NeurIPS 2025 Papers

When agents trade in a Duality-based Cost Function prediction market, they collectively implement the learning algorithm Follow-The-Regularized-Leader [Abernethy et al., 2013]. We ask whether other learning algorithms could be used to inspire the design of prediction markets. By decomposing and modifying the Duality-based Cost Function Market Maker's (DCFMM) pricing mechanism, we propose a new prediction market, called the Smooth Quadratic Prediction Market, the incentivizes agents to collectively implement general steepest gradient descent. Relative to the DCFMM, the Smooth Quadratic Prediction Market has a better worst-case monetary loss for AD securities while preserving axiom guarantees such as the existence of instantaneous price, information incorporation, expressiveness, no arbitrage, and a form of incentive compatibility. To motivate the application of the Smooth Quadratic Prediction Market, we independently examine agents' trading behavior under two realistic constraints: bounded budgets and buy-only securities. Finally, we provide an introductory analysis of an approach to facilitate adaptive liquidity using the Smooth Quadratic Prediction Market. Our results suggest future designs where the price update rule is separate from the fee structure, yet guarantees are preserved.

Graph Transformers (GTs) have emerged as a powerful paradigm for graph representation learning due to their ability to model diverse node interactions. However, existing GTs often rely on intricate architectural designs tailored to specific interactions, limiting their flexibly. To address this, we propose a unified hierarchical mask framework that reveals an underlying equivalence between model architecture and attention mask construction. This framework enables a consistent modeling paradigm by capturing diverse interactions through carefully designed attention masks. Theoretical analysis under this framework demonstrates that the probability of correct classification positively correlates with the receptive field size and label consistency, leading to a fundamental design principle: An effective attention mask should ensure both a sufficiently large receptive field and a high level of label consistency. While no single existing mask satisfies this principle across all scenarios, our analysis reveals that hierarchical masks offer complementary strengths—motivating their effective integration. Then, we introduce M$^3$Dphormer, a Mixture-of-Experts based Graph Transformer with Multi-Level Masking and Dual Attention Computation. M$^3$Dphormer incorporates three theoretically grounded hierarchical masks and employs a bi-level expert routing mechanism to adaptively integrate multi-level interaction information. To ensure scalability, we further introduce a dual attention computation scheme that dynamically switches between dense and sparse modes based on local mask sparsity. Extensive experiments across multiple benchmarks demonstrate that M$^3$Dphormer achieves state-of-the-art performance, validating the effectiveness of our unified framework and model design.

Many critical applications, from autonomous scientific discovery to personalized medicine, demand systems that can both strategically acquire the most informative data and instantaneously perform inference based upon it. While amortized methods for Bayesian inference and experimental design offer part of the solution, neither approach is optimal in the most general and challenging task, where new data needs to be collected for instant inference. To tackle this issue, we introduce the Amortized Active Learning and Inference Engine (ALINE), a unified framework for amortized Bayesian inference and active data acquisition. ALINE leverages a transformer architecture trained via reinforcement learning with a reward based on self-estimated information gain provided by its own integrated inference component. This allows it to strategically query informative data points while simultaneously refining its predictions. Moreover, ALINE can selectively direct its querying strategy towards specific subsets of model parameters or designated predictive tasks, optimizing for posterior estimation, data prediction, or a mixture thereof. Empirical results on regression-based active learning, classical Bayesian experimental design benchmarks, and a psychometric model with selectively targeted parameters demonstrate that ALINE delivers both instant and accurate inference along with efficient selection of informative points.

Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing RNA’s conformational flexibility, ensuring structural validity, and overcoming data scarcity. To address these challenges, we introduce RiboFlow, a synergistic flow matching model to co-design RNA structures and sequences based on target molecules. By integrating RNA backbone frames, torsion angles, and sequence features in an unified architecture, RiboFlow explicitly models RNA’s dynamic conformations while enforcing sequence-structure consistency to improve validity. Additionally, we curate RiboBind, a large-scale dataset of RNA-molecule interactions, to resolve the scarcity of high-quality structural data. Extensive experiments reveal that RiboFlow not only outperforms state-of-the-art RNA design methods by a large margin but also showcases controllable capabilities for achieving high binding affinity to target ligands. Our work bridges critical gaps in controllable RNA design, offering a framework for structure-aware, data-efficient generation.

