This textbook gives a systematic treatment of statistical machine learning for astronomical research, based on Bayesian inference. It shows how modern data analysis techniques connect to classical statistical methods and follow from familiar statistical principles. The Bayesian perspective, used throughout, gives priority to uncertainty quantification and statistical rigor, which scientific inference in astronomy needs. The textbook progresses from probability theory and Bayesian inference through supervised learning, including linear regression with measurement uncertainties, logistic regression and classification. Unsupervised learning topics cover Principal Component Analysis and clustering methods. We then introduce sampling and Markov Chain Monte Carlo, followed by Gaussian Processes as probabilistic nonparametric methods and neural networks in the broader statistical context. Our theory-focused approach derives each method from first principles with complete mathematical development and then shows its astronomical applications. We put statistical insight first and explain why algorithms work, when they are appropriate, and how they connect to broader statistical principles. From a solid grounding in classical methods and their theory, the treatment leads to modern techniques such as neural networks. With this grounding, readers can apply the methods to astronomical research with proper attention to assumptions, limits and uncertainty propagation, as large astronomical surveys require. The 22 companion tutorials apply the methods to astronomical data in Jupyter notebooks.
Bayesian optimization (BO) is a sequential decision-making tool widely used for optimizing expensive black-box functions. Recently, Large Language Models (LLMs) have shown remarkable adaptability in low-data regimes, making them promising tools for black-box optimization by leveraging contextual knowledge to propose high-quality query points. However, LLMs lack explicit surrogate modeling and calibrated uncertainty, and their internal mechanisms remain opaque. This structural opacity can result in unnecessary experiments, which are costly in BO and may prevent the search from approaching the optimum. To address this, we propose LLINBO: LLM-in-the-Loop BO, a general framework that wraps existing LLM-based BO approaches, deciding when and how to act on their suggestions and when to revert to classical BO. We introduce three mechanisms for this interaction, each accompanied by a no-harm theoretical guarantee that ensures sublinear cumulative regret for common kernels while requiring no performance assumptions on the LLM. Beyond these theoretical guarantees, we show through simulation studies that LLINBO makes existing LLM-based BO more reliable while still exploiting the LLM's few-shot learning ability to outperform classical BO. We further demonstrate its practical use on a real-world, expensive 3D printing experiment. Code is available at https://github.com/UMDataScienceLab/LLM-in-the-Loop-BO.
We present \texttt{MathOptAI.jl}, an open-source Julia library for embedding trained machine learning predictors into a JuMP model. \texttt{MathOptAI.jl} can embed a wide variety of neural networks, decision trees, and Gaussian Processes into a larger mathematical optimization model. In addition to interfacing a range of Julia-based machine learning libraries such as \texttt{Lux.jl} and \texttt{Flux.jl}, \texttt{MathOptAI.jl} uses Julia's Python interface to provide support for PyTorch models. When the PyTorch support is combined with \texttt{MathOptAI.jl}'s gray-box formulation, the function, Jacobian, and Hessian evaluations associated with the PyTorch model are offloaded to the GPU in Python, while the rest of the nonlinear oracles are evaluated on the CPU in Julia. \MathOptAI is available at https://github.com/lanl-ansi/MathOptAI.jl under a BSD-3 license.
Gaussian processes (GPs) are widely used as surrogate models for complicated functions in scientific and engineering applications. In many cases, prior knowledge about the function to be approximated, such as monotonicity, is available and can be leveraged to improve model fidelity. Incorporating such constraints into GP models enhances predictive accuracy and reduces uncertainty, but remains a computationally challenging task for high-dimensional problems. In this work, we present a novel virtual point-based framework for building constrained GP models under monotonicity constraints, based on regularized linear randomize-then-optimize (RLRTO), which enables efficient sampling from a constrained posterior distribution by means of solving randomized optimization problems. We also enhance two existing virtual point-based approaches by replacing Gibbs sampling with the No U-Turn Sampler (NUTS) for improved efficiency. A Python implementation of these methods is provided and can be easily applied to a wide range of problems. This implementation is then used to validate the approaches on approximating a range of synthetic functions, demonstrating comparable predictive performance between all considered methods and significant improvements in computational efficiency with the two NUTS methods and especially with the RLRTO method. The framework is further applied to construct surrogate models for systems of differential equations.
