune models even as they are scaled up, and automates much of the "black magic" of tuning. Among our results, we effectively solve the entire ProcGen benchmark just by tuning a simple baseline (PPO, as provided in the original ProcGen paper). We also reproduce the model size vs. training tokens scaling result from the Chinchilla project (Hoffmann et al. 2022), while simultaneously discovering scaling laws for every other hyperparameter, via an easy automated process that uses significantly less compute and is applicable to any deep learning problem (not just language models).

Completely randomized experiments, originally developed by Fisher and Neyman in the 1930s, are still widely used in practice, even in online experimentation. However, such designs are of limited value for answering standard questions in marketplaces, where multiple populations of agents interact strategically, leading to complex patterns of spillover effects. In this paper, we derive the finite-sample properties of tractable estimators for "Simple Multiple Randomization Designs" (SMRDs), a new class of experimental designs which account for complex spillover effects in randomized experiments. Our derivations are obtained under a natural and general form of cross-unit interference, which we call "local interference". We discuss the estimation of main effects, direct effects, and spillovers, and present associated central limit theorems.

Treatment effect estimation in continuous time is crucial for personalized medicine. However, existing methods for this task are limited to point estimates of the potential outcomes, whereas uncertainty estimates have been ignored. Needless to say, uncertainty quantification is crucial for reliable decision-making in medical applications. To fill this gap, we propose a novel Bayesian neural controlled differential equation (BNCDE) for treatment effect estimation in continuous time. In our BNCDE, the time dimension is modeled through a coupled system of neural controlled differential equations and neural stochastic differential equations, where the neural stochastic differential equations allow for tractable variational Bayesian inference. Thereby, for an assigned sequence of treatments, our BNCDE provides meaningful posterior predictive distributions of the potential outcomes. To the best of our knowledge, ours is the first tailored neural method to provide uncertainty estimates of treatment effects in continuous time. As such, our method is of direct practical value for promoting reliable decision-making in medicine.

Implicit feedback data is extensively explored in recommendation as it is easy to collect and generally applicable. However, predicting users' preference on implicit feedback data is a challenging task since we can only observe positive (voted) samples and unvoted samples. It is difficult to distinguish between the negative samples and unlabeled positive samples from the unvoted ones. Existing works, such as Bayesian Personalized Ranking (BPR), sample unvoted items as negative samples uniformly, therefore suffer from a critical noisy-label issue. To address this gap, we design an adaptive sampler based on noisy-label robust learning for implicit feedback data. To formulate the issue, we first introduce Bayesian Point-wise Optimization (BPO) to learn a model, e.g., Matrix Factorization (MF), by maximum likelihood estimation. We predict users' preferences with the model and learn it by maximizing likelihood of observed data labels, i.e., a user prefers her positive samples and has no interests in her unvoted samples. However, in reality, a user may have interests in some of her unvoted samples, which are indeed positive samples mislabeled as negative ones. We then consider the risk of these noisy labels, and propose a Noisy-label Robust BPO (NBPO). NBPO also maximizes the observation likelihood while connects users' preference and observed labels by the likelihood of label flipping based on the Bayes' theorem. In NBPO, a user prefers her true positive samples and shows no interests in her true negative samples, hence the optimization quality is dramatically improved. Extensive experiments on two public real-world datasets show the significant improvement of our proposed optimization methods.

Parameter inference, i.e. inferring the posterior distribution of the parameters of a statistical model given some data, is a central problem to many scientific disciplines. Generative models can be used as an alternative to Markov Chain Monte Carlo methods for conducting posterior inference, both in likelihood-based and simulation-based problems. However, assessing the accuracy of posteriors encoded in generative models is not straightforward. In this paper, we introduce `Tests of Accuracy with Random Points' (TARP) coverage testing as a method to estimate coverage probabilities of generative posterior estimators. Our method differs from previously-existing coverage-based methods, which require posterior evaluations. We prove that our approach is necessary and sufficient to show that a posterior estimator is accurate. We demonstrate the method on a variety of synthetic examples, and show that TARP can be used to test the results of posterior inference analyses in high-dimensional spaces. We also show that our method can detect inaccurate inferences in cases where existing methods fail.

