NeurIPS 2025 Papers

Previous research has investigated the application of Multimodal Large Language Models (MLLMs) in understanding 3D scenes by interpreting them as videos. These approaches generally depend on comprehensive 3D data inputs, such as point clouds or reconstructed Bird's-Eye View (BEV) maps. In our research, we advance this field by enhancing the capability of MLLMs to understand and reason in 3D spaces directly from video data, without the need for additional 3D input. We propose a novel and efficient method called the Video-3D Geometry Large Language Model (VG LLM). Our approach utilizes a 3D visual geometry encoder to extract 3D prior information from video sequences. This information is then integrated with visual tokens and input into the MLLM. Extensive experiments have shown that our method has achieved substantial improvements in various tasks related to 3D scene understanding and spatial reasoning, all directly learned from video sources. Impressively, our 4B model, which does not rely on explicit 3D data inputs, achieves competitive results compared to existing state-of-the-art methods, and even surpasses the Gemini-1.5-Pro in the VSI-Bench evaluations.

Despite the significant breakthrough of Mixture-of-Experts (MoE), the increasing scale of these MoE models presents huge memory and storage challenges. Existing MoE pruning methods, which involve reducing parameter size with a uniform sparsity across all layers, often lead to suboptimal outcomes and performance degradation due to varying expert redundancy in different MoE layers. To address this, we propose a non-uniform pruning strategy, dubbed Differentiable Expert Pruning (DiEP), which adaptively adjusts pruning rates at the layer level while jointly learning inter-layer importance, effectively capturing the varying redundancy across different MoE layers. By transforming the global discrete search space into a continuous one, our method handles exponentially growing non-uniform expert combinations, enabling adaptive gradient-based pruning. Extensive experiments on five advanced MoE models demonstrate the efficacy of our method across various NLP tasks. Notably, \textbf{DiEP} retains around 92\% of original performance on Mixtral 8$\times$7B with only half the experts, outperforming other pruning methods by up to 7.1% on the challenging MMLU dataset.

Large Language Models (LLMs) are transforming search engines into Conversational Search Engines (CSE). Consequently, Search Engine Optimization (SEO) is being shifted into Conversational Search Engine Optimization (C-SEO). We are beginning to see dedicated C-SEO methods for modifying web documents to increase their visibility in CSE responses. However, they are often tested only for a limited breadth of application domains; we do not know whether certain C-SEO methods would be effective for a broad range of domains. Moreover, existing evaluations consider only a single-actor scenario where only one web document adopts a C-SEO method; in reality, multiple players are likely to competitively adopt the cutting-edge C-SEO techniques, drawing an analogy from the dynamics we have seen in SEO. We present C-SEO Bench, the first benchmark designed to evaluate C-SEO methods across multiple tasks, domains, and number of actors. We consider two search tasks, question answering and product recommendation, with three domains each. We also formalize a new evaluation protocol with varying adoption rates among involved actors. Our experiments reveal that most current C-SEO methods are not only largely ineffective but also frequently have a negative impact on document ranking, which is opposite to what is expected. Instead, traditional SEO strategies, those aiming to improve the ranking of the source in the LLM context, are significantly more effective. We also observe that as we increase the number of C-SEO adopters, the overall gains decrease, depicting a congested and zero-sum nature of the problem.

Bayesian Optimization (BO) is a powerful tool for optimizing expensive black-box objective functions. While extensive research has been conducted on the single-objective optimization problem, the multi-objective optimization problem remains challenging. In this paper, we propose MOBO-OSD, a multi-objective Bayesian Optimization algorithm designed to generate a diverse set of Pareto optimal solutions by solving multiple constrained optimization problems, referred to as MOBO-OSD subproblems, along orthogonal search directions (OSDs) defined with respect to an approximated convex hull of individual objective minima. By employing a well-distributed set of OSDs, MOBO-OSD ensures broad coverage of the objective space, enhancing both solution diversity and hypervolume performance. To further improve the density of the set of the Pareto optimal candidate solutions without requiring an excessive number of subproblems, we leverage a Pareto Front Estimation technique to generate additional solutions in the neighborhood of existing solutions. Additionally, MOBO-OSD supports batch optimization, enabling parallel function evaluations to accelerate the optimization process when resources are available. Through extensive experiments and analysis on a variety of synthetic and real-world benchmark functions with two to six objectives, we demonstrate that MOBO-OSD consistently outperform the state-of-the-art algorithms.

