Bayesian inference provides a natural way of incorporating prior beliefs and assigning a probability measure to the space of hypotheses. Current solutions rely on iterative routines like Markov Chain Monte Carlo (MCMC) sampling and Variational Inference (VI), which need to be re-run whenever new observations are available. Amortization, through conditional estimation, is a viable strategy to alleviate such difficulties and has been the guiding principle behind simulation-based inference, neural processes and in-context methods using pre-trained models. In this work, we conduct a thorough comparative analysis of amortized in-context Bayesian posterior estimation methods from the lens of different optimization objectives and architectural choices. Such methods train an amortized estimator to perform posterior parameter inference by conditioning on a set of data examples passed as context to a sequence model such as a transformer. In contrast to language models, we leverage permutation invariant architectures as the true posterior is invariant to the ordering of context examples. Our empirical study includes generalization to out-of-distribution tasks, cases where the assumed underlying model is misspecified, and transfer from simulated to real problems. Subsequently, it highlights the superiority of the reverse KL estimator for predictive problems, especially when combined with the transformer architecture and normalizing flows.

Despite recent advances, sampling-based inference for Bayesian Neural Networks (BNNs) remains a significant challenge in probabilistic deep learning. While sampling-based approaches do not require a variational distribution assumption, current state-of-the-art samplers still struggle to navigate the complex and highly multimodal posteriors of BNNs. As a consequence, sampling still requires considerably longer inference times than non-Bayesian methods even for small neural networks, despite recent advances in making software implementations more efficient. Besides the difficulty of finding high-probability regions, the time until samplers provide sufficient exploration of these areas remains unpredictable. To tackle these challenges, we introduce an ensembling approach that leverages strategies from optimization and a recently proposed sampler called Microcanonical Langevin Monte Carlo (MCLMC) for efficient, robust and predictable sampling performance. Compared to approaches based on the state-of-the-art No-U-Turn Sampler, our approach delivers substantial speedups up to an order of magnitude, while maintaining or improving predictive performance and uncertainty quantification across diverse tasks and data modalities. The suggested Microcanonical Langevin Ensembles and modifications to MCLMC additionally enhance the method's predictability in resource requirements, facilitating easier parallelization. All in all, the proposed method offers a promising direction for practical, scalable inference for BNNs.

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language Models (LLMs) have demonstrated remarkable potential in predicting protein structures and interactions via automated mining of vast biomedical literature; yet their inherent uncertainty remains a key challenge for deriving reproducible findings, critical for biomedical applications. In this study, we present an uncertainty-aware adaptation of LLMs for PPI analysis, leveraging fine-tuned LLaMA-3 and BioMedGPT models. To enhance prediction reliability, we integrate LoRA ensembles and Bayesian LoRA models for uncertainty quantification (UQ), ensuring confidence-calibrated insights into protein behavior. Our approach achieves competitive performance in PPI identification across diverse disease contexts while addressing model uncertainty, thereby enhancing trustworthiness and reproducibility in computational biology. These findings underscore the potential of uncertainty-aware LLM adaptation for advancing precision medicine and biomedical research.

Credible forecasting and representation learning of dynamical systems are of ever-increasing importance for reliable decision-making. To that end, we propose a family of Gaussian processes (GP) for dynamical systems with linear time-invariant responses, which are nonlinear only in initial conditions. This linearity allows us to tractably quantify forecasting and representational uncertainty, simultaneously alleviating the challenge of computing the distribution of trajectories from a GP-based dynamical system and enabling a new probabilistic treatment of learning Koopman operator representations. Using a trajectory-based equivariance -- which we refer to as \textit{Koopman equivariance} -- we obtain a GP model with enhanced generalization capabilities. To allow for large-scale regression, we equip our framework with variational inference based on suitable inducing points. Experiments demonstrate on-par and often better forecasting performance compared to kernel-based methods for learning dynamical systems.

Conformal prediction methods create prediction bands with distribution-free guarantees but do not explicitly capture epistemic uncertainty, which can lead to overconfident predictions in data-sparse regions. Although recent conformal scores have been developed to address this limitation, they are typically designed for specific tasks, such as regression or quantile regression. Moreover, they rely on particular modeling choices for epistemic uncertainty, restricting their applicability. We introduce $\texttt{EPICSCORE}$, a model-agnostic approach that enhances any conformal score by explicitly integrating epistemic uncertainty. Leveraging Bayesian techniques such as Gaussian Processes, Monte Carlo Dropout, or Bayesian Additive Regression Trees, $\texttt{EPICSCORE}$ adaptively expands predictive intervals in regions with limited data while maintaining compact intervals where data is abundant. As with any conformal method, it preserves finite-sample marginal coverage. Additionally, it also achieves asymptotic conditional coverage. Experiments demonstrate its good performance compared to existing methods. Designed for compatibility with any Bayesian model, but equipped with distribution-free guarantees, $\texttt{EPICSCORE}$ provides a general-purpose framework for uncertainty quantification in prediction problems.

