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Probabilistic Methods · Gaussian Processes

Iskander Azangulov, Andrei Smolensky, Alexander Terenin, Viacheslav (Slava) Borovitskiy

Gaussian processes are arguably the most important class of spatiotemporal models within machine learning. They encode prior information about the modeled function and can be used for exact or approximate Bayesian learning. In many applications, particularly in physical sciences and engineering, but also in areas such as geostatistics and neuroscience, invariance to symmetries is one of the most fundamental forms of prior information one can consider. The invariance of a Gaussian process' covariance to such symmetries gives rise to the most natural generalization of the concept of stationarity to such spaces. In this work, we develop constructive and practical techniques for building stationary Gaussian processes on a very large class of non-Euclidean spaces arising in the context of symmetries. Our techniques make it possible to (i) calculate covariance kernels and (ii) sample from prior and posterior Gaussian processes defined on such spaces, both in a practical manner. This work is split into two parts, each involving different technical considerations: part I studies compact spaces, while part II studies non-compact spaces possessing certain structure. Our contributions make the non-Euclidean Gaussian process models we study compatible with well-understood computational techniques available in standard Gaussian process software packages, thereby making them accessible to practitioners.

Probabilistic Methods

Guy Moss, Leah Muhle, Reinhard Drews, Jakob H Macke, Cornelius Schröder

Simulation-based inference (SBI) is an established approach for performing Bayesian inference on scientific simulators. SBI so far works best on low-dimensional parametric models. However, it is difficult to infer function-valued parameters, which frequently occur in disciplines that model spatiotemporal processes such as the climate and earth sciences. Here, we introduce an approach for efficient posterior estimation, using a Fourier Neural Operator (FNO) architecture with a flow matching objective. We show that our approach, FNOPE, can perform inference of function-valued parameters at a fraction of the simulation budget of state of the art methods. In addition, FNOPE supports posterior evaluation at arbitrary discretizations of the domain, as well as simultaneous estimation of vector-valued parameters. We demonstrate the effectiveness of our approach on several benchmark tasks and a challenging spatial inference task from glaciology. FNOPE extends the applicability of SBI methods to new scientific domains by enabling the inference of function-valued parameters.

Probabilistic Methods · Everything Else

Kevin H. Lam, Thang Bui, George Deligiannidis, Yee Whye Teh

Latent Gaussian variables have been popularised in probabilistic machine learning. In turn, gradient estimators are the machinery that facilitates gradient-based optimisation for models with latent Gaussian variables. The reparameterisation trick is often used as the default estimator as it is simple to implement and yields low-variance gradients for variational inference. In this work, we propose the R2-G2 estimator as the Rao-Blackwellisation of the reparameterisation gradient estimator. Interestingly, we show that the local reparameterisation gradient estimator for Bayesian MLPs is an instance of the R2-G2 estimator and Rao-Blackwellisation. This lets us extend benefits of Rao-Blackwellised gradients to a suite of probabilistic models. We show that initial training with R2-G2 consistently yields better performance in models with multiple applications of the reparameterisation trick.

Probabilistic Methods · Bayesian Models and Methods

Hyungi Lee, Moonseok Choi, Hyunsu Kim, Kyunghyun Cho, Rajesh Ranganath, Juho Lee

Uncertainty-aware meta-learning aims not only for rapid adaptation to new tasks but also for reliable uncertainty estimation under limited supervision. Neural Processes (NPs) offer a flexible solution by learning implicit stochastic processes directly from data, often using a global latent variable to capture functional uncertainty. However, we empirically find that variational posteriors for this global latent variable are frequently miscalibrated, limiting both predictive accuracy and the reliability of uncertainty estimates. To address this issue, we propose Test Time Scaling for Neural Processes (TTSNPs), a sequential inference framework based on Sequential Monte Carlo Sampler (SMCS) that refines latent samples at test time without modifying the pre-trained NP model. TTSNPs iteratively transform variational samples into better approximations of the true posterior using neural transition kernels, significantly improving both prediction quality and uncertainty calibration. This makes NPs more robust and trustworthy, extending applicability to various scenarios requiring well-calibrated uncertainty estimates.