Mask-based pretraining has become a cornerstone of modern large-scale models across language, vision, and recently biology. Despite its empirical success, its role and limits in learning data representations have been unclear. In this work, we show that the behavior of mask-based pretraining can be directly characterized by test risk in high-dimensional minimum-norm ("ridge-less") linear regression, without relying on further model specifications. Further analysis of linear models uncovers several novel aspects of mask-based pretraining. The theoretical framework and its implications have been validated across diverse neural architectures (including MLPs, CNNs, and Transformers) applied to both vision and language tasks. Guided by our theory, we propose an embarrassingly simple yet overlooked pretraining scheme named *Randomly Random Mask AutoEncoding* (**R²MAE**), which enforces capturing multi-scale features from data and is able to outperform optimal fixed mask ratio settings in our linear model framework. We implement R²MAE in vision, language, DNA sequence, and single-cell models, where it consistently outperforms standard and more complicated masking schemes, leading to improvements for state-of-the-art models. Our code is available at [this URL](https://github.com/MingzeDong/r2mae).

Long-form video understanding presents significant challenges due to extensive temporal-spatial complexity and the difficulty of question answering under such extended contexts. While Large Language Models (LLMs) have demonstrated considerable advancements in video analysis capabilities and long context handling, they continue to exhibit limitations when processing information-dense hour-long videos. To overcome such limitations, we propose the $\textbf{D}eep \ \textbf{V}ideo \ \textbf{D}iscovery \ (\textbf{DVD})$ agent to leverage an $\textit{agentic search}$ strategy over segmented video clips. Different from previous video agents manually designing a rigid workflow, our approach emphasizes the autonomous nature of agents. By providing a set of search-centric tools on multi-granular video database, our DVD agent leverages the advanced reasoning capability of LLM to plan on its current observation state, strategically selects tools to orchestrate adaptive workflow for different queries in light of the gathered information. We perform comprehensive evaluation on multiple long video understanding benchmarks that demonstrates our advantage. Our DVD agent achieves state-of-the-art performance on the challenging LVBench dataset, reaching an accuracy of $\textbf{74.2\%}$, which substantially surpasses all prior works, and further improves to $\textbf{76.0\%}$ with transcripts.

Video Anomaly Detection (VAD) aims to identify abnormal frames from discrete events within video sequences. Existing VAD methods suffer from heavy annotation burdens in fully-supervised paradigm, insensitivity to subtle anomalies in semi-supervised paradigm, and vulnerability to noise in weakly-supervised paradigm. To address these limitations, we propose a novel paradigm: Single-Frame supervised VAD (SF-VAD), which uses a single annotated abnormal frame per abnormal video. SF-VAD ensures annotation efficiency while offering precise anomaly reference, facilitating robust anomaly modeling, and enhancing the detection of subtle anomalies in complex visual contexts. To validate its effectiveness, we construct three SF-VAD benchmarks by manually re-annotating the ShanghaiTech, UCF-Crime, and XD-Violence datasets in a practical procedure. Further, we devise Frame-guided Progressive Learning (FPL), to generalize sparse frame supervision to event-level anomaly understanding. FPL first leverages evidential learning to estimate anomaly relevance guided by annotated frames. Then it extends anomaly supervision by mining discrete abnormal events based on anomaly relevance and feature similarity. Meanwhile, FPL decouples normal patterns by isolating distinct normal frames outside abnormal events, reducing false alarms. Extensive experiments show SF-VAD achieves state-of-the-art detection results while offering a favorable trade-off between performance and annotation cost.