Machine learning models are often trained to predict the outcome resulting from a human decision. For example, if a doctor decides to test a patient for disease, will the patient test positive? A challenge is that historical decision-making determines whether the outcome is observed: we only observe test outcomes for patients doctors historically tested. Untested patients, for whom outcomes are unobserved, may differ from tested patients along observed and unobserved dimensions. We propose a Bayesian model class which captures this setting. The purpose of the model is to accurately estimate risk for both tested and untested patients. Estimating this model is challenging due to the wide range of possibilities for untested patients. To address this, we propose two domain constraints which are plausible in health settings: a prevalence constraint, where the overall disease prevalence is known, and an expertise constraint, where the human decision-maker deviates from purely risk-based decision-making only along a constrained feature set. We show theoretically and on synthetic data that domain constraints improve parameter inference. We apply our model to a case study of cancer risk prediction, showing that the model's inferred risk predicts cancer diagnoses, its inferred testing policy captures known public health policies, and it can identify suboptimalities in test allocation. Though our case study is in healthcare, our analysis reveals a general class of domain constraints which can improve model estimation in many settings.

We consider the stochastic linear contextual bandit problem with high-dimensional features. We analyze the Thompson sampling algorithm using special classes of sparsity-inducing priors (e.g., spike-and-slab) to model the unknown parameter and provide a nearly optimal upper bound on the expected cumulative regret. To the best of our knowledge, this is the first work that provides theoretical guarantees of Thompson sampling in high-dimensional and sparse contextual bandits. For faster computation, we use variational inference instead of Markov Chain Monte Carlo (MCMC) to approximate the posterior distribution. Extensive simulations demonstrate the improved performance of our proposed algorithm over existing ones.

Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the Controlled Monte Carlo Diffusion sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{\"o}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.

Epistemic Uncertainty is a measure of the lack of knowledge of a learner which diminishes with more evidence. While existing work focuses on using the variance of the Bayesian posterior due to parameter uncertainty as a measure of epistemic uncertainty, we argue that this does not capture the part of lack of knowledge induced by model misspecification. We discuss how the excess risk, which is the gap between the generalization error of a predictor and the Bayes predictor, is a sound measure of epistemic uncertainty which captures the effect of model misspecification. We thus propose a principled framework for directly estimating the excess risk by learning a secondary predictor for the generalization error and subtracting an estimate of aleatoric uncertainty, i.e., intrinsic unpredictability. We discuss the merits of this novel measure of epistemic uncertainty, and highlight how it differs from variance-based measures of epistemic uncertainty and addresses its major pitfall. Our framework, Direct Epistemic Uncertainty Prediction (DEUP) is particularly interesting in interactive learning environments, where the learner is allowed to acquire novel examples in each round. Through a wide set of experiments, we illustrate how existing methods in sequential model optimization can be improved with epistemic uncertainty estimates from DEUP, and how DEUP can be used to drive exploration in reinforcement learning. We also evaluate the quality of uncertainty estimates from DEUP for probabilistic image classification and predicting synergies of drug combinations.

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

Optimizing multiple competing black-box objectives is a challenging problem in many fields, including science, engineering, and machine learning. Multi-objective Bayesian optimization (MOBO) is a sample-efficient approach for identifying the optimal trade-offs between the objectives. However, many existing methods perform poorly when the observations are corrupted by noise. We propose a novel acquisition function, NEHVI, that overcomes this important practical limitation by applying a Bayesian treatment to the popular expected hypervolume improvement (EHVI) criterion and integrating over this uncertainty in the Pareto frontier. We argue that, even in the noiseless setting, generating multiple candidates in parallel is an incarnation of EHVI with uncertainty in the Pareto frontier and therefore can be addressed using the same underlying technique. Through this lens, we derive a natural parallel variant, qNEHVI, that reduces computational complexity of parallel EHVI from exponential to polynomial with respect to the batch size. qNEHVI is one-step Bayes-optimal for hypervolume maximization in both noisy and noiseless environments, and we show that it can be optimized effectively with gradient-based methods via sample average approximation. Empirically, we demonstrate not only that qNEHVI is substantially more robust to observation noise than existing MOBO approaches, but also that it achieves state-of-the-art optimization performance and competitive wall-times in large-batch environments.

