NeurIPS 2025 论文列表

We present scPilot, the first systematic framework to practice \textit{omics-native reasoning}: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and on-demand bioinformatics tools. scPilot converts core single-cell analyses, i.e., cell-type annotation, developmental-trajectory reconstruction, and transcription-factor targeting, into step-by-step reasoning problems that the model must solve, justify, and, when needed, revise with new evidence. To measure progress, we release \scbench, a suite of 9 expertly curated datasets and graders that faithfully evaluate the omics-native reasoning capability of scPilot w.r.t various LLMs. Experiments with o1 show that \textit{iterative} omics-native reasoning lifts average accuracy by 11\% for cell-type annotation and Gemini 2.5 Pro cuts trajectory graph-edit distance by 30\% versus one-shot prompting, while generating transparent reasoning traces that explain marker gene ambiguity and regulatory logic. By grounding LLMs in raw omics data, scPilot enables auditable, interpretable, and diagnostically informative single-cell analyses.

We introduce TAPIP3D, a novel approach for long-term 3D point tracking in monocular RGB and RGB-D videos. TAPIP3D represents videos as camera-stabilized spatio-temporal feature clouds, leveraging depth and camera motion information to lift 2D video features into a 3D world space where camera movement is effectively canceled out. Within this stabilized 3D representation, TAPIP3D iteratively refines multi-frame motion estimates, enabling robust point tracking over long time horizons. To handle the irregular structure of 3D point distributions, we propose a 3D Neighborhood-to-Neighborhood (N2N) attention mechanism—a 3D-aware contextualization strategy that builds informative, spatially coherent feature neighborhoods to support precise trajectory estimation. Our 3D-centric formulation significantly improves performance over existing 3D point tracking methods and even surpasses state-of-the-art 2D pixel trackers in accuracy when reliable depth is available. The model supports inference in both camera-centric (unstabilized) and world-centric (stabilized) coordinates, with experiments showing that compensating for camera motion leads to substantial gains in tracking robustness. By replacing the conventional 2D square correlation windows used in prior 2D and 3D trackers with a spatially grounded 3D attention mechanism, TAPIP3D achieves strong and consistent results across multiple 3D point tracking benchmarks. Our code and trained checkpoints will be public.

Creativity in AI imagery remains a fundamental challenge, requiring not only the generation of visually compelling content but also the capacity to add novel, expressive, and artistically rich transformations to images. Unlike conventional editing tasks that rely on direct prompt-based modifications, creative image editing demands an autonomous, iterative approach that balances originality, coherence, and artistic intent. To address this, we introduce CREA, a novel multi-agent collaborative framework that mimics the human creative process. Our framework leverages a team of specialized AI agents who dynamically collaborate to conceptualize, generate, critique, and enhance images. Through extensive qualitative and quantitative evaluations, we demonstrate that CREA significantly outperforms state-of-the-art methods in diversity, semantic alignment, and creative transformation. To the best of our knowledge, this is the first work to introduce the task of creative editing.

We study stochastic gradient descent (SGD) with gradient clipping on convex functions under a generalized smoothness assumption called $(L_0,L_1)$-smoothness. Using gradient clipping, we establish a high probability convergence rate that matches the SGD rate in the $L$ smooth case up to polylogarithmic factors and additive terms. We also propose a variation of adaptive SGD with gradient clipping, which achieves the same guarantee. We perform empirical experiments to examine our theory and algorithmic choices.

Large language models with Mixture-of-Experts (MoE) architectures achieve efficiency and scalability, yet their routing mechanisms introduce safety alignment challenges insufficiently addressed by techniques developed for dense models. In this work, the MoE-specific safety risk of positional vulnerability—that safety-aligned behaviors rely on specific expert modules—is formalized and systematically analyzed. An analytical framework, SAFEx, is presented to robustly identify, characterize, and validate safety-critical experts via a stability-based expert selection procedure, and to decompose them into two functional groups: the Harmful Content Detection Group (HCDG), which specializes in identifying and recognizing harmful content within user inputs, and the Harmful Response Control Group (HRCG), which specializes in controlling and enforcing model behaviors to generate appropriate safety responses. Expert-level interventions are conducted to probe causality and to test mitigation. Targeted masking of SAFEx-selected experts reveals that safety behavior is highly concentrated. On Qwen3-30B-A3B, configured with 48 MoE-FFN layers and 128 experts per layer under top-8 routing (48×128=6,144 experts in total), disabling 12 selected experts reduces the refusal rate by 22%. In addition, lightweight adaptation is performed using LoRA under three configurations—the HRCG, the union of HCDG and HRCG, and all experts—and the resulting updates are composed through negative weight merging targeted at the HRCG, leading to improved refusal under adversarial prompts without full-model retraining. These results establish positional vulnerability as a distinct MoE-specific safety challenge and provide a practical, compute-efficient pathway for expert-level safety interventions within routed architectures.