Associative learning--forming links between co-occurring items--is fundamental to human cognition, reshaping internal representations in complex ways. Testing hypotheses on how representational changes occur in biological systems is challenging, but large language models (LLMs) offer a scalable alternative. Building on LLMs' in-context learning, we adapt a cognitive neuroscience associative learning paradigm and investigate how representations evolve across six models. Our initial findings reveal a non-monotonic pattern consistent with the Non-Monotonic Plasticity Hypothesis, with moderately similar items differentiating after learning. Leveraging the controllability of LLMs, we further show that this differentiation is modulated by the overlap of associated items with the broader vocabulary--a factor we term vocabulary interference, capturing how new associations compete with prior knowledge. We find that higher vocabulary interference amplifies differentiation, suggesting that representational change is influenced by both item similarity and global competition. Our findings position LLMs not only as powerful tools for studying representational dynamics in human-like learning systems, but also as accessible and general computational models for generating new hypotheses about the principles underlying memory reorganization in the brain.

Instruction tuning is essential for Large Language Models (LLMs) to effectively follow user instructions. To improve training efficiency and reduce data redundancy, recent works use LLM-based scoring functions, e.g., Instruction-Following Difficulty (IFD), to select high–quality instruction-tuning data with scores above a threshold. While these data selection methods often lead to models that can match or even exceed the performance of models trained on the full datasets, we identify two key limitations: (i) they assess quality at the sample level, ignoring token-level informativeness; and (ii) they overlook the robustness of the scoring method, often selecting a sample due to superficial lexical features instead of its true quality. In this work, we propose Token-Selective HIeRarchical Data Selection for Instruction Tuning (T-SHIRT), a novel data selection framework that introduces a new scoring method to include only informative tokens in quality evaluation and also promote robust and reliable samples whose neighbors also show high quality with less local inconsistencies. We demonstrate that models instruction-tuned on a curated dataset (only 5% of the original size) using T-SHIRT can outperform those trained on the entire large-scale dataset by up to 5.48 points on average across eight benchmarks. Across various LLMs and training set scales, our method consistently surpasses existing state-of-the-art data selection techniques, while also remaining both cost-effective and highly efficient. For instance, by using GPT-2 for score computation, we are able to process a dataset of 52k samples in 40 minutes on a single GPU. Our code is available at https://github.com/Dynamite321/T-SHIRT.

Advancements in AI for science unlocks capabilities for critical drug discovery tasks such as protein-ligand binding affinity prediction. However, current models overfit to existing oversimplified datasets that does not represent naturally occurring and biologically relevant proteins with modifications. In this work, we curate a complete and modification-aware version of the widely used DAVIS dataset by incorporating 4,032 kinase–ligand pairs involving substitutions, insertions, deletions, and phosphorylation events. This enriched dataset enables benchmarking of predictive models under biologically realistic conditions. Based on this new dataset, we propose three benchmark settings—Augmented Dataset Prediction, Wild-Type to Modification Generalization, and Few-Shot Modification Generalization—designed to assess model robustness in the presence of protein modifications. Through extensive evaluation of both docking-free and docking-based methods, we find that docking-based model generalize better in zero-shot settings. In contrast, docking-free models tend to overfit to wild-type proteins and struggle with unseen modifications but show notable improvement when fine-tuned on a small set of modified examples. We anticipate that the curated dataset and benchmarks offer a valuable foundation for developing models that better generalize to protein modifications, ultimately advancing precision medicine in drug discovery. The benchmark is available at: https://github.com/ZhiGroup/DAVIS-complete

Learning rules—prescriptions for updating model parameters to improve performance—are typically assumed rather than derived. Why do some learning rules work better than others, and under what assumptions can a given rule be considered optimal? We propose a theoretical framework that casts learning rules as policies for navigating (partially observable) loss landscapes, and identifies optimal rules as solutions to an associated optimal control problem. A range of well-known rules emerge naturally within this framework under different assumptions: gradient descent from short-horizon optimization, momentum from longer-horizon planning, natural gradients from accounting for parameter space geometry, non-gradient rules from partial controllability, and adaptive optimizers like Adam from online Bayesian inference of loss landscape shape. We further show that continual learning strategies like weight resetting can be understood as optimal responses to task uncertainty. By unifying these phenomena under a single objective, our framework clarifies the computational structure of learning and offers a principled foundation for designing adaptive algorithms.