Functional ANOVA (FANOVA) is a widely used variance-based sensitivity analysis tool. However, studies on functional-output FANOVA remain relatively scarce, especially for black-box computer experiments, which often involve complex and nonlinear functional-output relationships with unknown data distribution. Conventional approaches often rely on predefined basis functions or parametric structures that lack the flexibility to capture complex nonlinear relationships. Additionally, strong assumptions about the underlying data distributions further limit their ability to achieve a data-driven orthogonal effect decomposition. To address these challenges, this study proposes a functional-output orthogonal additive Gaussian process (FOAGP) to efficiently perform the data-driven orthogonal effect decomposition. By enforcing a conditional orthogonality constraint on the separable prior process, the proposed functional-output orthogonal additive kernel enables data-driven orthogonality without requiring prior distributional assumptions. The FOAGP framework also provides analytical formulations for local Sobol' indices and expected conditional variance sensitivity indices, enabling comprehensive sensitivity analysis by capturing both global and local effect significance. Validation through two simulation studies and a real case study on fuselage shape control confirms the model's effectiveness in orthogonal effect decomposition and variance decomposition, demonstrating its practical value in engineering applications.
Surrogate modeling techniques have become indispensable in accelerating the discovery and optimization of high-entropy alloys(HEAs), especially when integrating computational predictions with sparse experimental observations. This study systematically evaluates the fitting performance of four prominent surrogate models conventional Gaussian Processes(cGP), Deep Gaussian Processes(DGP), encoder-decoder neural networks for multi-output regression and XGBoost applied to a hybrid dataset of experimental and computational properties in the AlCoCrCuFeMnNiV HEA system. We specifically assess their capabilities in predicting correlated material properties, including yield strength, hardness, modulus, ultimate tensile strength, elongation, and average hardness under dynamic and quasi-static conditions, alongside auxiliary computational properties. The comparison highlights the strengths of hierarchical and deep modeling approaches in handling heteroscedastic, heterotopic, and incomplete data commonly encountered in materials informatics. Our findings illustrate that DGP infused with machine learning-based prior outperform other surrogates by effectively capturing inter-property correlations and input-dependent uncertainty. This enhanced predictive accuracy positions advanced surrogate models as powerful tools for robust and data-efficient materials design.
This monograph studies the relations between two approaches using positive definite kernels: probabilistic methods using Gaussian processes, and non-probabilistic methods using reproducing kernel Hilbert spaces (RKHS). They are widely studied and used in machine learning, statistics, and numerical analysis. Connections and equivalences between them are reviewed for fundamental topics such as regression, interpolation, numerical integration, distributional discrepancies, and statistical dependence, as well as for sample path properties of Gaussian processes. A unifying perspective for these equivalences is established, based on the equivalence between the Gaussian Hilbert space and the RKHS. The monograph serves as a basis to bridge many other methods based on Gaussian processes and reproducing kernels, which are developed in parallel by the two research communities.
Short-term sentiment forecasting in financial markets (e.g., stocks, indices) is challenging due to volatility, non-linearity, and noise in OHLC (Open, High, Low, Close) data. This paper introduces a novel CMG (Chaos-Markov-Gaussian) framework that integrates chaos theory, Markov property, and Gaussian processes to improve prediction accuracy. Chaos theory captures nonlinear dynamics; the Markov chain models regime shifts; Gaussian processes add probabilistic reasoning. We enhance the framework with transformer-based deep learning models to capture temporal patterns efficiently. The CMG Framework is designed for fast, resource-efficient, and accurate forecasting of any financial instrument's OHLC time series. Unlike traditional models that require heavy infrastructure and instrument-specific tuning, CMG reduces overhead and generalizes well. We evaluate the framework on market indices, forecasting sentiment for the next trading day's first quarter. A comparative study against statistical, ML, and DL baselines trained on the same dataset with no feature engineering shows CMG consistently outperforms in accuracy and efficiency, making it valuable for analysts and financial institutions.
