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Zero-shot protein stability prediction by inverse folding models: a free energy interpretation

Neural Information Processing Systems

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying thermodynamic stability remains incompletely understood. A better understanding would be of interest not only from a theoretical perspective, but also potentially provide the basis for stronger zero-shot stability prediction. In this paper, we take steps to clarify the free-energy foundations of inverse folding models. Our derivation reveals the standard practice of likelihood ratios as a simplistic approximation and suggests several paths towards better estimates of the relative stability. We empirically assess these approaches and demonstrate that considerable gains in zero-shot performance can be achieved with fairly simple means.


Fast Zeroth-Order Convex Optimization with Quantum Gradient Methods

Neural Information Processing Systems

We study quantum algorithms based on quantum (sub)gradient estimation using noisy function evaluation oracles, and demonstrate the first dimension-independent query complexities (up to poly-logarithmic factors) for zeroth-order convex optimization in both smooth and nonsmooth settings. Interestingly, only using noisy function evaluation oracles, we match the first-order query complexities of classical gradient descent, thereby exhibiting exponential separation between quantum and classical zeroth-order optimization. We then generalize these algorithms to work in non-Euclidean settings by using quantum (sub)gradient estimation to instantiate mirror descent and its variants, including dual averaging and mirror prox. By leveraging a connection between semidefinite programming and eigenvalue optimization, we use our quantum mirror descent method to give a new quantum algorithm for solving semidefinite programs, linear programs, and zero-sum games. We identify a parameter regime in which our zero-sum games algorithm is faster than any existing classical or quantum approach.


Thompson Sampling for Multi-Objective Linear Contextual Bandit

Neural Information Processing Systems

We study the multi-objective linear contextual bandit problem, where multiple possible conflicting objectives must be optimized simultaneously. We propose MOL-TS, the first Thompson Sampling algorithm with Pareto regret guarantees for this problem. Unlike standard approaches that compute an empirical Pareto front each round, MOL-TS samples parameters across objectives and efficiently selects an arm from a novel effective Pareto front, which accounts for repeated selections over time. Our analysis shows that MOL-TSachieves a worst-case Pareto regret bound of eO(d3/2 T), where dis the dimension of the feature vectors, T is the total number of rounds, matching the best known order for randomized linear bandit algorithms for single objective. Empirical results confirm the benefits of our proposed approach, demonstrating improved regret minimization and strong multi-objective performance.


C3PO: Optimized Large Language Model Cascades with Probabilistic Cost Constraints for Reasoning

Neural Information Processing Systems

Large language models (LLMs) have achieved impressive results on complex reasoning tasks, but their high inference cost remains a major barrier to real-world deployment. A promising solution is to use cascaded inference, where small, cheap models handle easy queries, and only the hardest examples are escalated to more powerful models. However, existing cascade methods typically rely on supervised training with labeled data, offer no theoretical generalization guarantees, and provide limited control over test-time computational cost. We introduce C3PO (Cost Controlled Cascaded Prediction Optimization), a self-supervised framework for optimizing LLM cascades under probabilistic cost constraints. By focusing on minimizing regret with respect to the most powerful model (MPM), C3PO avoids the need for labeled data by constructing a cascade using only unlabeled model outputs. It leverages conformal prediction to bound the probability that inference cost exceeds a user-specified budget. We provide theoretical guarantees on both cost control and generalization error, and show that our optimization procedure is effective even with small calibration sets. Empirically, C3PO achieves stateof-the-art performance across a diverse set of reasoning benchmarks including GSM8K, MATH-500, BigBench-Hard and AIME, outperforming strong LLM cascading baselines in both accuracy and cost-efficiency. Our results demonstrate that principled, label-free cascade optimization can enable scalable LLM deployment.


GMM-based VAE model with Normalizing Flow for effective stochastic segmentation

Neural Information Processing Systems

While deep neural networks possess the capability to perform semantic segmentation, producing a single deterministic output limits reliability in safety-critical applications caused by uncertainty and annotation variability. To address this, stochastic segmentation models using Conditional Variational Autoencoders (CVAE), Bayesian networks, and diffusion have been explored. However, existing approaches suffer from limited latent expressiveness and interpretability. Furthermore, our experiments showed that models like Probabilistic U-Net rely excessively on high latent variance, leading to posterior collapse. This work propose a novel framework by integrating Gaussian Mixture Model (GMM) with Normalizing Flow (NF) in CVAE for stochastic segmentation. GMM structures the latent space into meaningful semantic clusters, while NF captures feature deformations with quantified uncertainty. Our method stabilizes latent distributions through constrained variance and mean ranges. Experiments on LIDC, Crack500, and Cityscapes datasets show that our approach outperformed state-of-the-art in curvilinear structure and medical image segmentation.