Classifier-free guidance (CFG) is a core technique powering state-of-the-art image generation systems, yet its underlying mechanisms remain poorly understood. In this work, we first analyze CFG in a simplified linear diffusion model, where we show its behavior closely resembles that observed in the nonlinear case. Our analysis reveals that linear CFG improves generation quality via three distinct components: (i) a mean-shift term that approximately steers samples in the direction of class means, (ii) a positive Contrastive Principal Components (CPC) term that amplifies class-specific features, and (iii) a negative CPC term that suppresses generic features prevalent in unconditional data. We then verify that these insights in real-world, nonlinear diffusion models: over a broad range of noise levels, linear CFG resembles the behavior of its nonlinear counterpart. Although the two eventually diverge at low noise levels, we discuss how the insights from the linear analysis still shed light on the CFG's mechanism within the nonlinear regime.

Kolmogorov-Arnold Networks (KANs) have demonstrated remarkable expressive capacity and predictive power in symbolic learning. However, existing generalization errors of KANs primarily focus on approximation errors while neglecting estimation errors, leading to a suboptimal bias-variance trade-off and poor generalization performance. Meanwhile, the unclear generalization mechanism hinders the design of more effective KANs variants. As the authors of KANs highlighted, they ``would like to explore ways to restrict KANs' hypothesis space so that they can achieve good performance''. To address these challenges, we explore the generalization mechanism of KANs and design more effective KANs with lower model complexity and better generalization. We define \textit{Lipschitz complexity} as the first structural measure for deep functions represented by KANs and derive novel generalization bounds based on \textit{Lipschitz complexity}, establishing a theoretical foundation for understanding their generalization behavior. To reduce \textit{Lipschitz complexity} and boost the generalization mechanism of KANs, we propose Lipschitz-Enhanced KANs ($\textbf{LipKANs}$) by integrating the Lip layer and pioneering the $L_{1.5}$-regularized loss, contributing to tighter generalization bounds. Empirical experiments validate that the proposed LipKANs enhance the generalization mechanism of KANs when modeling complex distributions. We hope our theoretical bounds and LipKANs lay a foundation for the future development of KANs.

Sampling multiple outputs from a Large Language Model (LLM) and selecting the most frequent (Self-consistency) or highest-scoring (Best-of-N) candidate is a popular approach to achieve higher accuracy in tasks with discrete final answers. Best-of-N (BoN) selects the output with the highest reward, and with perfect rewards, it often achieves near-perfect accuracy. With imperfect rewards from reward models, however, BoN fails to reliably find the correct answer and its performance degrades drastically. We consider the distribution of BoN’s outputs and highlight that, although the correct answer does not usually have a probability close to one under imperfect rewards, it is often the most likely outcome. This suggests that the mode of this distribution can be more reliably correct than a sample from it. Based on this idea, we propose Majority-of-the-Bests (MoB), a novel selection mechanism that estimates the output distribution of BoN via bootstrapping and selects its mode. Experimental results across five benchmarks, three different base LLMs, and two reward models demonstrate consistent improvements over BoN in 25 out of 30 setups. We also provide theoretical results for the consistency of the bootstrapping. MoB serves as a simple, yet strong alternative to BoN and self-consistency, and more broadly, motivates further research in more nuanced selection mechanisms.