In decentralized multi-agent deep reinforcement learning (MADRL), communication can help agents to gain a better understanding of the environment to better coordinate their behaviors. Nevertheless, communication may involve uncertainty, which potentially introduces variance to the learning of decentralized agents. In this paper, we focus on a specific decentralized MADRL setting with communication and conduct a theoretical analysis to study the variance that is caused by communication in policy gradients. We propose modular techniques to reduce the variance in policy gradients during training. We adopt our modular techniques into two existing algorithms for decentralized MADRL with communication and evaluate them on multiple tasks in the StarCraft Multi-Agent Challenge and Traffic Junction domains. The results show that decentralized MADRL communication methods extended with our proposed techniques not only achieve high-performing agents but also reduce variance in policy gradients during training.

In average reward Markov decision processes, state-of-the-art algorithms for regret minimization follow a well-established framework: They are model-based, optimistic and episodic. First, they maintain a confidence region from which optimistic policies are computed using a well-known subroutine called Extended Value Iteration (EVI). Second, these policies are used over time windows called episodes, each ended by the Doubling Trick (DT) rule or a variant thereof. In this work, without modifying EVI, we show that there is a significant advantage in replacing (DT) by another simple rule, that we call the Vanishing Multiplicative (VM) rule. When managing episodes with (VM), the algorithm's regret is, both in theory and in practice, as good if not better than with (DT), while the one-shot behavior is greatly improved. More specifically, the management of bad episodes (when sub-optimal policies are being used) is much better under (VM) than (DT) by making the regret of exploration logarithmic rather than linear. These results are made possible by a new in-depth understanding of the contrasting behaviors of confidence regions during good and bad episodes.

This paper addresses the problem of mixed-membership estimation in networks, where the goal is to efficiently estimate the latent mixed-membership structure from the observed network. Recognizing the widespread availability and valuable information carried by node covariates, we propose a novel network model that incorporates both community information, as represented by the Degree-Corrected Mixed Membership (DCMM) model, and node covariate similarities to determine connections. We investigate the regularized maximum likelihood estimation (MLE) for this model and demonstrate that our approach achieves optimal estimation accuracy for both the similarity matrix and the mixed-membership, in terms of both the Frobenius norm and the entrywise loss. Since directly analyzing the original convex optimization problem is intractable, we employ nonconvex optimization to facilitate the analysis. A key contribution of our work is identifying a crucial assumption that bridges the gap between convex and nonconvex solutions, enabling the transfer of statistical guarantees from the nonconvex approach to its convex counterpart. Importantly, our analysis extends beyond the MLE loss and the mean squared error (MSE) used in matrix completion problems, generalizing to all the convex loss functions. Consequently, our analysis techniques extend to a broader set of applications, including ranking problems based on pairwise comparisons. Finally, simulation experiments validate our theoretical findings, and real-world data analyses confirm the practical relevance of our model.

The particle filter (PF) and the ensemble Kalman filter (EnKF) are widely used for approximate inference in state-space models. From a Bayesian perspective, these algorithms represent the prior by an ensemble of particles and update it to the posterior with new observations over time. However, the PF often suffers from weight degeneracy in high-dimensional settings, whereas the EnKF relies on linear Gaussian assumptions that can introduce significant approximation errors. In this paper, we propose the Adversarial Transform Particle Filter (ATPF), a novel filtering framework that combines the strengths of the PF and the EnKF through adversarial learning. Specifically, importance sampling is used to ensure statistical consistency as in the PF, while adversarially learned transformations, such as neural networks, allow accurate posterior matching for nonlinear and non-Gaussian systems. In addition, we incorporate kernel methods to ease optimization and leverage regularization techniques based on optimal transport for better statistical properties and numerical stability. We provide theoretical guarantees, including generalization bounds for both the analysis and forecast steps of ATPF. Extensive experiments across various nonlinear and non-Gaussian scenarios demonstrate the effectiveness and practical advantages of our method.

Accurate prediction with multimodal data-encompassing tabular, textual, and visual inputs or outputs-is fundamental to advancing analytics in diverse application domains. Traditional approaches often struggle to integrate heterogeneous data types while maintaining high predictive accuracy. We introduce Generative Distribution Prediction (GDP), a novel framework that leverages multimodal synthetic data generation-such as conditional diffusion models-to enhance predictive performance across structured and unstructured modalities. GDP is model-agnostic, compatible with any high-fidelity generative model, and supports transfer learning for domain adaptation. We establish a rigorous theoretical foundation for GDP, providing statistical guarantees on its predictive accuracy when using diffusion models as the generative backbone. By estimating the data-generating distribution and adapting to various loss functions for risk minimization, GDP enables accurate point predictions across multimodal settings. We empirically validate GDP on four supervised learning tasks-tabular data prediction, question answering, image captioning, and adaptive quantile regression-demonstrating its versatility and effectiveness across diverse domains.