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 Bayesian Inference


Optimal Sample Complexity of M-wise Data for Top-K Ranking

Neural Information Processing Systems

We explore the top-K rank aggregation problem in which one aims to recover a consistent ordering that focuses on top-K ranked items based on partially revealed preference information. We examine an M-wise comparison model that builds on the Plackett-Luce (PL) model where for each sample, M items are ranked according to their perceived utilities modeled as noisy observations of their underlying true utilities. As our result, we characterize the minimax optimality on the sample size for top-K ranking. The optimal sample size turns out to be inversely proportional to M. We devise an algorithm that effectively converts M-wise samples into pairwise ones and employs a spectral method using the refined data. In demonstrating its optimality, we develop a novel technique for deriving tight $\ell_\infty$ estimation error bounds, which is key to accurately analyzing the performance of top-K ranking algorithms, but has been challenging. Recent work relied on an additional maximum-likelihood estimation (MLE) stage merged with a spectral method to attain good estimates in $\ell_\infty$ error to achieve the limit for the pairwise model. In contrast, although it is valid in slightly restricted regimes, our result demonstrates a spectral method alone to be sufficient for the general M-wise model. We run numerical experiments using synthetic data and confirm that the optimal sample size decreases at the rate of 1/M. Moreover, running our algorithm on real-world data, we find that its applicability extends to settings that may not fit the PL model.


Overcoming Selection Bias in Statistical Studies With Amortized Bayesian Inference

Arruda, Jonas, Chervet, Sophie, Staudt, Paula, Wieser, Andreas, Hoelscher, Michael, Sermet-Gaudelus, Isabelle, Binder, Nadine, Opatowski, Lulla, Hasenauer, Jan

arXiv.org Machine Learning

Selection bias arises when the probability that an observation enters a dataset depends on variables related to the quantities of interest, leading to systematic distortions in estimation and uncertainty quantification. For example, in epidemiological or survey settings, individuals with certain outcomes may be more likely to be included, resulting in biased prevalence estimates with potentially substantial downstream impact. Classical corrections, such as inverse-probability weighting or explicit likelihood-based models of the selection process, rely on tractable likelihoods, which limits their applicability in complex stochastic models with latent dynamics or high-dimensional structure. Simulation-based inference enables Bayesian analysis without tractable likelihoods but typically assumes missingness at random and thus fails when selection depends on unobserved outcomes or covariates. Here, we develop a bias-aware simulation-based inference framework that explicitly incorporates selection into neural posterior estimation. By embedding the selection mechanism directly into the generative simulator, the approach enables amortized Bayesian inference without requiring tractable likelihoods. This recasting of selection bias as part of the simulation process allows us to both obtain debiased estimates and explicitly test for the presence of bias. The framework integrates diagnostics to detect discrepancies between simulated and observed data and to assess posterior calibration. The method recovers well-calibrated posterior distributions across three statistical applications with diverse selection mechanisms, including settings in which likelihood-based approaches yield biased estimates. These results recast the correction of selection bias as a simulation problem and establish simulation-based inference as a practical and testable strategy for parameter estimation under selection bias.


PAC-Bayes Bounds for Gibbs Posteriors via Singular Learning Theory

Wang, Chenyang, Yang, Yun

arXiv.org Machine Learning

We derive explicit non-asymptotic PAC-Bayes generalization bounds for Gibbs posteriors, that is, data-dependent distributions over model parameters obtained by exponentially tilting a prior with the empirical risk. Unlike classical worst-case complexity bounds based on uniform laws of large numbers, which require explicit control of the model space in terms of metric entropy (integrals), our analysis yields posterior-averaged risk bounds that can be applied to overparameterized models and adapt to the data structure and the intrinsic model complexity. The bound involves a marginal-type integral over the parameter space, which we analyze using tools from singular learning theory to obtain explicit and practically meaningful characterizations of the posterior risk. Applications to low-rank matrix completion and ReLU neural network regression and classification show that the resulting bounds are analytically tractable and substantially tighter than classical complexity-based bounds. Our results highlight the potential of PAC-Bayes analysis for precise finite-sample generalization guarantees in modern overparameterized and singular models.


