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Probabilistic Methods

Gerardo Duran-Martin, Leandro Sánchez-Betancourt, Alvaro Cartea, Kevin Murphy

We introduce scalable algorithms for online learning of neural network parameters and Bayesian sequential decision making. Unlike classical Bayesian neural networks, which induce predictive uncertainty through a posterior over model parameters, our methods adopt a predictive-first perspective based on martingale posteriors. In particular, we work directly with the one-step-ahead posterior predictive, which we parameterize with a neural network and update sequentially with incoming observations. This decouples Bayesian decision-making from parameter-space inference: we sample from the posterior predictive for decision making, and update the parameters of the posterior predictive via fast, frequentist Kalman-filter-like recursions. Our algorithms operate in a fully online, replay-free setting, providing principled uncertainty quantification without costly posterior sampling. Empirically, they achieve competitive performance–speed trade-offs in non-stationary contextual bandits and Bayesian optimization, offering 10–100 times faster inference than classical Thompson sampling while maintaining comparable or superior decision performance.

General Machine Learning · Everything Else

Dongguen Kim, Young-Geun Choi, Minwoo Chae

Dynamic pricing algorithms typically assume continuous price variables, which may not reflect real-world scenarios where prices are often discrete. This paper demonstrates that leveraging discrete price information within a semi-parametric model can substantially improve performance, depending on the size of the support set of the price variable relative to the time horizon. Specifically, we propose a novel semi-parametric contextual dynamic pricing algorithm, namely BayesCoxCP, based on a Bayesian approach to the Cox proportional hazards model. Our theoretical analysis establishes high-probability regret bounds that adapt to the sparsity level $\gamma$, proving that our algorithm achieves a regret upper bound of $\widetilde{O}(T^{(1+\gamma)/2}+\sqrt{dT})$ for $\gamma < 1/3$ and $\widetilde{O}(T^{2/3}+\sqrt{dT})$ for $\gamma \geq 1/3$, where $\gamma$ represents the sparsity of the price grid relative to the time horizon $T$. Through numerical experiments, we demonstrate that our proposed algorithm significantly outperforms an existing method, particularly in scenarios with sparse discrete price points.

Probabilistic Methods

Abdellah Rahmani, Pascal Frossard

Understanding causal relationships in multivariate time series is crucial in many scenarios, such as those dealing with financial or neurological data. Many such time series exhibit multiple regimes, i.e., consecutive temporal segments with a priori unknown boundaries, with each regime having its own causal structure. Inferring causal dependencies and regime shifts is critical for analyzing the underlying processes. However, causal structure learning in this setting is challenging due to (1) non-stationarity, i.e., each regime can have its own causal graph and mixing function, and (2) complex noise distributions, which may be non-Gaussian or heteroscedastic. Existing causal discovery approaches cannot address these challenges, since generally assume stationarity or Gaussian noise with constant variance. Hence, we introduce FANTOM, a unified framework for causal discovery that handles non-stationary processes along with non-Gaussian and heteroscedastic noises. FANTOM simultaneously infers the number of regimes and their corresponding indices and learns each regime’s Directed Acyclic Graph. It uses a Bayesian Expectation Maximization algorithm that maximizes the evidence lower bound of the data log-likelihood. On the theoretical side, we prove, under mild assumptions, that temporal heteroscedastic causal models, introduced in FANTOM's formulation, are identifiable in both stationary and non-stationary settings. In addition, extensive experiments on synthetic and real data show that FANTOM outperforms existing methods.

Probabilistic Methods · Bayesian Models and Methods

Gongyu Chen, Ying Cui

We propose a generalized score-based diffusion framework for learning multivariate Gaussian mixture models with homoscedastic or heteroscedastic noise. Our goal is to nonparametrically estimate the latent location distribution and denoise the observations. Departing from the conventional maximum likelihood approach, we reinterpret each observation as a temporal slice of a family of stochastic diffusion processes. This modeling choice enables a principled characterization of the additive noise structure and supports a multi-step denoising procedure grounded in reverse-time dynamics. We introduce a score-based objective that explicitly models the latent distribution and accommodates observation-specific noise covariances. Theoretically, we establish that the score estimation error with $n$ independent observations achieves a near-parametric error rate of $\frac{\mathrm{polylog}(n)}{n}$, improving upon existing results in the diffusion literature. Empirically, our method outperforms the nonparametric maximum likelihood estimator in both density estimation and denoising fidelity, especially in high-dimensional settings. These findings suggest a promising direction for integrating nonparametric empirical Bayes with diffusion-based generative modeling for latent structure recovery.