The m-out-of-n bootstrap—proposed by \cite{bickel1992resampling}—approximates the distribution of a statistic by repeatedly drawing $m$ subsamples ($m \ll n$) without replacement from an original sample of size n; it is now routinely used for robust inference with heavy-tailed data, bandwidth selection, and other large-sample applications. Despite this broad applicability across econometrics, biostatistics, and machine-learning workflows, rigorous parameter-free guarantees for the soundness of the m-out-of-n bootstrap when estimating sample quantiles have remained elusive. This paper establishes such guarantees by analysing the estimator of sample quantiles obtained from m-out-of-n resampling of a dataset of length n. We first prove a central limit theorem for a fully data-driven version of the estimator that holds under a mild moment condition and involves no unknown nuisance parameters. We then show that the moment assumption is essentially tight by constructing a counter-example in which the CLT fails. Strengthening the assumptions slightly, we derive an Edgeworth expansion that delivers exact convergence rates and, as a corollary, a Berry–Esséen bound on the bootstrap approximation error. Finally, we illustrate the scope of our results by obtaining parameter-free asymptotic distributions for practical statistics, including the quantiles for random walk MH, and rewards of ergodic MDP's, thereby demonstrating the usefulness of our theory in modern estimation and learning tasks.

Reinforcement learning (RL) is a critical component of large language model (LLM) post-training. However, on-policy algorithms used for post-training are not naturally robust to a diversified content of experience replay buffers, which asynchronous off-policy actors can efficiently populate in parallel to training. We propose efficiently learning on such off-policy data via Trajectory Balance with Asynchrony (TBA), an approach to asynchronous RL for LLMs that leverages the principled off-policy TB objective. On math, preference-tuning, and automated red-teaming tasks, we post-train models ranging from Pythia 410M to Qwen 2.5 7B, finding TBA offers speed and performance boosts over strong baselines like Online DPO and Dr. GRPO. Beyond TBA's performance benefits (high accuracy even as asynchrony grows) and speedups ($4\times$ or more), we show its reward- and recency-prioritizing sampling enable further gains as data generation is scaled. Our code is available at https://github.com/bbartoldson/TBA.

Mixture-of-Experts (MoE) models achieve a favorable trade-off between performance and inference efficiency by activating only a subset of experts. However, the memory overhead of storing all experts remains a major limitation, especially in large-scale MoE models such as DeepSeek-R1 (671B). In this study, we investigate domain specialization and expert redundancy in large-scale MoE models and uncover a consistent behavior we term~\emph{few-shot expert localization}, with only a few in-domain demonstrations, the model consistently activates a sparse and stable subset of experts on tasks within the same domain. Building on this observation, we propose a simple yet effective pruning framework, \textbf{EASY-EP}, that leverages a few domain-specific demonstrations to identify and retain only the most relevant experts. EASY-EP comprises two key components: \textbf{output-aware expert importance assessment} and \textbf{expert-level token contribution estimation}. The former evaluates the importance of each expert for the current token by considering the gating scores and L2 norm of the outputs of activated experts, while the latter assesses the contribution of tokens based on representation similarities before and after routed experts. Experiments on DeepSeek-R1 and DeepSeek-V3-0324 show that our method can achieve comparable performances and $2.99\times$ throughput under the same memory budget as the full model, with only half the experts. Our code is available at https://github.com/RUCAIBox/EASYEP.

We study the greedy (exploitation-only) algorithm in bandit problems with a known reward structure. We allow arbitrary finite reward structures, while prior work focused on a few specific ones. We fully characterize when the greedy algorithm asymptotically succeeds or fails, in the sense of sublinear vs. linear regret as a function of time. Our characterization identifies a partial identifiability property of the problem instance as the necessary and sufficient condition for the asymptotic success. Notably, once this property holds, the problem becomes easy—\emph{any} algorithm will succeed (in the same sense as above), provided it satisfies a mild non-degeneracy condition. Our characterization extends to contextual bandits and interactive decision-making with arbitrary feedback. Examples demonstrating broad applicability and extensions to infinite reward structures are provided.

With advancements in reasoning capabilities, Large Language Models (LLMs) are increasingly employed for automated judgment tasks. While LLMs-as-Judges offer promise in automating evaluations, current approaches often rely on simplistic aggregation methods (e.g., majority voting), which can fail even when individual agents provide correct answers. To address this, we propose a multi-agent debate judge framework where agents collaboratively reason and iteratively refine their responses. We formalize the debate process mathematically, analyzing agent interactions and proving that debate amplifies correctness compared to static ensembles. To enhance efficiency, we introduce a stability detection mechanism that models judge consensus dynamics via a time-varying Beta-Binomial mixture, with adaptive stopping based on distributional similarity (Kolmogorov-Smirnov test). This mechanism models the judges' collective correct rate dynamics using a time-varying mixture of Beta-Binomial distributions and employs an adaptive stopping criterion based on distributional similarity (Kolmogorov-Smirnov statistic). Experiments across multiple benchmarks and models demonstrate that our framework improves judgment accuracy over majority voting while maintaining computational efficiency.