Gaussian process upper confidence bound (GP-UCB) is a theoretically promising approach for black-box optimization; however, the confidence parameter beta is considerably large in the theorem and chosen heuristically in practice. Then, randomized GP-UCB (RGP-UCB) uses a randomized confidence parameter, which follows the Gamma distribution, to mitigate the impact of manually specifying beta. This study first generalizes the regret analysis of RGP-UCB to a wider class of distributions, including the Gamma distribution. Furthermore, we propose improved RGP-UCB (IRGP-UCB) based on a two-parameter exponential distribution, which achieves tighter Bayesian regret bounds. IRGP-UCB does not require an increase in the confidence parameter in terms of the number of iterations, which avoids over-exploration in the later iterations. Finally, we demonstrate the effectiveness of IRGP-UCB through extensive experiments.

The performance of acquisition functions for Bayesian optimisation to locate the global optimum of continuous functions is investigated in terms of the Pareto front between exploration and exploitation. We show that Expected Improvement (EI) and the Upper Confidence Bound (UCB) always select solutions to be expensively evaluated on the Pareto front, but Probability of Improvement is not guaranteed to do so and Weighted Expected Improvement does so only for a restricted range of weights. We introduce two novel epsilon-greedy acquisition functions. Extensive empirical evaluation of these together with random search, purely exploratory, and purely exploitative search on 10 benchmark problems in 1 to 10 dimensions shows that epsilon-greedy algorithms are generally at least as effective as conventional acquisition functions (e.g., EI and UCB), particularly with a limited budget. In higher dimensions epsilon-greedy approaches are shown to have improved performance over conventional approaches. These results are borne out on a real world computational fluid dynamics optimisation problem and a robotics active learning problem. Our analysis and experiments suggest that the most effective strategy, particularly in higher dimensions, is to be mostly greedy, occasionally selecting a random exploratory solution.

Bayesian inference provides principled uncertainty quantification but is often limited by challenges of prior elicitation, likelihood misspecification, and computational burden. The martingale posterior (MGP, Fong et al., 2023) offers an alternative, replacing prior-likelihood elicitation with a predictive rule - namely, a sequence of one-step-ahead predictive distributions - for forward data generation. The utility of MGPs depends on the choice of predictive rule, yet the literature has offered few compelling examples. Foundation transformers are well-suited here, as their autoregressive generation mirrors this forward simulation and their general-purpose design enables rich predictive modeling. We introduce TabMGP, an MGP built on TabPFN, a transformer foundation model that is currently state-of-the-art for tabular data. TabMGP produces credible sets with near-nominal coverage and often outperforms both existing MGP constructions and standard Bayes.

The Bayesian treatment of neural networks dictates that a prior distribution is specified over their weight and bias parameters. This poses a challenge because modern neural networks are characterized by a large number of parameters, and the choice of these priors has an uncontrolled effect on the induced functional prior, which is the distribution of the functions obtained by sampling the parameters from their prior distribution. We argue that this is a hugely limiting aspect of Bayesian deep learning, and this work tackles this limitation in a practical and effective way. Our proposal is to reason in terms of functional priors, which are easier to elicit, and to "tune" the priors of neural network parameters in a way that they reflect such functional priors. Gaussian processes offer a rigorous framework to define prior distributions over functions, and we propose a novel and robust framework to match their prior with the functional prior of neural networks based on the minimization of their Wasserstein distance. We provide vast experimental evidence that coupling these priors with scalable Markov chain Monte Carlo sampling offers systematically large performance improvements over alternative choices of priors and state-of-the-art approximate Bayesian deep learning approaches. We consider this work a considerable step in the direction of making the long-standing challenge of carrying out a fully Bayesian treatment of neural networks, including convolutional neural networks, a concrete possibility.