Probabilistic Methods · Gaussian Processes

Marshal Sinaga, Julien Martinelli, Samuel Kaski

Gaussian processes (GPs) are widely used for regression and optimization tasks such as Bayesian optimization (BO) due to their expressiveness and principled uncertainty estimates. However, in settings with large datasets corrupted by outliers, standard GPs and their sparse approximations struggle with computational tractability and robustness. We introduce Robust Computation-aware Gaussian Process (RCaGP), a novel GP model that jointly addresses these challenges by combining a principled treatment of approximation-induced uncertainty with robust generalized Bayesian updating. The key insight is that robustness and approximation-awareness are not orthogonal but intertwined: approximations can exacerbate the impact of outliers, and mitigating one without the other is insufficient. Unlike previous work that focuses narrowly on either robustness or approximation quality, RCaGP combines both in a principled and scalable framework, thus effectively managing both outliers and computational uncertainties introduced by approximations such as low-rank matrix multiplications. Our model ensures more conservative and reliable uncertainty estimates, a property we rigorously demonstrate. Additionally, we establish a robustness property and show that the mean function is key to preserving it, motivating a tailored model selection scheme for robust mean functions. Empirical results confirm that solving these challenges jointly leads to superior performance across both clean and outlier-contaminated settings, both on regression and high-throughput Bayesian optimization benchmarks.

Probabilistic Methods

Julius Vetter, Manuel Gloeckler, Daniel Gedon, Jakob H Macke

Simulation-based inference (SBI) offers a flexible and general approach to performing Bayesian inference: In SBI, a neural network is trained on synthetic data simulated from a model and used to rapidly infer posterior distributions for observed data. A key goal for SBI is to achieve accurate inference with as few simulations as possible, especially for expensive simulators. In this work, we address this challenge by repurposing recent probabilistic foundation models for tabular data: We show how tabular foundation models---specifically TabPFN---can be used as pre-trained autoregressive conditional density estimators for SBI. We propose Neural Posterior Estimation with Prior-data Fitted Networks (NPE-PFN) and show that it is competitive with current SBI approaches in terms of accuracy for both benchmark tasks and two complex scientific inverse problems. Crucially, it often substantially outperforms them in terms of simulation efficiency, sometimes requiring orders of magnitude fewer simulations. NPE-PFN eliminates the need for selecting and training an inference network and tuning its hyperparameters. We also show that it exhibits superior robustness to model misspecification and can be scaled to simulation budgets that exceed the context size limit of TabPFN. NPE-PFN provides a new direction for SBI, where training-free, general-purpose inference models offer efficient, easy-to-use, and flexible solutions for a wide range of stochastic inverse problems.

Probabilistic Methods · Bayesian Models and Methods

Luckeciano Carvalho Melo, Alessandro Abate, Yarin Gal

Machine Learning models in real-world applications must continuously learn new tasks to adapt to shifts in the data-generating distribution. Yet, for Continual Learning (CL), models often struggle to balance learning new tasks (plasticity) with retaining previous knowledge (memory stability). Consequently, they are susceptible to Catastrophic Forgetting, which degrades performance and undermines the reliability of deployed systems. In the Bayesian CL literature, variational methods tackle this challenge by employing a learning objective that recursively updates the posterior distribution while constraining it to stay close to its previous estimate. Nonetheless, we argue that these methods may be ineffective due to compounding approximation errors over successive recursions. To mitigate this, we propose new learning objectives that integrate the regularization effects of multiple previous posterior estimations, preventing individual errors from dominating future posterior updates and compounding over time. We reveal insightful connections between these objectives and Temporal-Difference methods, a popular learning mechanism in Reinforcement Learning and Neuroscience. Experiments on challenging CL benchmarks show that our approach effectively mitigates Catastrophic Forgetting, outperforming strong Variational CL methods.

