NeurIPS 2025 论文列表

Generating diverse, all‐atom conformational ensembles of dynamic proteins such as G‐protein‐coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational diversity altogether. We present latent diffusion for full protein generation (LD-FPG), a framework that constructs complete all‐atom protein structures, including every side‐chain heavy atom, directly from molecular dynamics (MD) trajectories. LD-FPG employs a Chebyshev graph neural network (ChebNet) to obtain low‐dimensional latent embeddings of protein conformations, which are processed using three pooling strategies: blind, sequential and residue‐based. A diffusion model trained on these latent representations generates new samples that a decoder, optionally regularized by dihedral‐angle losses, maps back to Cartesian coordinates. Using D2R-MD, a $2\mu\text{s}$ MD trajectory (12 000 frames) of the human dopamine D$2$ receptor in a membrane environment, the sequential and residue-based pooling strategies reproduce the reference ensemble with high structural fidelity (all‐atom lDDT \~ $0.7$; $C\alpha$-lDDT \~ $0.8$) and recovers backbone and side‐chain dihedral‐angle distributions with a Jensen–Shannon divergence $<0.03$ compared to the MD data. LD-FPG thereby offers a practical route to system‐specific, all‐atom ensemble generation for large proteins, providing a promising tool for structure‐based therapeutic design on complex, dynamic targets. The D2R-MD dataset and our implementation are freely available to facilitate further research.

Machine unlearning has become a focal point in recent research, yet the specific area of feature unlearning has not been thoroughly explored. Feature unlearning involves the elimination of specific features' effects from an already trained model, presenting distinct challenges that are still not comprehensively addressed. This paper presents a novel and straightforward approach to feature unlearning that employs a tactical shuffling of the features designated for removal. By redistributing the values of the features targeted for unlearning throughout the original training dataset and subsequently fine-tuning the model with this shuffled data, our proposed method provides a theoretical guarantee for effective feature unlearning. Under mild assumptions, our method can effectively disrupt the established correlations between unlearned features and the target outcomes, while preserving the relationships between the remaining features and the predicted outcomes. Our empirical studies across various datasets,validate that our approach not only successfully removes the effects of specified features but also maintains the informational integrity of the remaining features while achieving a faster convergence rate.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

Contrastive learning is a powerful framework for learning discriminative representations from image-text pairs. Despite its success, its theoretical foundations, especially when the image-text pair exhibits misalignment, remain underexplored. This paper provides the first theoretical analysis of contrastive learning under data misalignment, proving how the ground-truth modality-paired features are amplified while spurious features are suppressed through the training dynamics analysis. Specifically, we study two nonlinear encoders trained jointly with a contrastive loss and demonstrate that noisy (or misaligned) data pairs result in mixed representations and degrade the model's generalization ability. In contrast, recaptioning and filtering improve the data alignment, which in turn purifies the features learned by neurons and subsequently enhances generalization. Our analysis identifies feature purity as a key factor in the success of contrastive learning and offers insights into how data quality and training procedures impact representation learning and downstream generalization. Theoretical insights are supported by experiments on standard benchmarks.

In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of $T$ black-box objective functions, $f_1, \ldots f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In contrast, we consider a problem setting that departs from this paradigm: finding a small set of $K < T$ solutions, that collectively "cover" the $T$ objectives. A set of solutions is defined as "covering" if, for each objective $f_1, \ldots f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have $T$ pathogens and aim to identify a set of $K < T$ antibiotics such that at least one antibiotic can be used to treat each pathogen. This problem, known as coverage optimization, has yet to be tackled with the Bayesian optimization (BO) framework. To fill this void, we develop Multi-Objective Coverage Bayesian Optimization (MOCOBO), a BO algorithm for solving coverage optimization. Our approach is based on a new acquisition function reminiscent of expected improvement in the vanilla BO setup. We demonstrate the performance of our method on high-dimensional black-box optimization tasks, including applications in peptide and molecular design. Results show that the coverage of the $K < T$ solutions found by MOCOBO matches or nearly matches the coverage of $T$ solutions obtained by optimizing each objective individually. Furthermore, in *in vitro* experiments, the peptides found by MOCOBO exhibited high potency against drug-resistant pathogens, further demonstrating the potential of MOCOBO for drug discovery. All of our code is publicly available at the following link: https://github.com/nataliemaus/mocobo.