Selecting a compact subset of visual instruction–following data has emerged as an effective way to align large multimodal models with human intentions while avoiding the high cost of full-dataset training. Yet we observe that both full-data training and existing state-of-the-art data selection methods tend to inherit underlying dataset biases such as position bias and spurious correlations, leading to biased model behaviors. To address this issue, we introduce ARDS, a robustness-aware targeted visual instruction-selection framework that explicitly mitigates these weaknesses, sidestepping the need for access to downstream data or time-consuming gradient computation. Specifically, we first identify the worst-case evaluation subgroups through visual and textual task-specific perturbations. The robust training mixture is then constructed by prioritizing samples that are semantically closer to these subgroups in a rich multimodal embedding space. Extensive experiments demonstrate that ARDS substantially boosts both robustness and data efficiency for visual instruction tuning. We also showcase that the robust mixtures produced with a smaller model transfer effectively to larger architectures. Our code and selected datasets that have been demonstrated transferable across models are available at https://github.com/xyang583/ARDS.

Large language model (LLM) agents have demonstrated remarkable capabilities in complex reasoning and decision-making by leveraging external tools. However, this tool-centric paradigm introduces a previously underexplored attack surface, where adversaries can manipulate tool metadata---such as names, descriptions, and parameter schemas---to influence agent behavior. We identify this as a new and stealthy threat surface that allows malicious tools to be preferentially selected by LLM agents, without requiring prompt injection or access to model internals. To demonstrate and exploit this vulnerability, we propose the Attractive Metadata Attack (AMA), a black-box in-context learning framework that generates highly attractive but syntactically and semantically valid tool metadata through iterative optimization. The proposed attack integrates seamlessly into standard tool ecosystems and requires no modification to the agent’s execution framework. Extensive experiments across ten realistic, simulated tool-use scenarios and a range of popular LLM agents demonstrate consistently high attack success rates (81\%-95\%) and significant privacy leakage, with negligible impact on primary task execution. Moreover, the attack remains effective even against prompt-level defenses, auditor-based detection, and structured tool-selection protocols such as the Model Context Protocol, revealing systemic vulnerabilities in current agent architectures. These findings reveal that metadata manipulation constitutes a potent and stealthy attack surface. Notably, AMA is orthogonal to injection attacks and can be combined with them to achieve stronger attack efficacy, highlighting the need for execution-level defenses beyond prompt-level and auditor-based mechanisms. Code is available at \url{https://github.com/SEAIC-M/AMA}.

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained molecular annotations across multiple levels, bridging the gap between molecules and textual descriptions. Additionally, we propose chemically-informative molecular representation, effectively addressing limitations in existing molecular representation strategies. Building upon these innovations, we develop KnowMol, a state-of-the-art multi-modal molecular large language model. Extensive experiments demonstrate that KnowMol achieves superior performance across molecular understanding and generation tasks.

Music-driven 3D dance generation has attracted increasing attention in recent years, with promising applications in choreography, virtual reality, and creative content creation. Previous research has generated promising realistic dance movement from audio signals. However, traditional methods underutilize genre conditioning, often treating it as auxiliary modifiers rather than core semantic drivers. This oversight compromises music-motion synchronization and disrupts dance genre continuity, particularly during complex rhythmic transitions, thereby leading to visually unsatisfactory effects. To address the challenge, we propose MEGADance, a novel architecture for music-driven 3D dance generation. By decoupling choreographic consistency into dance generality and genre specificity, MEGADance demonstrates significant dance quality and strong genre controllability. It consists of two stages: (1) High-Fidelity Dance Quantization Stage (HFDQ), which encodes dance motions into a latent representation by Finite Scalar Quantization (FSQ) and reconstructs them with kinematic-dynamic constraints, and (2) Genre-Aware Dance Generation Stage (GADG), which maps music into the latent representation by synergistic utilization of Mixture-of-Experts (MoE) mechanism with Mamba-Transformer hybrid backbone. Extensive experiments on the FineDance and AIST++ dataset demonstrate the state-of-the-art performance of MEGADance both qualitatively and quantitatively. Code will be released upon acceptance.