Computer Vision · 3D Rendering & Reconstruction

Hyunjin Kim, Haebeom Jung, Jaesik Park

We propose an adaptive sampling framework for 3D Gaussian Splatting (3DGS) that leverages comprehensive multi-view photometric error signals within a unified Metropolis-Hastings approach. Vanilla 3DGS heavily relies on heuristic-based density-control mechanisms (e.g., cloning, splitting, and pruning), which can lead to redundant computations or premature removal of beneficial Gaussians. Our framework overcomes these limitations by reformulating densification and pruning as a probabilistic sampling process, dynamically inserting and relocating Gaussians based on aggregated multi-view errors and opacity scores. Guided by Bayesian acceptance tests derived from these error-based importance scores, our method substantially reduces reliance on heuristics, offers greater flexibility, and adaptively infers Gaussian distributions without requiring predefined scene complexity. Experiments on benchmark datasets, including Mip-NeRF360, Tanks and Temples and Deep Blending, show that our approach reduces the number of Gaussians needed, achieving faster convergence while matching or modestly surpassing the view-synthesis quality of state-of-the-art models.

Probabilistic Methods

Jeffrey Alido, Tongyu Li, Yu Sun, Lei Tian

Conventional score-based diffusion models (DMs) may struggle with anisotropic Gaussian diffusion processes due to the required inversion of covariance matrices in the denoising score matching training objective \cite{vincent_connection_2011}. We propose Whitened Score (WS) diffusion models, a novel framework based on stochastic differential equations that learns the Whitened Score function instead of the standard score. This approach circumvents covariance inversion, extending score-based DMs by enabling stable training of DMs on arbitrary Gaussian forward noising processes. WS DMs establish equivalence with flow matching for arbitrary Gaussian noise, allow for tailored spectral inductive biases, and provide strong Bayesian priors for imaging inverse problems with structured noise. We experiment with a variety of computational imaging tasks using the CIFAR, CelebA ($64\times64$), and CelebA-HQ ($256\times256$) datasets and demonstrate that WS diffusion priors trained on anisotropic Gaussian noising processes consistently outperform conventional diffusion priors based on isotropic Gaussian noise.

Data-centric AI · Data-centric AI methods and tools

Thomson Yen, Andrew Siah, Haozhe Chen, C. Guetta, Tianyi Peng, Hongseok Namkoong

Careful curation of data sources can significantly improve the performance of LLM pre-training, but predominant approaches rely heavily on intuition or costly trial-and-error, making them difficult to generalize across different data domains and downstream tasks. Although scaling laws can provide a principled and general approach for data curation, standard deterministic extrapolation from small-scale experiments to larger scales requires strong assumptions on the reliability of such extrapolation, whose brittleness has been highlighted in prior works. In this paper, we introduce a probabilistic extrapolation framework for data mixture optimization that avoids rigid assumptions and explicitly models the uncertainty in performance across decision variables. We formulate data curation as a sequential decision-making problem–multi-fidelity, multi-scale Bayesian optimization–where {data mixtures, model scale, training steps} are adaptively selected to balance training cost and potential information gain. Our framework naturally gives rise to algorithm prototypes that leverage noisy information from inexpensive experiments to systematically inform costly training decisions. To accelerate methodological progress, we build a simulator based on 472 language model pre-training runs with varying data compositions from the SlimPajama dataset. We observe that even simple kernels and acquisition functions can enable principled decisions across training models from 20M to 1B parameters and achieve 2.6x and 3.3x speedups compared to multi-fidelity BO and random search baselines. Taken together, our framework underscores potential efficiency gains achievable by developing principled and transferable data mixture optimization methods. Our code is publicly available at https://github.com/namkoong-lab/data-recipes.