This paper investigates Reinforcement Learning (RL) on data without explicit labels for reasoning tasks in Large Language Models (LLMs). The core challenge of the problem is reward estimation during inference while not having access to ground-truth information. While this setting appears elusive, we find that common practices in Test-Time Scaling (TTS), such as majority voting, yield surprisingly effective rewards suitable for driving RL training. In this work, we introduce Test-Time Reinforcement Learning (TTRL), a novel method for training LLMs using RL on unlabeled data. TTRL enables self-evolution of LLMs by utilizing the priors in the pre-trained models. Our experiments demonstrate that TTRL consistently improves performance across a variety of tasks and models. Notably, TTRL boosts the pass@1 performance of Qwen-2.5-Math-7B by approximately 211% on the AIME 2024 with only unlabeled test data. Furthermore, although TTRL is only supervised by the Maj@N metric, TTRL has demonstrated performance to consistently surpass the upper limit of the initial model, and approach the performance of models trained directly on test data with ground-truth labels. Our experimental findings validate the general effectiveness of TTRL across various tasks and highlight TTRL's potential for broader tasks and domains.

We introduce Neural Hamiltonian Diffusion, a unified framework for learning stochastic Hamiltonian dynamics on differentiable manifolds. While Hamiltonian Neural Networks (HNNs) model conservative systems in flat Euclidean space, they fail to account for geometric structure and intrinsic stochasticity. Conversely, diffusion models on Riemannian manifolds offer geometry-aware stochastic modeling but lack physical inductive biases. Our method parameterizes a Hamiltonian with a neural network and defines its dynamics as a stochastic differential equation on a (pseudo-)Riemannian manifold equipped with a Poisson structure. This enables physically consistent modeling of dynamics on curved, periodic, or causally structured spaces. We demonstrate that the proposed geometric dynamics generalizes existing approaches and applies to systems ranging from molecular dynamics to relativistic n-body problems.

Discrete state space diffusion models have shown significant advantages in applications involving discrete data, such as text and image generation. It has also been observed that their performance is highly sensitive to the choice of rate matrices, particularly between uniform and absorbing rate matrices. While empirical results suggest that absorbing rate matrices often yield better generation quality compared to uniform rate matrices, existing theoretical works have largely focused on the uniform rate matrices case. Notably, convergence guarantees and error analyses for absorbing diffusion models are still missing. In this work, we provide the first finite-time error bounds and convergence rate analysis for discrete diffusion models using absorbing rate matrices. We begin by deriving an upper bound on the KL divergence of the forward process, introducing a surrogate initialization distribution to address the challenge posed by the absorbing stationary distribution, which is a singleton and causes the KL divergence to be ill-defined. We then establish the first convergence guarantees for both the $\tau$-leaping and uniformization samplers under absorbing rate matrices, demonstrating improved rates over their counterparts using uniform rate matrices. Furthermore, under suitable assumptions, we provide convergence guarantees without early stopping. Our analysis introduces several new technical tools to address challenges unique to absorbing rate matrices. These include a Jensen-type argument for bounding forward process convergence, novel techniques for bounding absorbing score functions, and a non-divergent upper bound on the score near initialization that removes the need of early-stopping.

Scaling video diffusion transformers (DiTs) is limited by their quadratic 3D attention, even though most of the attention mass concentrates on a small subset of positions. We turn this observation into VSA, a trainable, hardware-efficient sparse attention that replaces full attention at both training and inference. In VSA, a lightweight coarse stage pools tokens into tiles and identifies high-weight critical tokens; a fine stage computes token-level attention only inside those tiles subjecting to block computing layout to ensure hard efficiency. This leads to a single differentiable kernel that trains end-to-end, requires no post-hoc profiling, and sustains 85\% of FlashAttention3 MFU. We perform a large sweep of ablation studies and scaling-law experiments by pretraining DiTs from 60M to 1.4B parameters. VSA reaches a Pareto point that cuts training FLOPS by 2.53$\times$ with no drop in diffusion loss. Retrofitting the open-source Wan2.1-1.3B model speeds up attention time by 6$\times$ and lowers end-to-end generation time from 31s to 18s with comparable quality, while for the 14B model, end-to-end generation time is reduced from 1274s to 576s. Furthermore, we introduce a preliminary study of Sparse-Distill, the first method to enable sparse attention and distillation concurrently, achieving 50.9x speed up for Wan-1.3B while maintaining quality. These results establish trainable sparse attention as a practical alternative to full attention and a key enabler for further scaling of video diffusion models. Code is available at https://github.com/hao-ai-lab/FastVideo.