The interface between stochastic analysis and machine learning is a rapidly evolving field, with path signatures - iterated integrals that provide faithful, hierarchical representations of paths - offering a principled and universal feature map for sequential and structured data. Rooted in rough path theory, path signatures are invariant to reparameterization and well-suited for modelling evolving dynamics, long-range dependencies, and irregular sampling - common challenges in real-world time series and graph data. This thesis investigates how to harness the expressive power of path signatures within scalable machine learning pipelines. It introduces a suite of models that combine theoretical robustness with computational efficiency, bridging rough path theory with probabilistic modelling, deep learning, and kernel methods. Key contributions include: Gaussian processes with signature kernel-based covariance functions for uncertainty-aware time series modelling; the Seq2Tens framework, which employs low-rank tensor structure in the weight space for scalable deep modelling of long-range dependencies; and graph-based models where expected signatures over graphs induce hypo-elliptic diffusion processes, offering expressive yet tractable alternatives to standard graph neural networks. Further developments include Random Fourier Signature Features, a scalable kernel approximation with theoretical guarantees, and Recurrent Sparse Spectrum Signature Gaussian Processes, which combine Gaussian processes, signature kernels, and random features with a principled forgetting mechanism for multi-horizon time series forecasting with adaptive context length. We hope this thesis serves as both a methodological toolkit and a conceptual bridge, and provides a useful reference for the current state of the art in scalable, signature-based learning for sequential and structured data.
Bayesian Optimization, leveraging Gaussian process models, has proven to be a powerful tool for minimizing expensive-to-evaluate objective functions by efficiently exploring the search space. Extensions such as constrained Bayesian Optimization have further enhanced Bayesian Optimization's utility in practical scenarios by focusing the search within feasible regions defined by a black-box constraint function. However, constrained Bayesian Optimization in is developed based on the independence Gaussian processes assumption between objective and constraint functions, which may not hold in real-world applications. To address this issue, we use the bivariate Gaussian process model to characterize the dependence between the objective and constraint functions and developed the constrained expected improvement acquisition function under this model assumption. We show case the performance of the proposed approach with an application to cure process optimization in Manufacturing.
This paper presents a real-time capable algorithm for the learning of Gaussian Processes (GP) for submodels. It extends an existing recursive Gaussian Process (RGP) algorithm which requires a measurable output. In many applications, however, an envisaged GP output is not directly measurable. Therefore, we present the integration of an RGP into an Extended Kalman Filter (EKF) for the combined state estimation and GP learning. The algorithm is successfully tested in simulation studies and outperforms two alternative implementations -- especially if high measurement noise is present. We conclude the paper with an experimental validation within the control structure of a Vapor Compression Cycle typically used in refrigeration and heat pumps. In this application, the algorithm is used to learn a GP model for the heat-transfer values in dependency of several process parameters. The GP model significantly improves the tracking performance of a previously published model-based controller.