The attention mechanism is a core primitive in modern large language models (LLMs) and AI more broadly. Since attention by itself is permutation-invariant, position encoding is essential for modeling structured domains such as language. Rotary position encoding (RoPE) has emerged as the de facto standard approach for position encoding and is part of many modern LLMs. However, in RoPE the key/query transformation between two elements in a sequence is only a function of their relative position and otherwise independent of the actual input. This limits the expressivity of RoPE-based transformers. This paper describes PaTH, a flexible data-dependent position encoding scheme based on accumulated products of Householder(like) transformations, where each transformation is data-dependent, i.e., a function of the input. We derive an efficient parallel algorithm for training through exploiting a compact representation of products of Householder matrices, and implement a FlashAttention-style blockwise algorithm. Across both targeted synthetic benchmarks and moderate-scale real-world language modeling experiments, we find that PaTH improves upon RoPE and other recent baselines. Finally, we show that we can convert pretrained RoPE transformers into PaTH with continued pretraining.

Engineering design optimization seeks to automatically determine the shapes, topologies, or parameters of components that maximize performance under given conditions. This process often depends on physics-based simulations, which are difficult to install, computationally expensive, and require domain-specific expertise. To mitigate these challenges, we introduce EngiBench, the first open‐source library and datasets spanning diverse domains for data‐driven engineering design. EngiBench provides a unified API and a curated set of benchmarks---covering aeronautics, heat conduction, photonics, and more---that enable fair, reproducible comparisons of optimization and machine learning algorithms, such as generative or surrogate models. We also release EngiOpt, a companion library offering a collection of such algorithms compatible with the EngiBench interface. Both libraries are modular, letting users plug in novel algorithms or problems, automate end-to-end experiment workflows, and leverage built-in utilities for visualization, dataset generation, feasibility checks, and performance analysis. We demonstrate their versatility through experiments comparing state-of-the-art techniques across multiple engineering design problems, an undertaking that was previously prohibitively time-consuming to perform. Finally, we show that these problems pose significant challenges for standard machine learning methods due to highly sensitive and constrained design manifolds.

The augmentation of algorithms with predictions of the optimal solution, such as from a machine-learning algorithm, has garnered significant attention in recent years, particularly in facility location problems. Moving beyond the traditional focus on utilitarian and egalitarian objectives, we design learning-augmented facility location mechanisms for the envy ratio objective, a fairness metric defined as the maximum ratio between the utilities of any two agents. For the deterministic setting, we propose a mechanism which utilizes predictions to achieve $\alpha$-consistency and $\frac{\alpha}{\alpha - 1}$-robustness for a selected parameter $\alpha \in [1,2]$, and prove its optimality. We also resolve open questions raised by Ding et al. [2020], devising a randomized mechanism without predictions to improve upon the best-known approximation ratio from $2$ to $1.8944$. Building upon these advancements, we construct a novel randomized mechanism which incorporates predictions to achieve improved performance guarantees.

With AI advancement and increasing circuit complexity, efficient chip design through Electronic Design Automation (EDA) is critical. Fast and accurate congestion prediction in chip layout and routing can significantly enhance automated design performance. Existing congestion modeling methods are limited by **(i)** ineffective processing and fusion of multi-view circuit data information, and **(ii)** insufficient reliability and interpretability in the prediction process. To address these challenges, We propose **M**ulti-view **I**nterpretable **H**ypergraph for **C**hip (**MIHC**), a trustworthy 'multi-view hypergraph neural network'-based framework that **(i)** processes both graph and image information in unified hypergraph representations, capturing topological and geometric circuit data, and **(ii)** implements a novel subgraph Information Bottleneck mechanism identifying critical congestion-correlated regions to guide predictions. This represents the first attempt to incorporate such interpretability into congestion prediction through informative graph reasoning. Experiments show our model reduces NMAE by 16.67% and 8.57% in cell-based and grid-based predictions on ISPD2015, and 5.26% and 2.44% on CircuitNet-N28, respectively, compared to state-of-the-art methods. Rigorous cross-design generalization experiments further validate our method’s capability to handle entirely unseen circuit designs.