A Bayesian Updating Framework for Long-term Multi-Environment Trial Data in Plant Breeding

Bark, Stephan, Malik, Waqas Ahmed, Prus, Maryna, Piepho, Hans-Peter, Schmid, Volker

arXiv.org Machine Learning

In variety testing, multi-environment trials (MET) are essential for evaluating the genotypic performance of crop plants. A persistent challenge in the statistical analysis of MET data is the estimation of variance components, which are often still inaccurately estimated or shrunk to exactly zero when using residual (restricted) maximum likelihood (REML) approaches. At the same time, institutions conducting MET typically possess extensive historical data that can, in principle, be leveraged to improve variance component estimation. However, these data are rarely incorporated sufficiently. The purpose of this paper is to address this gap by proposing a Bayesian framework that systematically integrates historical information to stabilize variance component estimation and better quantify uncertainty. Our Bayesian linear mixed model (BLMM) reformulation uses priors and Markov chain Monte Carlo (MCMC) methods to maintain the variance components as positive, yielding more realistic distributional estimates. Furthermore, our model incorporates historical prior information by managing MET data in successive historical data windows. Variance component prior and posterior distributions are shown to be conjugate and belong to the inverse gamma and inverse Wishart families. While Bayesian methodology is increasingly being used for analyzing MET data, to the best of our knowledge, this study comprises one of the first serious attempts to objectively inform priors in the context of MET data. This refers to the proposed Bayesian updating approach. To demonstrate the framework, we consider an application where posterior variance component samples are plugged into an A-optimality experimental design criterion to determine the average optimal allocations of trials to agro-ecological zones in a sub-divided target population of environments (TPE).


Early-stopped aggregation: Adaptive inference with computational efficiency

Ohn, Ilsang, Fan, Shitao, Jun, Jungbin, Lin, Lizhen

arXiv.org Machine Learning

When considering a model selection or, more generally, an aggregation approach for adaptive statistical inference, it is often necessary to compute estimators over a wide range of model complexities including unnecessarily large models even when the true data-generating process is relatively simple, due to the lack of prior knowledge. This requirement can lead to substantial computational inefficiency. In this work, we propose a novel framework for efficient model aggregation called the early-stopped aggregation (ESA): instead of computing and aggregating estimators for all candidate models, we compute only a small number of simpler ones using an early-stopping criterion and aggregate only these for final inference. Our framework is versatile and applies to both Bayesian model selection, in particular, within the variational Bayes framework, and frequentist estimation, including a general penalized estimation setting. We investigate adaptive optimal property of the ESA approach across three learning paradigms. We first show that ESA achieves optimal adaptive contraction rates in the variational Bayes setting under mild conditions. We extend this result to variational empirical Bayes, where prior hyperparameters are chosen in a data-dependent manner. In addition, we apply the ESA approach to frequentist aggregation including both penalization-based and sample-splitting implementations, and establish corresponding theory. As we demonstrate, there is a clear unification between early-stopped Bayes and frequentist penalized aggregation, with a common "energy" functional comprising a data-fitting term and a complexity-control term that drives both procedures. We further present several applications and numerical studies that highlight the efficiency and strong performance of the proposed approach.


Doubly Outlier-Robust Online Infinite Hidden Markov Model

Yiu, Horace, Sánchez-Betancourt, Leandro, Cartea, Álvaro, Duran-Martin, Gerardo

arXiv.org Machine Learning

We derive a robust update rule for the online infinite hidden Markov model (iHMM) for when the streaming data contains outliers and the model is misspecified. Leveraging recent advances in generalised Bayesian inference, we define robustness via the posterior influence function (PIF), and provide conditions under which the online iHMM has bounded PIF. Imposing robustness inevitably induces an adaptation lag for regime switching. Our method, which is called Batched Robust iHMM (BR-iHMM), balances adaptivity and robustness with two additional tunable parameters. Across limit order book data, hourly electricity demand, and a synthetic high-dimensional linear system, BR-iHMM reduces one-step-ahead forecasting error by up to 67% relative to competing online Bayesian methods. Together with theoretical guarantees of bounded PIF, our results highlight the practicality of our approach for both forecasting and interpretable online learning.


