Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring heuristic MSA subsampling approaches for generating alternative states. In parallel, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for imaging near-native structural heterogeneity, but is challenged by arduous pipelines to transform raw experimental data into atomic models. Here, we bridge the gap between these modalities, combining cryo-EM density maps with the rich sequence and biophysical priors learned by protein structure prediction models. Our method, CryoBoltz, guides the sampling trajectory of a pretrained biomolecular structure prediction model using both global and local structural constraints derived from density maps, driving predictions towards conformational states consistent with the experimental data. We demonstrate that this flexible yet powerful inferencetime approach allows us to build atomic models into heterogeneous cryo-EM maps across a variety of dynamic biomolecular systems including transporters and antibodies.

Large language models (LLMs) are now pivotal in real-world applications. Model editing has emerged as a promising paradigm for efficiently modifying LLMs without full retraining. However, current editing approaches face significant limitations due to parameter drift, which stems from inconsistencies between newly edited knowledge and the model's existing knowledge. In sequential editing scenarios, cumulative drifts progressively lead to model collapse characterized by general capability degradation and balance between acquiring new knowledge and catastrophic forgetting of existing knowledge. Drawing inspiration from the hippocampal trisynaptic circuit for continual memorizing and forgetting, we propose a Hippocampal-like Sequential Editing (HSE) framework that designs the unlearning of obsolete knowledge, domain-specific knowledge update separation and replay for edited knowledge. Specifically, the HSE framework designs three core mechanisms: (1) Machine unlearning selectively erases outdated knowledge to facilitate integration of new information, (2) Fisher information matrix-guided parameter updates prevents cross-domain knowledge interference, and (3) Parameter replay consolidates long-term editing memory through lightweight and global replay of editing data in a parametric form. Theoretical analysis demonstrates that HSE achieves smaller generalization error bounds, more stable convergence and higher computational efficiency.

This paper introduces the Quotient Bayesian Learning Rule, an extension of natural-gradient Bayesian updates to probability models that fall outside the exponential family. Building on the observation that many heavy-tailed and otherwise non-exponential distributions arise as marginals of minimal exponential families, we prove that such marginals inherit a unique Fisher-Rao information geometry via the quotient-manifold construction. Exploiting this geometry, we derive the Quotient Natural Gradient algorithm, which takes steepest-descent steps in the well-structured covering space, thereby guaranteeing parameterization-invariant optimization in the target space. Empirical results on the Student-t distribution confirm that our method converges more rapidly and attains higher-quality solutions than previous variants of the Bayesian Learning Rule.

Understanding causal relationships in multivariate time series is crucial in many scenarios, such as those dealing with financial or neurological data.

The distribution of data changes over time; models operating in dynamic environments need retraining. But knowing when to retrain, without access to labels, is an open challenge since some, but not all shifts degrade model performance. This paper formalizes and addresses the problem of post-deployment deterioration (PDD) monitoring. We propose D3M, a practical and efficient monitoring algorithm based on the disagreement of predictive models, achieving low false positive rates under non-deteriorating shifts and provides sample complexity bounds for high true positive rates under deteriorating shifts. Empirical results on both standard benchmark and a real-world large-scale internal medicine dataset demonstrate the effectiveness of the framework and highlight its viability as an alert mechanism for high-stakes machine learning pipelines.

While RLHF has demonstrated promising results, many algorithms are highly sensitive to misspecifications in the underlying preference model (e.g., the Bradley-Terry model), the reference policy, or the reward function, resulting in undesirable fine-tuning. To address model misspecification, we propose a doubly robust preference optimization algorithm that remains consistent when either the preference model or the reference policy is correctly specified (without requiring both). Our proposal demonstrates superior and more robust performance than state-of-the-art algorithms, both in theory and in practice.

The softmax-contaminated mixture of experts (MoE) model is deployed when a large-scale pre-trained model, which plays the role of a fixed expert, is fine-tuned for learning downstream tasks by including a new contamination part, or prompt, functioning as a new, trainable expert. Despite its popularity and relevance, the theoretical properties of the softmax-contaminated MoE have remained unexplored in the literature. In the paper, we study the convergence rates of the maximum likelihood estimator of gating and prompt parameters in order to gain insights into the statistical properties and potential challenges of fine-tuning with a new prompt. We find that the estimability of these parameters is compromised when the prompt acquires overlapping knowledge with the pre-trained model, in the sense that we make precise by formulating a novel analytic notion of distinguishability. Under distinguishability of the pre-trained and prompt models, we derive minimax optimal estimation rates for all the gating and prompt parameters. By contrast, when the distinguishability condition is violated, these estimation rates become significantly slower due to their dependence on the prompt convergence rate to the pre-trained model. Finally, we empirically corroborate our theoretical findings through several numerical experiments.

The prediction of learning curves for Natural Language Processing (NLP) models enables informed decision-making to meet specific performance objectives, while reducing computational overhead and lowering the costs associated with dataset acquisition and curation. In this work, we formulate the prediction task as a multitask learning problem, where each task's data is modelled as being organized within a two-layer hierarchy. To model the shared information and dependencies across tasks and hierarchical levels, we employ latent variable multi-output Gaussian Processes, enabling to account for task correlations and supporting zero-shot prediction of learning curves (LCs). We demonstrate that this approach facilitates the development of probabilistic scaling laws at lower costs. Applying an active learning strategy, LCs can be queried to reduce predictive uncertainty and provide predictions close to ground truth scaling laws.

Variational mean field approximations tend to struggle with contemporary overparametrized deep neural networks. Where a Bayesian treatment is usually associated with high-quality predictions and uncertainties, the practical reality has been the opposite, with unstable training, poor predictive power, and subpar calibration. Building upon recent work on reparametrizations of neural networks, we propose a simple variational family that considers two independent linear subspaces of the parameter space. These represent functional changes inside and outside the support of training data. This allows us to build a fully-correlated approximate posterior reflecting the overparametrization that tunes easy-to-interpret hyperparameters. We develop scalable numerical routines that maximize the associated evidence lower bound (ELBO) and sample from the approximate posterior. Empirically, we observe state-of-the-art performance across tasks, models, and datasets compared to a wide array of baseline methods. Our results show that approximate Bayesian inference applied to deep neural networks is far from a lost cause when constructing inference mechanisms that reflect the geometry of reparametrizations.

Recent advances in large language models (LLMs) have enabled automated dataset labeling with minimal human supervision. While majority voting across multiple LLMs can improve label reliability by mitigating individual model biases, it incurs high computational costs due to repeated querying. In this work, we propose a novel online framework, Cost-aware Majority Voting (CaMVo), for efficient and accurate LLM-based dataset annotation. CaMVo adaptively selects a subset of LLMs for each data instance based on contextual embeddings, balancing confidence and cost without requiring pre-training or ground-truth labels. Leveraging a LinUCB-based selection mechanism and a Bayesian estimator over confidence scores, CaMVo estimates a lower bound on labeling accuracy for each LLM and aggregates responses through weighted majority voting. Our empirical evaluation on the MMLU and IMDBMovie Review datasets demonstrates that CaMVo achieves comparable or superior accuracy to full majority voting while significantly reducing labeling costs. This establishes CaMVo as a practical and robust solution for cost-efficient annotation in dynamic labeling environments.