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.

Recently, Cella and Martin proved how, under an assumption called consonance, a credal set (i.e. a closed and convex set of probabilities) can be derived from the conformal transducer associated with transductive conformal prediction. We show that the Imprecise Highest Density Region (IHDR) associated with such a credal set corresponds to the classical Conformal Prediction Region. In proving this result, we relate the set of probability density/mass functions (pdf/pmf's) associated with the elements of the credal set to the imprecise probabilistic concept of a cloud. As a result, we establish new relationships between Conformal Prediction and Imprecise Probability (IP) theories. A byproduct of our presentation is the discovery that consonant plausibility functions are monoid homomorphisms, a new algebraic property of an IP tool.

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.

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.

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.

We propose Joint Moment Estimation (JME), a method for continually and privately estimating both the first and second moments of data with reduced noise compared to naive approaches. JME uses the matrix mechanism and a joint sensitivity analysis to allow the second moment estimation with no additional privacy cost, thereby improving accuracy while maintaining privacy. We demonstrate JME's effectiveness in two applications: estimating the running mean and covariance matrix for Gaussian density estimation, and model training with DP-Adam on CIFAR-10.

Previous methods for posterior sampling A recent line of research has exploited pre-trained generative with diffusion priors, while providing impressive diffusion models as priors for solving Bayesian results on tasks like image reconstruction (Kawar et al., inverse problems. We contribute to this research direction 2022; Chung et al., 2023; Song et al., 2023), often rely by designing a sequential Monte Carlo method on approximations and fail or perform poorly on simple for linear-Gaussian inverse problems which builds on tasks (Cardoso et al., 2024, and our Section 5.1), "decoupled diffusion", where the generative process is making it uncertain to what extent they can solve designed such that larger updates to the sample are Bayesian inference problems in general.

The central challenge in probabilistic inference is numerical integration, to average over ensembles of models or unknown (hyper-)parameters (for example to compute the marginal likelihood or a partition function).