Gaussian processes (GP) are one of the most successful frameworks to model uncertainty. However, GP optimization (e.g., GP-UCB) suffers from major scalability issues. Experimental time grows linearly with the number of evaluations, unless candidates are selected in batches (e.g., using GP-BUCB) and evaluated in parallel. Furthermore, computational cost is often prohibitive since algorithms such as GP-BUCB require a time at least quadratic in the number of dimensions and iterations to select each batch. In this paper, we introduce BBKB (Batch Budgeted Kernel Bandits), the first no-regret GP optimization algorithm that provably runs in near-linear time and selects candidates in batches. This is obtained with a new guarantee for the tracking of the posterior variances that allows BBKB to choose increasingly larger batches, improving over GP-BUCB. Moreover, we show that the same bound can be used to adaptively delay costly updates to the sparse GP approximation used by BBKB, achieving a near-constant per-step amortized cost. These findings are then confirmed in several experiments, where BBKB is much faster than state-of-the-art methods.

In Causal Bayesian Optimization (CBO), an agent intervenes on an unknown structural causal model to maximize a downstream reward variable. In this paper, we consider the generalization where other agents or external events also intervene on the system, which is key for enabling adaptiveness to non-stationarities such as weather changes, market forces, or adversaries. We formalize this generalization of CBO as Adversarial Causal Bayesian Optimization (ACBO) and introduce the first algorithm for ACBO with bounded regret: Causal Bayesian Optimization with Multiplicative Weights (CBO-MW). Our approach combines a classical online learning strategy with causal modeling of the rewards. To achieve this, it computes optimistic counterfactual reward estimates by propagating uncertainty through the causal graph. We derive regret bounds for CBO-MW that naturally depend on graph-related quantities. We further propose a scalable implementation for the case of combinatorial interventions and submodular rewards. Empirically, CBO-MW outperforms non-causal and non-adversarial Bayesian optimization methods on synthetic environments and environments based on real-word data. Our experiments include a realistic demonstration of how CBO-MW can be used to learn users' demand patterns in a shared mobility system and reposition vehicles in strategic areas.

In meta reinforcement learning (meta RL), an agent seeks a Bayes-optimal policy -- the optimal policy when facing an unknown task that is sampled from some known task distribution. Previous approaches tackled this problem by inferring a belief over task parameters, using variational inference methods. Motivated by recent successes of contrastive learning approaches in RL, such as contrastive predictive coding (CPC), we investigate whether contrastive methods can be used for learning Bayes-optimal behavior. We begin by proving that representations learned by CPC are indeed sufficient for Bayes optimality. Based on this observation, we propose a simple meta RL algorithm that uses CPC in lieu of variational belief inference. Our method, ContraBAR, achieves comparable performance to state-of-the-art in domains with state-based observation and circumvents the computational toll of future observation reconstruction, enabling learning in domains with image-based observations. It can also be combined with image augmentations for domain randomization and used seamlessly in both online and offline meta RL settings.

In this report we review memory-based meta-learning as a tool for building sample-efficient strategies that learn from past experience to adapt to any task within a target class. Our goal is to equip the reader with the conceptual foundations of this tool for building new, scalable agents that operate on broad domains. To do so, we present basic algorithmic templates for building near-optimal predictors and reinforcement learners which behave as if they had a probabilistic model that allowed them to efficiently exploit task structure. Furthermore, we recast memory-based meta-learning within a Bayesian framework, showing that the meta-learned strategies are near-optimal because they amortize Bayes-filtered data, where the adaptation is implemented in the memory dynamics as a state-machine of sufficient statistics. Essentially, memory-based meta-learning translates the hard problem of probabilistic sequential inference into a regression problem.