Optimization · Bayesian & Black-box Optimization

Paul Brunzema, Sebastian Trimpe

We introduce BayeSQP, a novel algorithm for general black-box optimization that merges the structure of sequential quadratic programming with concepts from Bayesian optimization. BayeSQP employs second-order Gaussian process surrogates for both the objective and constraints to jointly model the function values, gradients, and Hessian from only zero-order information. At each iteration, a local subproblem is constructed using the GP posterior estimates and solved to obtain a search direction. Crucially, the formulation of the subproblem explicitly incorporates uncertainty in both the function and derivative estimates, resulting in a tractable second-order cone program for high probability improvements under model uncertainty. A subsequent one-dimensional line search via constrained Thompson sampling selects the next evaluation point. Empirical results show that BayeSQP outperforms state-of-the-art methods in specific high-dimensional settings. Our algorithm offers a principled and flexible framework that bridges classical optimization techniques with modern approaches to black-box optimization.

Applications · Language, Speech and Dialog

Yufan Zhuang, Liyuan Liu, Chandan Singh, Jingbo Shang, Jianfeng Gao

In standard autoregressive generation, an LLM predicts the next-token distribution, samples a discrete token, and then discards the distribution, passing only the sampled token as new input. To preserve this distribution’s rich information, we propose Mixture of Inputs (MoI), a training-free method for autoregressive generation. After generating a token following the standard paradigm, we construct a new input that blends the generated discrete token with the previously discarded token distribution. Specifically, we employ a Bayesian estimation method that treats the token distribution as the prior, the sampled token as the observation, and replaces the conventional one-hot vector with the continuous posterior expectation as the new model input. MoI allows the model to maintain a richer internal representation throughout the generation process, resulting in improved text quality and reasoning capabilities. On mathematical reasoning, code generation, and PhD-level QA tasks, MoI consistently improves performance across multiple models including QwQ-32B, Nemotron-Super-49B, Gemma-3-27B, and DAPO-Qwen-32B, with no additional training and negligible computational overhead.

Probabilistic Methods · Bayesian Models and Methods

Bálint Mucsányi, Nathaël Da Costa, Philipp Hennig

In classification tasks, softmax functions are ubiquitously used as output activations to produce predictive probabilities. Such outputs only capture aleatoric uncertainty. To capture epistemic uncertainty, approximate Gaussian inference methods have been proposed. We develop a common formalism to describe such methods, which we view as outputting Gaussian distributions over the logit space. Predictives are then obtained as the expectations of the Gaussian distributions pushed forward through the softmax. However, such softmax Gaussian integrals cannot be solved analytically, and Monte Carlo (MC) approximations can be costly and noisy. We propose to replace the softmax activation with element-wise normCDF or sigmoid, which allows for the accurate sampling-free approximation of predictives. This also enables the approximation of the Gaussian pushforwards by Dirichlet distributions with moment matching. This approach entirely eliminates the runtime and memory overhead associated with MC sampling. We evaluate it combined with several approximate Gaussian inference methods (Laplace, HET, SNGP) on large- and small-scale datasets (ImageNet, CIFAR-100, CIFAR-10), demonstrating improved uncertainty quantification capabilities compared to softmax MC sampling. Our code is available at https://github.com/bmucsanyi/probit.

Optimization · Bayesian & Black-box Optimization

Hanyang Wang, Juergen Branke, Matthias Poloczek

Many real-world black-box optimization problems have multiple conflicting objectives. Rather than attempting to approximate the entire set of Pareto-optimal solutions, interactive preference learning, i.e., optimization with a decision maker in the loop, allows to focus the search on the most relevant subset. However, few previous studies have exploited the fact that utility functions are usually monotonic. In this paper, we address the Bayesian Optimization with Preference Exploration (BOPE) problem and propose using a neural network ensemble as a utility surrogate model. This approach naturally integrates monotonicity and allows to learn the decision maker's preferences from pairwise comparisons. Our experiments demonstrate that the proposed method outperforms state-of-the-art approaches and exhibits robustness to noise in utility evaluations. An ablation study highlights the critical role of monotonicity in enhancing performance.

Applications · Neuroscience, Cognitive Science

Victor Geadah, Amin Nejatbakhsh, David Lipshutz, Jonathan Pillow, Alex Williams

Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop *Conditionally Linear Dynamical System* (CLDS) models as a general-purpose method to characterize these dynamics. These models use Gaussian Process priors to capture the nonlinear dependence of circuit dynamics on task and behavioral variables. Conditioned on these covariates, the data is modeled with linear dynamics. This allows for transparent interpretation and tractable Bayesian inference. We find that CLDS models can perform well even in severely data-limited regimes (e.g. one trial per condition) due to their Bayesian formulation and ability to share statistical power across nearby task conditions. In example applications, we apply CLDS to model thalamic neurons that nonlinearly encode heading direction and to model motor cortical neurons during a cued-reaching task.