We present Ambient Protein Diffusion, a framework for training protein diffusion models that generates structures with unprecedented diversity and quality. State-of-the-art generative models are trained on computationally derived structures from AlphaFold2 (AF), as experimentally determined structures are relatively scarce. The resulting models are therefore limited by the quality of synthetic datasets. Since the accuracy of AF predictions degrades with increasing protein length and complexity, de novo generation of long, complex proteins remains challenging. Ambient Protein Diffusion overcomes this problem by treating low-confidence AF structures as corrupted data. Rather than simply filtering out low-quality AF structures, our method adjusts the diffusion objective for each structure based on its corruption level, allowing the model to learn from both high and low quality structures. Empirically, ambient protein diffusion yields major improvements: on proteins with 700 residues, diversity increases from 45% to 85% from the previous state-of-the-art, and designability improves from 70% to 88%.

Motivated by applications such as cloud platforms allocating GPUs to users or governments deploying mobile health units across competing regions, we study the constrained dynamic allocation of a reusable resource to a group of strategic agents. Our objective is to simultaneously (i) maximize social welfare, (ii) satisfy multi-dimensional long-term cost constraints, and (iii) incentivize truthful reporting. We begin by numerically evaluating primal-dual methods widely used in constrained online optimization and find them to be highly fragile in strategic settings -- agents can easily manipulate their reports to distort future dual updates for future gain. To address this vulnerability, we develop an incentive-aware framework that makes primal-dual methods robust to strategic behavior. Our primal-side design combines epoch-based lazy updates -- discouraging agents from distorting dual updates -- with dual-adjust pricing and randomized exploration techniques that extract approximately truthful signals for learning. On the dual side, we design a novel online learning subroutine to resolve a circular dependency between actions and predictions; this makes our mechanism achieve $\tilde{\mathcal{O}}(\sqrt{T})$ social welfare regret (where $T$ is the number of allocation rounds), satisfies all cost constraints, and ensures incentive alignment. This $\tilde{\mathcal{O}}(\sqrt{T})$ performance matches that of non-strategic allocation approaches while additionally exhibiting robustness to strategic agents.

Surrogate models are widely used to approximate complex systems across science and engineering to reduce computational costs. Despite their widespread adoption, the field lacks standardisation across key stages of the modelling pipeline, including data sampling, model selection, evaluation, and downstream analysis. This fragmentation limits reproducibility and cross-domain utility – a challenge further exacerbated by the rapid proliferation of AI-driven surrogate models. We argue for the urgent need to establish a structured reporting standard, the Surrogate Model Reporting Standard (SMRS), that systematically captures essential design and evaluation choices while remaining agnostic to implementation specifics. By promoting a standardised yet flexible framework, we aim to improve the reliability of surrogate modelling, foster interdisciplinary knowledge transfer, and, as a result, accelerate scientific progress in the AI era.

Recent probing studies reveal that large language models exhibit linear subspaces that separate true from false statements, yet the mechanism behind their emergence is unclear. We introduce a transparent, one-layer transformer toy model that reproduces such truth subspaces end-to-end and exposes one concrete route by which they can arise. We study one simple setting in which truth encoding can emerge: a data distribution where factual statements co-occur with other factual statements (and vice-versa), encouraging the model to learn this distinction in order to lower the LM loss on future tokens. We corroborate this pattern with experiments in pretrained language models. Finally, in the toy setting we observe a two-phase learning dynamic: networks first memorize individual factual associations in a few steps, then---over a longer horizon---learn to linearly separate true from false, which in turn lowers language-modeling loss. Together, these results provide both a mechanistic demonstration and an empirical motivation for how and why linear truth representations can emerge in language models.