Recent advancements in text-to-video (T2V) diffusion models have enabled high-fidelity and realistic video synthesis. However, current T2V models often struggle to generate physically plausible content due to their limited inherent ability to accurately understand physics. We found that while the representations within T2V models possess some capacity for physics understanding, they lag significantly behind those from recent video self-supervised learning methods. To this end, we propose a novel framework called {VideoREPA}, which distills physics understanding capability from video understanding foundation models into T2V models by aligning token-level relations. This closes the physics understanding gap and enables more physics-plausible generation. Specifically, we introduce the {Token Relation Distillation (TRD) loss}, leveraging spatio-temporal alignment to provide soft guidance suitable for finetuning powerful pre-trained T2V models—a critical departure from prior representation alignment (REPA) methods. To our knowledge, VideoREPA is the first REPA method designed for finetuning T2V models and specifically for injecting physical knowledge. Empirical evaluations show that VideoREPA substantially enhances the physics commonsense of baseline method, CogVideoX, achieving significant improvement on relevant benchmarks and demonstrating a strong capacity for generating videos consistent with intuitive physics. Code and more video results are available at https://videorepa.github.io/.

As AI models are deployed with increasing autonomy, it is important to ensure they do not take harmful actions unnoticed. As a potential mitigation, we investigate Chain-of-Thought (CoT) monitoring, wherein a weaker trusted monitor model continuously oversees the intermediate reasoning steps of a more powerful but untrusted model. We compare CoT monitoring to action-only monitoring, where only final outputs are reviewed, in a red-teaming setup where the untrusted model is instructed to pursue harmful side tasks while completing a coding problem. We find that while CoT monitoring is more effective than overseeing only model outputs in scenarios where action-only monitoring fails to reliably identify sabotage, reasoning traces can contain misleading rationalizations that deceive the CoT monitors, reducing performance in obvious sabotage cases. To address this, we introduce a hybrid protocol that independently scores model reasoning and actions, and combines them using a weighted average. Our hybrid monitor consistently outperforms both CoT and action-only monitors across all tested models and tasks, with detection rates twice higher than action-only monitoring for subtle deception scenarios.

Recent advancements in static feed-forward scene reconstruction have demonstrated significant progress in high-quality novel view synthesis. However, these models often struggle with generalizability across diverse environments and fail to effectively handle dynamic content. We present BTimer (short for Bullet Timer), the first motion-aware feed-forward model for real-time reconstruction and novel view synthesis of dynamic scenes. Our approach reconstructs the full scene in a 3D Gaussian Splatting representation at a given target (‘bullet’) timestamp by aggregating information from all the context frames. Such a formulation allows BTimer to gain scalability and generalization by leveraging both static and dynamic scene datasets. Given a casual monocular dynamic video, BTimer reconstructs a bullet-time scene within 150ms while reaching state-of-the-art performance on both static and dynamic scene datasets, even compared with optimization-based approaches.

Recent advancements in diffusion policies have demonstrated promising performance in decision-making tasks. To align these policies with human preferences, a common approach is incorporating Preference-based Reinforcement Learning (PbRL) into policy tuning. However, since preference data is practically collected from populations with different backgrounds, a key challenge lies in handling the inherent uncertainties in people's preferences during policy updates. To address this challenge, we propose the Diff-UAPA algorithm, designed for uncertainty-aware preference alignment in diffusion policies. Specifically, Diff-UAPA introduces a novel iterative preference alignment framework in which the diffusion policy adapts incrementally to preferences from different user groups. To accommodate this online learning paradigm, Diff-UAPA employs a maximum posterior objective, which aligns the diffusion policy with regret-based preferences under the guidance of an informative Beta prior. This approach enables direct optimization of the diffusion policy without specifying any reward functions, while effectively mitigating the influence of inconsistent preferences across different user groups. We conduct extensive experiments across both simulated and real-world robotics tasks, and diverse human preference configurations, demonstrating the robustness and reliability of Diff-UAPA in achieving effective preference alignment. The project page is available at https://anonymous.4open.science/w/Diff-UAPA-5827.