Probabilistic Methods · Bayesian Models and Methods

Fuyuan Xiao, Yu Zhou, Witold Pedrycz

In pattern classification, efficient uncertainty reasoning plays a critical role, particularly in real-time applications involving noisy data, ambiguous class boundaries, or overlapping categories. Leveraging the advanced computational power of quantum computing, an Adaptive Quantum Circuit for Dempster’s Rule of Combination (AQC-DRC) is proposed to address efficient classification under uncertain environments. The AQC-DRC is developed within the framework of quantum evidence theory (QET) and facilitates decision-making based on quantum basic probability and plausibility levels, which is a generalized Bayesian inference method. The AQC-DRC provides a deterministic computation of DRC, ensuring that quantum fusion outcomes in uncertain pattern classification are exactly aligned with those of the classical method, while simultaneously achieving exponential reductions in the computational complexity of evidence combination and significantly improving fusion efficiency. It is founded that the quantum basic probability amplitude function in QET, as a generalized quantum probability amplitude, can be naturally utilized to express the quantum amplitude encoding. In addition, the quantum basic probability in QET, as a generalized quantum probability, naturally forms a quantum basic probability distribution and can be used to represent quantum measurement outcomes for quantum basic probability level decision-making. Furthermore, the quantum plausibility function in QET also can be naturally used to express the quantum measurement outcomes for quantum plausibility level decision-making. These findings enrich the physical understanding of quantum amplitude encoding and quantum measurement outcomes, offering broad application prospects for representing and processing uncertain knowledge in pattern classification.

Probabilistic Methods · Monte Carlo and Sampling Methods

Han Cui, Jingbo Liu

Conditional sampling is a fundamental task in Bayesian statistics and generative modeling. Consider the problem of sampling from the posterior distribution $P\_{X|Y=y^\*}$ for some observation $y^\*$, where the likelihood $P\_{Y|X}$ is known, and we are given $n$ i.i.d. samples $D=\\{X\_i\\}\_{i=1}^n$ drawn from an unknown prior distribution $\pi\_X$. Suppose that $f(\hat{\pi}\_{X^n})$ is the distribution of a posterior sample generated by an algorithm (e.g. a conditional generative model or the Bayes rule) when $\hat{\pi}\_{X^n}$ is the empirical distribution of the training data. Although averaging over the randomness of the training data $D$, we have $\mathbb{E}\_D\left(\hat{\pi}\_{X^n}\right)= \pi\_X$, we do not have $\mathbb{E}\_D\left\\{f(\hat{\pi}\_{X^n})\right\\}= f(\pi\_X)$ due to the nonlinearity of $f$, leading to a bias. In this paper we propose a black-box debiasing scheme that improves the accuracy of such a naive plug-in approach. For any integer $k$ and under boundedness of the likelihood and smoothness of $f$, we generate samples $\hat{X}^{(1)},\dots,\hat{X}^{(k)}$ and weights $w\_1,\dots,w\_k$ such that $\sum_{i=1}^kw_iP\_{\hat{X}^{(i)}}$ is a $k$-th order approximation of $f(\pi\_X)$, where the generation process treats $f$ as a black-box. Our generation process achieves higher accuracy when averaged over the randomness of the training data, without degrading the variance, which can be interpreted as improving memorization without compromising generalization in generative models.

Probabilistic Methods · Bayesian Models and Methods

Hadi Vafaii, Dekel Galor, Jacob Yates

Inference in both brains and machines can be formalized by optimizing a shared objective: maximizing the evidence lower bound (ELBO) in machine learning, or minimizing variational free energy ($\mathcal{F}$) in neuroscience (ELBO = $-\mathcal{F}$). While this equivalence suggests a unifying framework, it leaves open how inference is implemented in neural systems. Here, we introduce FOND (*Free energy Online Natural-gradient Dynamics*), a framework that derives neural inference dynamics from three principles: (1) natural gradients on $\mathcal{F}$, (2) online belief updating, and (3) iterative refinement. We apply FOND to derive iP-VAE (*iterative Poisson variational autoencoder*), a recurrent spiking neural network that performs variational inference through membrane potential dynamics, replacing amortized encoders with iterative inference updates. Theoretically, iP-VAE yields several desirable features such as emergent normalization via lateral competition, and hardware-efficient integer spike count representations. Empirically, iP-VAE outperforms both standard VAEs and Gaussian-based predictive coding models in sparsity, reconstruction, and biological plausibility, and scales to complex color image datasets such as CelebA. iP-VAE also exhibits strong generalization to out-of-distribution inputs, exceeding hybrid iterative-amortized VAEs. These results demonstrate how deriving inference algorithms from first principles can yield concrete architectures that are simultaneously biologically plausible and empirically effective.