Self-driving labs (SDLs), employing automation and machine learning (ML) to accelerate experimental procedures, have enormous potential in the discovery of new materials. However, in thin film science, SDLs are mainly restricted to solution-based synthetic methods which are easier to automate but cannot access the broad chemical space of inorganic materials. This work presents an SDL based on magnetron co-sputtering. We are using combinatorial frameworks, obtaining accurate composition maps on multi-element, compositionally graded thin films. This normally requires time-consuming ex-situ analysis prone to systematic errors. We present a rapid and calibration-free in-situ, ML driven approach to produce composition maps for arbitrary source combinations and sputtering conditions. We develop a method to predict the composition distribution in a multi-element combinatorial thin film, using in-situ measurements from quartz-crystal microbalance sensors placed in a sputter chamber. For a given source, the sensor readings are learned as a function of the sputtering pressure and magnetron power, through active learning using Gaussian processes (GPs). The final GPs are combined with a geometric model of the deposition flux distribution in the chamber, which allows interpolation of the deposition rates from each source, at any position across the sample. We investigate several acquisition functions for the ML procedure. A fully Bayesian GP - BALM (Bayesian active learning MacKay) - achieved the best performance, learning the deposition rates for a single source in 10 experiments. Prediction accuracy for co-sputtering composition distributions was verified experimentally. Our framework dramatically increases throughput by avoiding the need for extensive characterisation or calibration, thus demonstrating the potential of ML-guided SDLs to accelerate materials exploration.
In multi-task Bayesian optimization, the goal is to leverage experience from optimizing existing tasks to improve the efficiency of optimizing new ones. While approaches using multi-task Gaussian processes or deep kernel transfer exist, the performance improvement is marginal when scaling beyond a moderate number of tasks. We introduce a novel approach leveraging large language models (LLMs) to learn from, and improve upon, previous optimization trajectories, scaling to approximately 1500 distinct tasks. Specifically, we propose a feedback loop in which an LLM is fine-tuned on the high quality solutions to specific tasks found by Bayesian optimization (BO). This LLM is then used to generate initialization points for future BO searches for new tasks. The trajectories of these new searches provide additional training data for fine-tuning the LLM, completing the loop. We evaluate our method on two distinct domains: database query optimization and antimicrobial peptide design. Results demonstrate that our approach creates a positive feedback loop, where the LLM's generated initializations gradually improve, leading to better optimization performance. As this feedback loop continues, we find that the LLM is eventually able to generate solutions to new tasks in just a few shots that are better than the solutions produced by "from scratch" by Bayesian optimization while simultaneously requiring significantly fewer oracle calls.
Developments in Deep Learning have significantly improved time series forecasting by enabling more accurate modeling of complex temporal dependencies inherent in sequential data. The effectiveness of such models is often demonstrated on limited sets of specific real-world data. Although this allows for comparative analysis, it still does not demonstrate how specific data characteristics align with the architectural strengths of individual models. Our research aims at uncovering clear connections between time series characteristics and particular models. We introduce a novel dataset generated using Gaussian Processes, specifically designed to display distinct, known characteristics for targeted evaluations of model adaptability to them. Furthermore, we present TimeFlex, a new model that incorporates a modular architecture tailored to handle diverse temporal dynamics, including trends and periodic patterns. This model is compared to current state-of-the-art models, offering a deeper understanding of how models perform under varied time series conditions.
I present a novel approach to estimating the temporal and spatial patterns of violent conflict. I show how we can use highly temporally and spatially disaggregated data on conflict events in tandem with Gaussian processes to estimate temporospatial conflict trends. These trends can be studied to gain insight into conflict traps, diffusion and tempo-spatial conflict exposure in general; they can also be used to control for such phenomenons given other estimation tasks; lastly, the approach allow us to extrapolate the estimated tempo-spatial conflict patterns into future temporal units, thus facilitating powerful, stat-of-the-art, conflict forecasts. Importantly, these results are achieved via a relatively parsimonious framework using only one data source: past conflict patterns.