LLM unlearning aims to remove sensitive or harmful information within the model, thus reducing the potential risk of generating unexpected information. However, existing Preference Optimization (PO)-based unlearning methods suffer two limitations. First, their rigid reward setting limits the effect of unlearning. Second, the lack of robustness causes unlearned information to reappear. To remedy these two weaknesses, we present a novel LLM unlearning optimization framework, namely Elastic Robust Unlearning (ERU), to efficiently and robustly remove specific knowledge from LLMs. We design the elastic reward setting instead of the rigid reward setting to enhance the unlearning performance. Meanwhile, we incorporate the refusal feature ablation into the unlearning process to trigger specific failure patterns for efficiently enhancing the robustness of the PO-based unlearning methods in multiple scenarios. Experimental results show that ERU can improve the unlearning effectiveness significantly while maintaining a high utility performance. Especially, on the WMDP-Bio benchmark, ERU shows a 9\% improvement over the second-best method, and maintains 83\% performance even under 1,000 sample fine-tuned retraining attacks, significantly better than the baseline method.

Predicting a sequence of actions has been crucial in the success of recent behavior cloning algorithms in robotics. Can similar ideas improve reinforcement learning (RL)? We answer affirmatively by observing that incorporating action sequences when predicting ground-truth return-to-go leads to lower validation loss. Motivated by this, we introduce Coarse-to-fine Q-Network with Action Sequence (CQN-AS), a novel value-based RL algorithm that learns a critic network that outputs Q-values over a sequence of actions, i.e., explicitly training the value function to learn the consequence of executing action sequences. Our experiments show that CQN-AS outperforms several baselines on a variety of sparse-reward humanoid control and tabletop manipulation tasks from BiGym and RLBench.

Frontier models that generate extended reasoning traces inadvertently produce token sequences that can facilitate model distillation. Recognizing this vulnerability, model owners may seek sampling strategies that limit the effectiveness of distillation without compromising model performance. *Antidistillation sampling* provides exactly this capability. By strategically modifying a model's next-token probability distribution, antidistillation sampling poisons reasoning traces, rendering them significantly less effective for distillation while preserving the model's utility.

We investigate the problem of finding second-order stationary points (SOSP) in differentially private (DP) stochastic non-convex optimization. Existing methods suffer from two key limitations: \textbf{(i)} inaccurate convergence error rate due to overlooking gradient variance in the saddle point escape analysis, and \textbf{(ii)} dependence on auxiliary private model selection procedures for identifying DP-SOSP, which can significantly impair utility, particularly in distributed settings. To address these issues, we propose a generic perturbed stochastic gradient descent (PSGD) framework built upon Gaussian noise injection and general gradient oracles. A core innovation of our framework is using model drift distance to determine whether PSGD escapes saddle points, ensuring convergence to approximate local minima without relying on second-order information or additional DP-SOSP identification. By leveraging the adaptive DP-SPIDER estimator as a specific gradient oracle, we develop a new DP algorithm that rectifies the convergence error rates reported in prior work. We further extend this algorithm to distributed learning with arbitrarily heterogeneous data, providing the first formal guarantees for finding DP-SOSP in such settings. Our analysis also highlights the detrimental impacts of private selection procedures in distributed learning under high-dimensional models, underscoring the practical benefits of our design. Numerical experiments on real-world datasets validate the efficacy of our approach.

Understanding perspective is fundamental to human visual perception, yet the extent to which multimodal large language models (MLLMs) internalize perspective geometry remains unclear. We introduce MMPerspective, the first benchmark specifically designed to systematically evaluate MLLMs' understanding of perspective through 10 carefully crafted tasks across three complementary dimensions: Perspective Perception, Reasoning, and Robustness. Our benchmark comprises 2,711 real-world and synthetic image instances with 5,083 question-answer pairs that probe key capabilities, such as vanishing point perception and counting, perspective type reasoning, line relationship understanding in 3D space, invariance to perspective-preserving transformations, etc. Through a comprehensive evaluation of 43 state-of-the-art MLLMs, we uncover significant limitations: while models demonstrate competence on surface-level perceptual tasks, they struggle with compositional reasoning and maintaining spatial consistency under perturbations. Our analysis further reveals intriguing patterns between model architecture, scale, and perspective capabilities, highlighting both robustness bottlenecks and the benefits of chain-of-thought prompting. MMPerspective establishes a valuable testbed for diagnosing and advancing spatial understanding in vision-language systems. Resources are available at https://yunlong10.github.io/MMPerspective/