Rigorous performance evaluation is essential for developing robust algorithms for high-throughput computational chemistry. Traditional benchmarking, however, often struggles to account for system-specific variability, making it difficult to form actionable conclusions. We present a Bayesian hierarchical modeling framework that rigorously quantifies performance metrics and their uncertainty, enabling a nuanced comparison of algorithmic strategies. We apply this framework to analyze the Dimer method, comparing Conjugate Gradient (CG) and L-BFGS rotation optimizers, with and without the removal of external rotations, across a benchmark of 500 molecular systems. Our analysis confirms that CG offers higher overall robustness than L-BFGS in this context. While the theoretically-motivated removal of external rotations led to higher computational cost (>40% more energy and force calls) for most systems in this set, our models also reveal a subtle interplay, hinting that this feature may improve the reliability of the L-BFGS optimizer. Rather than identifying a single superior method, our findings support the design of adaptive "chain of methods" workflows. This work showcases how a robust statistical paradigm can move beyond simple performance rankings to inform the intelligent, context-dependent application of computational chemistry methods.

The efficiency of Bayesian optimization (BO) relies heavily on the choice of the Gaussian process (GP) kernel, which plays a central role in balancing exploration and exploitation under limited evaluation budgets. Traditional BO methods often rely on fixed or heuristic kernel selection strategies, which can result in slow convergence or suboptimal solutions when the chosen kernel is poorly suited to the underlying objective function. To address this limitation, we propose a freshly-baked Context-Aware Kernel Evolution (CAKE) to enhance BO with large language models (LLMs). Concretely, CAKE leverages LLMs as the crossover and mutation operators to adaptively generate and refine GP kernels based on the observed data throughout the optimization process. To maximize the power of CAKE, we further propose BIC-Acquisition Kernel Ranking (BAKER) to select the most effective kernel through balancing the model fit measured by the Bayesian information criterion (BIC) with the expected improvement at each iteration of BO. Extensive experiments demonstrate that our fresh CAKE-based BO method consistently outperforms established baselines across a range of real-world tasks, including hyperparameter optimization, controller tuning, and photonic chip design. Our code is publicly available at https://github.com/cake4bo/cake.

In the field of decision trees, most previous studies have difficulty ensuring the statistical optimality of a prediction of new data and suffer from overfitting because trees are usually used only to represent prediction functions to be constructed from given data. In contrast, some studies, including this paper, used the trees to represent stochastic data observation processes behind given data. Moreover, they derived the statistically optimal prediction, which is robust against overfitting, based on the Bayesian decision theory by assuming a prior distribution for the trees. However, these studies still have a problem in computing this Bayes optimal prediction because it involves an infeasible summation for all division patterns of a feature space, which is represented by the trees and some parameters. In particular, an open problem is a summation with respect to combinations of division axes, i.e., the assignment of features to inner nodes of the tree. We solve this by a Markov chain Monte Carlo method, whose step size is adaptively tuned according to a posterior distribution for the trees.

Recent advances in deep reinforcement learning have made significant strides in performance on applications such as Go and Atari games. However, developing practical methods to balance exploration and exploitation in complex domains remains largely unsolved. Thompson Sampling and its extension to reinforcement learning provide an elegant approach to exploration that only requires access to posterior samples of the model. At the same time, advances in approximate Bayesian methods have made posterior approximation for flexible neural network models practical. Thus, it is attractive to consider approximate Bayesian neural networks in a Thompson Sampling framework. To understand the impact of using an approximate posterior on Thompson Sampling, we benchmark well-established and recently developed methods for approximate posterior sampling combined with Thompson Sampling over a series of contextual bandit problems. We found that many approaches that have been successful in the supervised learning setting underperformed in the sequential decision-making scenario. In particular, we highlight the challenge of adapting slowly converging uncertainty estimates to the online setting.