Dirichlet-to-Neumann maps enable the coupling of multiphysics simulations across computational subdomains by ensuring continuity of state variables and fluxes at artificial interfaces. We present a novel method for learning Dirichlet-to-Neumann maps on graphs using Gaussian processes, specifically for problems where the data obey a conservation constraint from an underlying partial differential equation. Our approach combines discrete exterior calculus and nonlinear optimal recovery to infer relationships between vertex and edge values. This framework yields data-driven predictions with uncertainty quantification across the entire graph, even when observations are limited to a subset of vertices and edges. By optimizing over the reproducing kernel Hilbert space norm while applying a maximum likelihood estimation penalty on kernel complexity, our method ensures that the resulting surrogate strictly enforces conservation laws without overfitting. We demonstrate our method on two representative applications: subsurface fracture networks and arterial blood flow. Our results show that the method maintains high accuracy and well-calibrated uncertainty estimates even under severe data scarcity, highlighting its potential for scientific applications where limited data and reliable uncertainty quantification are critical.
In this paper, we investigate a class of approximate Gaussian processes (GP) obtained by taking a linear combination of compactly supported basis functions with the basis coefficients endowed with a dependent Gaussian prior distribution. This general class includes a popular approach that uses a finite element approximation of the stochastic partial differential equation (SPDE) associated with Mat\'ern GP. We explored another scalable alternative popularly used in the computer emulation literature where the basis coefficients at a lattice are drawn from a Gaussian process with an inverse-Gamma bandwidth. For both approaches, we study concentration rates of the posterior distribution. We demonstrated that the SPDE associated approach with a fixed smoothness parameter leads to a suboptimal rate despite how the number of basis functions and bandwidth are chosen when the underlying true function is sufficiently smooth. On the flip side, we showed that the later approach is rate-optimal adaptively over all smoothness levels of the underlying true function if an appropriate prior is placed on the number of basis functions. Efficient computational strategies are developed and numerics are provided to illustrate the theoretical results.
Bayesian models based on Gaussian processes (GPs) offer a flexible framework to predict spatially distributed variables with uncertainty. But the use of nonstationary priors, often necessary for capturing complex spatial patterns, makes sampling from the predictive posterior distribution (PPD) computationally intractable. In this paper, we propose a two-step approach based on diffusion generative models (DGMs) to mimic PPDs associated with non-stationary GP priors: we replace the GP prior by a DGM surrogate, and leverage recent advances on training-free guidance algorithms for DGMs to sample from the desired posterior distribution. We apply our approach to a rich non-stationary GP prior from which exact posterior sampling is untractable and validate that the issuing distributions are close to their GP counterpart using several statistical metrics. We also demonstrate how one can fine-tune the trained DGMs to target specific parts of the GP prior. Finally we apply the proposed approach to solve inverse problems arising in environmental sciences, thus yielding state-of-the-art predictions.
Fitting Gaussian Processes (GPs) provides interpretable aleatoric uncertainty quantification for estimation of spatio-temporal fields. Spatio-temporal deep learning models, while scalable, typically assume a simplistic independent covariance matrix for the response, failing to capture the underlying correlation structure. However, spatio-temporal GPs suffer from issues of scalability and various forms of approximation bias resulting from restrictive assumptions of the covariance kernel function. We propose STACI, a novel framework consisting of a variational Bayesian neural network approximation of non-stationary spatio-temporal GP along with a novel spatio-temporal conformal inference algorithm. STACI is highly scalable, taking advantage of GPU training capabilities for neural network models, and provides statistically valid prediction intervals for uncertainty quantification. STACI outperforms competing GPs and deep methods in accurately approximating spatio-temporal processes and we show it easily scales to datasets with millions of observations.
In this paper, we develop and analyze an integral fixed-time sliding mode control method for a scenario in which the system model is only partially known, utilizing Gaussian processes. We present two theorems on fixed-time convergence. The first theorem addresses the fully known system model, while the second considers situations where the system's drift is approximated utilizing Gaussian processes (GP) for approximating unknown dynamics. Both theorems establish the global fixed-time stability of the closed-loop system. The stability analysis is based on a straightforward quadratic Lyapunov function. Our proposed method outperforms an established adaptive fixed-time sliding mode control approach, especially when ample training data is available.