Probabilistic Methods · Bayesian Models and Methods

Ben Adcock, Zi Yuan (Nick) Huang

We study the sample complexity of Bayesian recovery for solving inverse problems with general prior, forward operator and noise distributions. We consider posterior sampling according to an approximate prior $\mathcal{P}$, and establish sufficient conditions for stable and accurate recovery with high probability. Our main result is a non-asymptotic bound that shows that the sample complexity depends on (i) the intrinsic complexity of $\mathcal{P}$, quantified by its *approximate covering number*, and (ii) concentration bounds for the forward operator and noise distributions. As a key application, we specialize to generative priors, where $\mathcal{P}$ is the pushforward of a latent distribution via a Deep Neural Network (DNN). We show that the sample complexity scales log-linearly with the latent dimension $k$, thus establishing the efficacy of DNN-based priors. Generalizing existing results on deterministic (i.e., non-Bayesian) recovery for the important problem of random sampling with an orthogonal matrix $U$, we show how the sample complexity is determined by the *coherence* of $U$ with respect to the support of $\mathcal{P}$. Hence, we establish that coherence plays a fundamental role in Bayesian recovery as well. Overall, our framework unifies and extends prior work, providing rigorous guarantees for the sample complexity of solving Bayesian inverse problems with arbitrary distributions.

Probabilistic Methods · Bayesian Models and Methods

Lu Xu, Tsai Hor Chan, Lequan Yu, Kwok Lam, Guosheng Yin

Density estimation is essential for generative modeling, particularly with the rise of modern neural networks. While existing methods capture complex data distributions, they often lack interpretability and uncertainty quantification. Bayesian nonparametric methods, especially the \polya tree, offer a robust framework that addresses these issues by accurately capturing function behavior over small intervals. Traditional techniques like Markov chain Monte Carlo (MCMC) face high computational complexity and scalability limitations, hindering the use of Bayesian nonparametric methods in deep learning. To tackle this, we introduce the variational \polya tree (VPT) model, which employs stochastic variational inference to compute posterior distributions. This model provides a flexible, nonparametric Bayesian prior that captures latent densities and works well with stochastic gradient optimization. We also leverage the joint distribution likelihood for a more precise variational posterior approximation than traditional mean-field methods. We evaluate the model performance on both real data and images, and demonstrate its competitiveness with other state-of-the-art deep density estimation methods. We also explore its ability in enhancing interpretability and uncertainty quantification. Code is available at \url{https://github.com/howardchanth/var-polya-tree}.

Optimization · Bayesian & Black-box Optimization

Seunghee Ryu, Donghoon Kwon, Seongjin Choi, Aryan Deshwal, Seungmo Kang, Carolina Osorio

We introduce BO4Mob, a new benchmark framework for high-dimensional Bayesian Optimization (BO), driven by the challenge of origin-destination (OD) travel demand estimation in large urban road networks. Estimating OD travel demand from limited traffic sensor data is a difficult inverse optimization problem, particularly in real-world, large-scale transportation networks. This problem involves optimizing over high-dimensional continuous spaces where each objective evaluation is computationally expensive, stochastic, and non-differentiable. BO4Mob comprises five scenarios based on real-world San Jose, CA road networks, with input dimensions scaling up to 10,100. These scenarios utilize high-resolution, open-source traffic simulations that incorporate realistic nonlinear and stochastic dynamics. We demonstrate the benchmark's utility by evaluating five optimization methods: three state-of-the-art BO algorithms and two non-BO baselines. This benchmark is designed to support both the development of scalable optimization algorithms and their application for the design of data-driven urban mobility models, including high-resolution digital twins of metropolitan road networks. Code and documentation are available at https://github.com/UMN-Choi-Lab/BO4Mob.