Improving Generative Behavior Cloning via Self-Guidance and Adaptive Chunking

Neural Information Processing Systems

Generative Behavior Cloning (GBC) is a simple yet effective framework for robot learning, particularly in multi-task settings. Recent GBC methods often employ diffusion policies with open-loop (OL) control, where actions are generated via a diffusion process and executed in multi-step chunks without replanning. While this approach has demonstrated strong success rates and generalization, its inherent stochasticity can result in erroneous action sampling, occasionally leading to unexpected task failures. Moreover, OL control suffers from delayed responses, which can degrade performance in noisy or dynamic environments. To address these limitations, we propose two novel techniques to enhance the consistency and reactivity of diffusion policies: (1) self-guidance, which improves action fidelity by leveraging past observations and implicitly promoting future-aware behavior; and (2) adaptive chunking, which selectively updates action sequences when the benefits of reactivity outweigh the need for temporal consistency. Extensive experiments show that our approach substantially improves GBC performance across a wide range of simulated and real-world robotic manipulation tasks. Our code is available at https://github.com/junhyukso/SGAC.


Generalizing while preserving monotonicity in comparison-based preference learning models

Neural Information Processing Systems

If you tell a learning model that you prefer an alternative a over another alternative b, then you probably expect the model to be monotone, that is, the valuation of a increases, and that of bdecreases. Yet, perhaps surprisingly, many widely deployed comparison-based preference learning models, including large language models, fail to have this guarantee. Until now, the only comparison-based preference learning algorithms that were proved to be monotone are the Generalized BradleyTerry models [10]. Yet, these models are unable to generalize to uncompared data. In this paper, we advance the understanding of the set of models with generalization ability that are monotone. Namely, we propose a new class of Linear Generalized Bradley-Terry models with Diffusion Priors, and identify sufficient conditions on alternatives' embeddings that guarantee monotonicity. Our experiments show that this monotonicity is far from being a general guarantee, and that our new class of generalizing models improves accuracy, especially when the dataset is limited.


Routing Mamba: Scaling State Space Models with Mixture-of-Experts Projection

Neural Information Processing Systems

Recent advances, such as Mamba, further enhance SSMs with inputdependent gating and hardware-aware implementations, positioning them as strong alternatives to Transformers for long sequence modeling. However, efficiently scaling the expressive power of SSMs, particularly with Mixture of Experts (MoE), remains challenging, as naive integration attempts often falter or degrade performance. In this work, we introduce Routing Mamba (RoM), a novel approach that scales SSM parameters using sparse mixtures of linear projection experts.


STEER-ME: Assessing the Microeconomic Reasoning of Large Language Models

Neural Information Processing Systems

Large language models (LLMs) are increasingly being asked to make economically rational decisions and indeed are already being applied to economic tasks like stock picking and financial analysis. Existing LLM benchmarks tend to focus on specific applications, making them insufficient for characterizing economic reasoning more broadly. In previous work, we offered a blueprint for comprehensively benchmarking strategic decision-making Raman et al. [2024]. However, this work did not engage with the even larger microeconomic literature on non-strategic settings. We address this gap here, taxonomizing microeconomic reasoning into 58distinct elements, each grounded in up to 10distinct domains, 5perspectives, and 3types. The generation of benchmark data across this combinatorial space is powered by a novel LLM-assisted data generation protocol that we dub auto-STEER, which generates a set of questions by adapting handwritten templates to target new domains and perspectives. By generating fresh questions for each element, auto-STEER induces diversity which could help to reduce the risk of data contamination. We use this benchmark to evaluate 27LLMs spanning a range of scales and adaptation strategies, comparing performance across multiple formats--multiple-choice and free-text question answering--and scoring schemes. Our results surface systematic limitations in current LLMs' ability to generalize economic reasoning across types, formats, and textual perturbations, and establish a foundation for evaluating and improving economic competence in foundation models.