A Bayesian Perspective on the Role of Epistemic Uncertainty for Delayed Generalization in In-Context Learning

Qchohi, Abdessamed, Rossi, Simone

arXiv.org Machine Learning

In-context learning enables transformers to adapt to new tasks from a few examples at inference time, while grokking highlights that this generalization can emerge abruptly only after prolonged training. We study task generalization and grokking in in-context learning using a Bayesian perspective, asking what enables the delayed transition from memorization to generalization. Concretely, we consider modular arithmetic tasks in which a transformer must infer a latent linear function solely from in-context examples and analyze how predictive uncertainty evolves during training. We combine approximate Bayesian techniques to estimate the posterior distribution and we study how uncertainty behaves across training and under changes in task diversity, context length, and context noise. We find that epistemic uncertainty collapses sharply when the model groks, making uncertainty a practical label-free diagnostic of generalization in transformers. Additionally, we provide theoretical support with a simplified Bayesian linear model, showing that asymptotically both delayed generalization and uncertainty peaks arise from the same underlying spectral mechanism, which links grokking time to uncertainty dynamics.


Monte Carlo Stochastic Depth for Uncertainty Estimation in Deep Learning

Müller, Adam T., Rögelein, Tobias, Stache, Nicolaj C.

arXiv.org Machine Learning

The deployment of deep neural networks in safety-critical systems necessitates reliable and efficient uncertainty quantification (UQ). A practical and widespread strategy for UQ is repurposing stochastic regularizers as scalable approximate Bayesian inference methods, such as Monte Carlo Dropout (MCD) and MC-DropBlock (MCDB). However, this paradigm remains under-explored for Stochastic Depth (SD), a regularizer integral to the residual-based backbones of most modern architectures. While prior work demonstrated its empirical promise for segmentation, a formal theoretical connection to Bayesian variational inference and a benchmark on complex, multi-task problems like object detection are missing. In this paper, we first provide theoretical insights connecting Monte Carlo Stochastic Depth (MCSD) to principled approximate variational inference. We then present the first comprehensive empirical benchmark of MCSD against MCD and MCDB on state-of-the-art detectors (YOLO, RT-DETR) using the COCO and COCO-O datasets. Our results position MCSD as a robust and computationally efficient method that achieves highly competitive predictive accuracy (mAP), notably yielding slight improvements in calibration (ECE) and uncertainty ranking (AUARC) compared to MCD. We thus establish MCSD as a theoretically-grounded and empirically-validated tool for efficient Bayesian approximation in modern deep learning.


Slithering Through Gaps: Capturing Discrete Isolated Modes via Logistic Bridging

Mohanty, Pinaki, Zhang, Ruqi

arXiv.org Machine Learning

High-dimensional and complex discrete distributions often exhibit multimodal behavior due to inherent discontinuities, posing significant challenges for sampling. Gradient-based discrete samplers, while effective, frequently become trapped in local modes when confronted with rugged or disconnected energy landscapes. This limits their ability to achieve adequate mixing and convergence in high-dimensional multimodal discrete spaces. To address these challenges, we propose \emph{Hyperbolic Secant-squared Gibbs-Sampling (HiSS)}, a novel family of sampling algorithms that integrates a \emph{Metropolis-within-Gibbs} framework to enhance mixing efficiency. HiSS leverages a logistic convolution kernel to couple the discrete sampling variable with the continuous auxiliary variable in a joint distribution. This design allows the auxiliary variable to encapsulate the true target distribution while facilitating easy transitions between distant and disconnected modes. We provide theoretical guarantees of convergence and demonstrate empirically that HiSS outperforms many popular alternatives on a wide variety of tasks, including Ising models, binary neural networks, and combinatorial optimization.


Performance of weakly-supervised electronic health record-based phenotyping methods in rare-outcome settings

Hong, Yunjing, Nelson, Jennifer C., Williamson, Brian D.

arXiv.org Machine Learning

Accurately identifying patients with specific medical conditions is a key challenge when using clinical data from electronic health records. Our objective was to comprehensively assess when weakly-supervised prediction methods, which use silver-standard labels (proxy measures of the true outcome) rather than gold-standard true labels, perform well in rare-outcome settings like vaccine safety studies. We compared three methods (PheNorm, MAP, and sureLDA) that combine structured features and features derived from clinical text using natural language processing, through an extensive simulation study with data-generating mechanisms ranging from simple to complex, varying outcome rates, and varying degrees of informative silver labels. We also considered using predicted probabilities to design a chart review validation study. No single method dominated the other across all prediction performance metrics. Probability-guided sampling selected a cohort enriched for patients with more mentions of important concepts in chart notes. SureLDA, the most complex of the three algorithms we considered, often performed well in simulations. Performance depended greatly on selected tuning parameters. Care should be taken when using weakly-supervised prediction methods in rare-outcome settings, particularly if the probabilities will be used in downstream analysis, but these methods can work well when silver labels are strong predictors of true outcomes.