Optimization · Bayesian & Black-box Optimization

Xunzhao Yu

Meta-learning has been demonstrated to be useful to improve the sampling efficiency of Bayesian optimization (BO) and surrogate-assisted evolutionary algorithms (SAEAs) when solving expensive optimization problems (EOPs). Existing studies mainly focus on either combinations of existing meta-learning modeling methods with optimization algorithms, or the development of meta-learning acquisition functions for specific meta BO. However, the meta-learning models used in the literature are not designed for optimization purpose, and the generalization ability of meta-learning acquisition functions is limited. In this work, we develop a novel architecture of meta-learning model for optimization purpose and propose a generalized few-shot evolutionary optimization (FSEO) framework to solve EOPs. We focus on the scenario of expensive multi-objective EOPs (EMOPs) in the context of few-shot optimization as there are few studies on it and its high requirement on surrogate modeling performance. The surrogates in FSEO framework combines neural network with Gaussian Processes (GPs), their network parameters and some parameters of GPs represent task-independent experience and are meta-learned across related optimization tasks, the remaining GPs parameters are task-specific parameters that represent unique features of the target task. We demonstrate that our FSEO framework is able to improve the sampling efficiency of existing SAEAs on EMOPs.

Probabilistic Methods · Gaussian Processes

Pratik Rathore, Zachary Frangella, Sachin Garg, Shaghayegh Fazliani, Michal Derezinski, Madeleine Udell

Gaussian processes (GPs) play an essential role in biostatistics, scientific machine learning, and Bayesian optimization for their ability to provide probabilistic predictions and model uncertainty. However, GP inference struggles to scale to large datasets (which are common in modern applications), since it requires the solution of a linear system whose size scales quadratically with the number of samples in the dataset. We propose an approximate, distributed, accelerated sketch-and-project algorithm ($\texttt{ADASAP}$) for solving these linear systems, which improves scalability. We use the theory of determinantal point processes to show that the posterior mean induced by sketch-and-project rapidly converges to the true posterior mean. In particular, this yields the first efficient, condition number-free algorithm for estimating the posterior mean along the top spectral basis functions, showing that our approach is principled for GP inference. $\texttt{ADASAP}$ outperforms state-of-the-art solvers based on conjugate gradient and coordinate descent across several benchmark datasets and a large-scale Bayesian optimization task. Moreover, $\texttt{ADASAP}$ scales to a dataset with $> 3 \cdot 10^8$ samples, a feat which has not been accomplished in the literature.

General Machine Learning · Causality

Vahid Balazadeh, Hamidreza Kamkari, Valentin Thomas, Junwei Ma, Bingru Li, Jesse Cresswell, Rahul Krishnan

Causal effect estimation from observational data is fundamental across various applications. However, selecting an appropriate estimator from dozens of specialized methods demands substantial manual effort and domain expertise. We present CausalPFN, a single transformer that *amortizes* this workflow: trained once on a large library of simulated data-generating processes that satisfy ignorability, it infers causal effects for new observational datasets out of the box. CausalPFN combines ideas from Bayesian causal inference with the large-scale training protocol of prior-fitted networks (PFNs), learning to map raw observations directly to causal effects without any task-specific adjustment. Our approach achieves superior average performance on heterogeneous and average treatment effect estimation benchmarks (IHDP, Lalonde, ACIC). Moreover, it shows competitive performance for real-world policy making on uplift modeling tasks. CausalPFN provides calibrated uncertainty estimates to support reliable decision-making based on Bayesian principles. This ready-to-use model requires no further training or tuning and takes a step toward automated causal inference (https://github.com/vdblm/CausalPFN/).

Applications · Health

Ke Liu, Shangde Gao, Yichao Fu, Shangqi Gao

Retinal vessel segmentation is critical for medical diagnosis, yet existing models often struggle to generalize across domains due to appearance variability, limited annotations, and complex vascular morphology. We propose GraphSeg, a variational Bayesian framework that integrates anatomical graph priors with structure-aware image decomposition to enhance cross-domain segmentation. GraphSeg factorizes retinal images into structure-preserved and structure-degraded components, enabling domain-invariant representation. A deformable graph prior, derived from a statistical retinal atlas, is incorporated via a differentiable alignment and guided by an unsupervised energy function. Experiments on three public benchmarks (CHASE, DRIVE, HRF) show that GraphSeg consistently outperforms existing methods under domain shifts. These results highlight the importance of jointly modeling anatomical topology and image structure for robust generalizable vessel segmentation.