Probabilistic Methods · Bayesian Models and Methods

Guohao Sun, Hang Hua, Jian Wang, Jiebo Luo, Sohail Dianat, MAJID RABBANI, Raghuveer Rao, Zhiqiang Tao

Chain-of-thought (CoT) reasoning is critical for improving the interpretability and reliability of Large Vision-Language Models (LVLMs). However, existing training algorithms such as SFT, PPO, and GRPO may not generalize well across unseen reasoning tasks and heavily rely on a biased reward model. To address this challenge, we reformulate reasoning in LVLMs as posterior inference and propose a scalable training algorithm based on amortized variational inference. By leveraging diversity-seeking reinforcement learning algorithms, we introduce a novel sparse reward function for token-level learning signals that encourage diverse, high-likelihood latent CoT, overcoming deterministic sampling limitations and avoiding reward hacking. Additionally, we implement a Bayesian inference-scaling strategy that replaces costly Best-of-N and Beam Search with a marginal likelihood to efficiently rank optimal rationales and answers. We empirically demonstrate that the proposed method enhances the state-of-the-art LVLMs on four reasoning benchmarks, in terms of effectiveness, generalization, and interpretability.

Applications · Neuroscience, Cognitive Science

Matthias Schultheis, Jana-Sophie Schönfeld, Constantin Rothkopf, Heinz Koeppl

Human behavior is characterized by continuous learning to reduce uncertainties about the world in pursuit of goals. When trying to understand such behavior from observations, it is essential to account for this adaptive nature and reason about the uncertainties that may have led to seemingly suboptimal decisions. Nevertheless, most inverse approaches to sequential decision-making focus on inferring cost functions underlying stationary behavior or are limited to low-dimensional tasks. In this paper, we address this gap by considering the problem of inferring an agent's knowledge or awareness about the environment based on a given trajectory. We assume that the agent aims to reach a goal in an environment they only partially know, and integrates new information into their plan as they act. We propose a Bayesian approach to infer their latent knowledge state, leveraging an approximate navigation model that optimistically incorporates partial information while accounting for uncertainty. By combining sample-based Bayesian inference with dynamic graph algorithms, we achieve an efficient method for computing posterior beliefs about the agent's knowledge. Empirical validation using simulated behavioral data and human data from an online experiment demonstrates that our model effectively captures human navigation under uncertainty and reveals interpretable insights into their environmental knowledge.

General Machine Learning · Everything Else

En Yu, Jie Lu, Xiaoyu Yang, Guangquan Zhang, Zhen Fang

Modern machine learning models struggle to maintain performance in dynamic environments where temporal distribution shifts, \textit{i.e., concept drift}, are prevalent. Temporal Domain Generalization (TDG) seeks to enable model generalization across evolving domains, yet existing approaches typically assume smooth incremental changes, struggling with complex real-world drifts involving both long-term structure (incremental evolution/periodicity) and local uncertainties. To overcome these limitations, we introduce FreKoo, which tackles these challenges through a novel frequency-domain analysis of parameter trajectories. It leverages the Fourier transform to disentangle parameter evolution into distinct spectral bands. Specifically, the low-frequency components with dominant dynamics are learned and extrapolated using the Koopman operator, robustly capturing diverse drift patterns including both incremental and periodic drifts. Simultaneously, potentially disruptive high-frequency variations are smoothed via targeted temporal regularization, preventing overfitting to transient noise and domain uncertainties. In addition, this dual-spectral strategy is rigorously grounded through theoretical analysis, providing stability guarantees for the Koopman prediction, a principled Bayesian justification for the high-frequency regularization, and culminating in a multiscale generalization bound connecting spectral dynamics to improved generalization. Extensive experiments demonstrate FreKoo's significant superiority over state-of-the-art TDG methods, particularly excelling in real-world streaming scenarios with complex drifts and uncertainties.