We present a novel prior for tree topology within Bayesian Additive Regression Trees (BART) models. This approach quantifies the hypothetical loss in information and the loss due to complexity associated with choosing the wrong tree structure. The resulting prior distribution is compellingly geared toward sparsity, a critical feature considering BART models' tendency to overfit. Our method incorporates prior knowledge into the distribution via two parameters that govern the tree's depth and balance between its left and right branches. Additionally, we propose a default calibration for these parameters, offering an objective version of the prior. We demonstrate our method's efficacy on both simulated and real datasets.

Bayesian inference usually requires running potentially costly inference procedures separately for every new observation. In contrast, the idea of amortized Bayesian inference is to initially invest computational cost in training an inference network on simulated data, which can subsequently be used to rapidly perform inference (i.e., to return estimates of posterior distributions) for new observations. This approach has been applied to many real-world models in the sciences and engineering, but it is unclear how robust the approach is to adversarial perturbations in the observed data. Here, we study the adversarial robustness of amortized Bayesian inference, focusing on simulation-based estimation of multi-dimensional posterior distributions. We show that almost unrecognizable, targeted perturbations of the observations can lead to drastic changes in the predicted posterior and highly unrealistic posterior predictive samples, across several benchmark tasks and a real-world example from neuroscience. We propose a computationally efficient regularization scheme based on penalizing the Fisher information of the conditional density estimator, and show how it improves the adversarial robustness of amortized Bayesian inference.

Sequential Bayesian inference can be used for continual learning to prevent catastrophic forgetting of past tasks and provide an informative prior when learning new tasks. We revisit sequential Bayesian inference and test whether having access to the true posterior is guaranteed to prevent catastrophic forgetting in Bayesian neural networks. To do this we perform sequential Bayesian inference using Hamiltonian Monte Carlo. We propagate the posterior as a prior for new tasks by fitting a density estimator on Hamiltonian Monte Carlo samples. We find that this approach fails to prevent catastrophic forgetting demonstrating the difficulty in performing sequential Bayesian inference in neural networks. From there we study simple analytical examples of sequential Bayesian inference and CL and highlight the issue of model misspecification which can lead to sub-optimal continual learning performance despite exact inference. Furthermore, we discuss how task data imbalances can cause forgetting. From these limitations, we argue that we need probabilistic models of the continual learning generative process rather than relying on sequential Bayesian inference over Bayesian neural network weights. In this vein, we also propose a simple baseline called Prototypical Bayesian Continual Learning, which is competitive with state-of-the-art Bayesian continual learning methods on class incremental continual learning vision benchmarks.

Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a mechanistic, causal model, not a curve fit; and learning such a model requires experiments, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is data efficiency. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a proposer of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that discovery and design reinforce: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, wiemann2026discoverphysics), chemistry (\CHEMbench, kabra2026autoscilab) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) --- we show that MDA sets a new SOTA in terms of data-efficient model learning and reliable interventional prediction ability.

The framework of reinforcement learning or optimal control provides a mathematical formalization of intelligent decision making that is powerful and broadly applicable. While the general form of the reinforcement learning problem enables effective reasoning about uncertainty, the connection between reinforcement learning and inference in probabilistic models is not immediately obvious. However, such a connection has considerable value when it comes to algorithm design: formalizing a problem as probabilistic inference in principle allows us to bring to bear a wide array of approximate inference tools, extend the model in flexible and powerful ways, and reason about compositionality and partial observability. In this article, we will discuss how a generalization of the reinforcement learning or optimal control problem, which is sometimes termed maximum entropy reinforcement learning, is equivalent to exact probabilistic inference in the case of deterministic dynamics, and variational inference in the case of stochastic dynamics. We will present a detailed derivation of this framework, overview prior work that has drawn on this and related ideas to propose new reinforcement learning and control algorithms, and describe perspectives on future research.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.