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.

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.

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.

Even though heterogeneous databases can be found in a broad variety of applications, there exists a lack of tools for estimating missing data in such databases. In this paper, we provide an efficient and robust table completion tool, based on a Bayesian nonparametric latent feature model. In particular, we propose a general observation model for the Indian buffet process (IBP) adapted to mixed continuous (real-valued and positive real-valued) and discrete (categorical, ordinal and count) observations. Then, we propose an inference algorithm that scales linearly with the number of observations. Finally, our experiments over five real databases show that the proposed approach provides more robust and accurate estimates than the standard IBP and the Bayesian probabilistic matrix factorization with Gaussian observations.

Implementing inference procedures for each new probabilistic model is timeconsuming and error-prone. Probabilistic programming addresses this problem by allowing a user to specify the model and then automatically generating the inference procedure. To make this practical it is important to generate high performance inference code. In turn, on modern architectures, high performance requires parallel execution. In this paper we present Augur, a probabilistic modeling language and compiler for Bayesian networks designed to make effective use of data-parallel architectures such as GPUs. We show that the compiler can generate data-parallel inference code scalable to thousands of GPU cores by making use of the conditional independence relationships in the Bayesian network.

We revisit from a statistical learning perspective the classical decision-theoretic problem of weighted expert voting. In particular, we examine the consistency (both asymptotic and finitary) of the optimal Nitzan-Paroush weighted majority and related rules. In the case of known expert competence levels, we give sharp error estimates for the optimal rule. When the competence levels are unknown, they must be empirically estimated. We provide frequentist and Bayesian analyses for this situation. Some of our proof techniques are non-standard and may be of independent interest. The bounds we derive are nearly optimal, and several challenging open problems are posed.

We propose a semi-parametric and dynamic rank factor model for topic modeling, capable of (i) discovering topic prevalence over time, and (ii) learning contemporary multi-scale dependence structures, providing topic and word correlations as a byproduct. The high-dimensional and time-evolving ordinal/rank observations (such as word counts), after an arbitrary monotone transformation, are well accommodated through an underlying dynamic sparse factor model. The framework naturally admits heavy-tailed innovations, capable of inferring abrupt temporal jumps in the importance of topics. Posterior inference is performed through straightforward Gibbs sampling, based on the forward-filtering backwardsampling algorithm. Moreover, an efficient data subsampling scheme is leveraged to speed up inference on massive datasets. The modeling framework is illustrated on two real datasets: the US State of the Union Address and the JSTOR collection from Science.

Attention has long been proposed by psychologists to be important for efficiently dealing with the massive amounts of sensory stimulus in the neocortex. Inspired by the attention models in visual neuroscience and the need for object-centered data for generative models, we propose a deep-learning based generative framework using attention. The attentional mechanism propagates signals from the region of interest in a scene to an aligned canonical representation for generative modeling. By ignoring scene background clutter, the generative model can concentrate its resources on the object of interest. A convolutional neural net is employed to provide good initializations during posterior inference which uses Hamiltonian Monte Carlo. Upon learning images of faces, our model can robustly attend to the face region of novel test subjects. More importantly, our model can learn generative models of new faces from a novel dataset of large images where the face locations are not known.