Optimization · Large Scale, Parallel and Distributed

Maximilian Egger, Rawad Bitar, Antonia Wachter-Zeh, Nir Weinberger, Deniz Gunduz

Federated Learning (FL) incurs high communication costs in both uplink and downlink. The literature largely focuses on lossy compression of model updates in deterministic FL. In contrast, stochastic (Bayesian) FL considers distributions over parameters, enabling uncertainty quantification, better generalization, and, crucially, inherent communication-regularized training through a mirror-descent structure. In this paper, we consider both uplink and downlink communication in stochastic FL, and propose a communication framework based on remote source generation. Employing Minimal Random Coding (MRC) for remote generation, we allow the server and the clients to sample from local and global posteriors (sources), respectively, rather than transmitting locally sampled updates. The framework encompasses communication-regularized local optimization and principled compression of model updates, leveraging gradually updated prior distributions as side information. Through extensive simulations, we show that our method achieves $5-32\times$ reduction in total communication cost while preserving accuracy. We further analyze the communication cost, refining existing MRC bounds and enabling precise quantification of uplink and downlink trade-offs. We also extend our method to conventional FL via stochastic quantization and prove a contraction property for the biased MRC compressor to facilitate convergence analysis.

Applications · Chemistry and Drug Discovery

Rubo Wang, Xingyu Gao, Peilin Zhao

With the development of biotechnology, RNA therapies have shown great potential. However, different from proteins, the sequences corresponding to a single RNA three-dimensional structure are more abundant. Most of the existing RNA design methods merely take into account the secondary structure of RNA, or are only capable of generating a limited number of candidate sequences. To address these limitations, we propose a geometric-algebra-enhanced $\textbf{B}$ayesian $\textbf{F}$low $\textbf{N}$etwork for the inverse design of $\textbf{R}$NA, called $\textbf{RBFN}$. RBFN uses a Bayesian Flow Network to model the distribution of nucleotide sequences in RNA, enabling the generation of more reasonable RNA sequences. Meanwhile, considering the more flexible characteristics of RNA conformations, we utilize geometric algebra to enhance the modeling ability of the RNA three-dimensional structure, facilitating a better understanding of RNA structural properties. In addition, due to the scarcity of RNA structures and the limitation that there are only four types of nucleic acids, we propose a new time-step distribution sampling to address the scarcity of RNA structure data and the relatively small number of nucleic acid types. Evaluation on the single-state fixed-backbone re-design benchmark and multi-state fixed-backbone benchmark indicates that RBFN can outperform existing RNA design methods in various RNA design tasks, enabling effective RNA sequence design.

Probabilistic Methods · Bayesian Models and Methods

Tianyu Chen, Vansh Bansal, James Scott

We consider the problem of validating whether a neural posterior estimate $q(\theta \mid x)$ is an accurate approximation to the true, unknown true posterior $p(\theta \mid x)$. Existing methods for evaluating the quality of an NPE estimate are largely derived from classifier-based tests or divergence measures, but these suffer from several practical drawbacks. As an alternative, we introduce the *Conditional Localization Test* (**CoLT**), a principled method designed to detect discrepancies between $p(\theta \mid x)$ and $q(\theta \mid x)$ across the full range of conditioning inputs. Rather than relying on exhaustive comparisons or density estimation at every $x$, CoLT learns a localization function that adaptively selects points $\theta_l(x)$ where the neural posterior $q$ deviates most strongly from the true posterior $p$ for that $x$. This approach is particularly advantageous in typical simulation-based inference settings, where only a single draw $\theta \sim p(\theta \mid x)$ from the true posterior is observed for each conditioning input, but where the neural posterior $q(\theta \mid x)$ can be sampled an arbitrary number of times. Our theoretical results establish necessary and sufficient conditions for assessing distributional equality across all $x$, offering both rigorous guarantees and practical scalability. Empirically, we demonstrate that CoLT not only performs better than existing methods at comparing $p$ and $q$, but also pinpoints regions of significant divergence, providing actionable insights for model refinement. These properties position CoLT as a state-of-the-art solution for validating neural posterior estimates.

Probabilistic Methods · Bayesian Models and Methods

Hongshuo Yang, Elias Bareinboim

Graphical models have been widely used as parsimonious encoders of assumptions of the underlying causal system and provide a basis for causal inferences. Models encoding stronger constraints tend to require higher expressive power, which are also harder, and sometimes impossible to empirically falsify. In this paper, we introduce two new collections of distributions that include counterfactual quan- tities which are experimentally accessible under counterfactual randomizations. Correspondingly, we define two new classes of graphical models for encoding empirically testable constraints in these distributions. We further present a sound and complete calculus, based on counterfactual calculus, which licenses inferences in these two new models with rules that are within the empirically falsifiable bound- ary. Finally, we formulate a hierarchy over several graphical models based on the constraints they encode and study the fundamental trade-off between the expressive power and empirical falsifiability of different models across the hierarchy.

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.