Deep Learning · Generative Models and Autoencoders

I. Shavindra Jayasekera, Jacob Si, Filippo Valdettaro, Wenlong Chen, Aldo Faisal, Yingzhen Li

As large language models (LLMs) gain popularity in conducting prediction tasks in-context, understanding the sources of uncertainty in in-context learning becomes essential to ensuring reliability. The recent hypothesis of in-context learning performing predictive Bayesian inference opens the avenue for Bayesian uncertainty estimation, particularly for decomposing uncertainty into epistemic uncertainty due to lack of in-context data and aleatoric uncertainty inherent in the in-context prediction task. However, the decomposition idea remains under-explored due to the intractability of the latent parameter posterior from the underlying Bayesian model. In this work, we introduce a variational uncertainty decomposition framework for in-context learning without explicitly sampling from the latent parameter posterior, by optimising auxiliary inputs as probes to obtain an upper bound to the aleatoric uncertainty of an LLM's in-context learning procedure. Through experiments on synthetic and real-world tasks, we show quantitatively and qualitatively that the decomposed uncertainties obtained from our method exhibit desirable properties of epistemic and aleatoric uncertainty.

Deep Learning · Algorithms

Boyuan Zhang, Yingjun Du, Xiantong Zhen, Ling Shao

Task vectors capture how a model changes during fine-tuning by recording the difference between pre-trained and task-specific weights. The composition of task vectors, a key operator in task arithmetic, enables models to integrate knowledge from multiple tasks without incurring significant additional inference costs. In this paper, we propose variational task vector composition (VTVC), where composition coefficients are taken as latent variables and estimated in a Bayesian inference framework. Unlike previous methods that operate at the task level, our framework focuses on sample-specific composition. Motivated by the observation of structural redundancy in task vectors, we introduce a Spike-and-Slab prior that promotes sparsity and aims to preserve the most informative components. To further address the high variance and sampling inefficiency in sparse, high-dimensional spaces, we develop a gated sampling mechanism that constructs a controllable posterior by filtering the composition coefficients based on both uncertainty and importance. This yields a more stable and interpretable variational framework by deterministically selecting reliable task components, reducing sampling variance while improving transparency and generalization. Experimental results demonstrate that our method achieves state-of-the-art average performance across a diverse range of benchmarks, including image classification and natural language understanding. These findings highlight the practical value of our approach, offering a new, efficient, and effective framework for task vector composition.

Dong Bok Lee, Aoxuan Zhang, Byungjoo Kim, Junhyeon Park, Steven Adriaensen, Juho Lee, Sung Ju Hwang, Hae Beom Lee

In this paper, we address the problem of cost-sensitive hyperparameter optimization (HPO) built upon freeze-thaw Bayesian optimization (BO). Specifically, we assume a scenario where users want to early-stop the HPO process when the expected performance improvement is not satisfactory with respect to the additional computational cost. Motivated by this scenario, we introduce \emph{utility} in the freeze-thaw framework, a function describing the trade-off between the cost and performance that can be estimated from the user's preference data. This utility function, combined with our novel acquisition function and stopping criterion, allows us to dynamically continue training the configuration that we expect to maximally improve the utility in the future, and also automatically stop the HPO process around the maximum utility. Further, we improve the sample efficiency of existing freeze-thaw methods with transfer learning to develop a specialized surrogate model for the cost-sensitive HPO problem. We validate our algorithm on established multi-fidelity HPO benchmarks and show that it outperforms all the previous freeze-thaw BO and transfer-BO baselines we consider, while achieving a significantly better trade-off between the cost and performance.