One main challenge in time series anomaly detection for industrial IoT lies in the complex spatio-temporal couplings within multivariate data. However, as traditional anomaly detection methods focus on modeling spatial or temporal dependencies independently, resulting in suboptimal representation learning and limited sensitivity to anomalous dispersion in high-dimensional spaces. In this work, we conduct an empirical analysis showing that both normal and anomalous samples tend to scatter in high-dimensional space, especially anomalous samples are markedly more dispersed. We formalize this dispersion phenomenon as scattering, quantified by the mean pairwise distance among sample representations, and leverage it as an inductive signal to enhance spatio-temporal anomaly detection. Technically, we propose ScatterAD to model representation scattering across temporal and topological dimensions. ScatterAD incorporates a topological encoder for capturing graph-structured scattering and a temporal encoder for constraining over-scattering through mean squared error minimization between neighboring time steps. We introduce a contrastive fusion mechanism to ensure the complementarity of the learned temporal and topological representations. Additionally, we theoretically show that maximizing the conditional mutual information between temporal and topological views improves cross-view consistency and enhances more discriminative representations. Extensive experiments on multiple public benchmarks show that ScatterAD achieves state-of-the-art performance on multivariate time series anomaly detection.

Long-context large language models (LLMs) have achieved remarkable advancements, driven by techniques like Rotary Position Embedding (RoPE) (Su et al., 2023) and its extensions (Chen et al., 2023; Liu et al., 2024c; Peng et al., 2023). By adjusting RoPE parameters and incorporating training data with extended contexts, we can train performant models with considerably longer input sequences. However, existing RoPE-based methods exhibit performance limitations when applied to extended context lengths. This paper presents a comprehensive analysis of various attention mechanisms, including RoPE, No Positional Embedding (NoPE), and Query-Key Normalization (QK-Norm), identifying their strengths and shortcomings in long-context modeling. Our investigation identifies distinctive attention patterns in these methods and highlights their impact on long-context performance, providing valuable insights for architectural design. on long context performance, providing valuable insights for architectural design. Building on these findings, we propose a novel architecture featuring a hybrid attention mechanism that integrates global and local attention spans. This design not only surpasses conventional RoPE-based transformer models with full attention in both long and short context tasks but also delivers substantial efficiency gains during training and inference.

Understanding neural network' (NN) generalizability remains a central question in deep learning research. The special phenomenon of grokking, where NNs abruptly generalize long after the training performance reaches near-perfect level, offers a unique window to investigate the underlying mechanisms of NNs' generalizability. Here we propose an interpretation for grokking by framing it as a computational glass relaxation: viewing NNs as a physical system where parameters are the degrees of freedom and train loss is the system energy, we find memorization process resembles a rapid cooling of liquid into non-equilibrium glassy state at low temperature and the later generalization is like a slow relaxation towards a more stable configuration. This mapping enables us to sample NNs' Boltzmann entropy (states of density) landscape as a function of training loss and test accuracy. Our experiments in transformers on arithmetic tasks suggests that there is NO entropy barrier in the memorization-to-generalization transition of grokking, challenging previous theory that defines grokking as a first-order phase transition. We identify a high-entropy advantage under grokking, an extension of prior work linking entropy to generalizability but much more significant. Inspired by grokking's far-from-equilibrium nature, we develop a toy optimizer WanD based on Wang-landau molecular dynamics, which can eliminate grokking without any constraints and find high-norm generalizing solutions. This provides strictly-defined counterexamples to theory attributing grokking solely to weight norm evolution towards the Goldilocks zone and also suggests new potential ways for optimizer design.

In multi-armed bandits with network interference (MABNI), the action taken by one node can influence the rewards of others, creating complex interdependence. While existing research on MABNI largely concentrates on minimizing regret, it often overlooks the crucial concern that an excessive emphasis on the optimal arm can undermine the inference accuracy for sub-optimal arms. Although initial efforts have been made to address this trade-off in single-unit scenarios, these challenges have become more pronounced in the context of MABNI. In this paper, we establish, for the first time, a theoretical Pareto frontier characterizing the trade-off between regret minimization and inference accuracy in adversarial (design-based) MABNI. We further introduce an anytime-valid asymptotic confidence sequence along with a corresponding algorithm, $\texttt{EXP3-N-CS}$, specifically designed to balance the trade-off between regret minimization and inference accuracy in this setting.