Generative steganography has emerged as an active research area, yet its practical system is constrained by the inherent secret payload limitation caused by low entropy in generating stego texts. This payload limitation necessitates the use of lengthy stego texts or frequent transmissions, which increases the risk of suspicion by adversaries. Previous studies have mainly focused on payload enhancement through optimized entropy utilization while overlooking the crucial role of secret message processing. To address this gap, we propose StegoZip, a framework that leverages large language models to optimize secret message processing. StegoZip consists of two core components: semantic redundancy pruning and index-based compression coding. The former dynamically prunes the secret message to extract a low-semantic representation, whereas the latter further compresses it into compact binary codes. When integrated with state-of-the-art steganographic methods under lossless decoding, StegoZip achieves 2.5$\times$ the payload of the baselines while maintaining comparable processing time in practice. This enhanced payload significantly improves covertness by mitigating the risks associated with frequent transmissions while maintaining provable content security.

Modern Text-to-Image (T2I) models deploy multi-layered defenses to block Not-Safe-For-Work (NSFW) content generation. These defenses typically include sequential layers such as prompt filters, concept erasers and image filters. While existing adversarial attacks have demonstrated vulnerabilities in isolated defense layers, they prove largely ineffective against multi-layered defenses deployed in real-world T2I systems. In this paper, we demonstrate that exploiting overlapping vulnerabilities across these distinct defense layers enables adversaries to systematically bypass the entire safeguard of T2I systems. We propose Transstratal Adversarial Attack (TAA, a novel black-box framework to compromise T2I models with multi-layered protection. It generates transstratal adversarial prompts to evade all defense layers simultaneously. This is accomplished through transstratal adversarial candidate generation using LLMs to fulfill implicit and subjective adversarial requirements against different defense layers, combined with adversarial genetic optimization for efficient black-box search to maximize the bypass rates and generated image harmfulness. Evaluated across 14 T2I models (e.g., Stable Diffusion, DALL·E, and Midjourney) and 17 safety modules, our attack achieves an average attack success rate of 85.6\%, surpassing state-of-the-art methods by 73.5\%. Our findings challenge the isolated design of safety mechanisms and establish the first benchmark for holistic robustness evaluation in multi-layered safeguarded T2I models. The code can be found in https://github.com/Bluedask/TAA-T2I.

The continuous nature of belief states in POMDPs presents significant computational challenges in learning the optimal policy. In this paper, we consider an approach that solves a Partially Observable Reinforcement Learning (PORL) problem by approximating the corresponding POMDP model into a finite-state Markov Decision Process (MDP) (called Superstate MDP). We first derive theoretical guarantees that improve upon prior work that relate the optimal value function of the transformed Superstate MDP to the optimal value function of the original POMDP. Next, we propose a policy-based learning approach with linear function approximation to learn the optimal policy for the Superstate MDP. Consequently, our approach shows that a POMDP can be approximately solved using TD-learning followed by Policy Optimization by treating it as an MDP, where the MDP state corresponds to a finite history. We show that the approximation error decreases exponentially with the length of this history. To the best of our knowledge, our finite-time bounds are the first to explicitly quantify the error introduced when applying standard TD learning to a setting where the true dynamics are not Markovian.

Multimodal language analysis is a rapidly evolving field that leverages multiple modalities to enhance the understanding of high-level semantics underlying human conversational utterances. Despite its significance, little research has investigated the capability of multimodal large language models (MLLMs) to comprehend cognitive-level semantics. In this paper, we introduce MMLA, a comprehensive benchmark specifically designed to address this gap. MMLA comprises over 61K multimodal utterances drawn from both staged and real-world scenarios, covering six core dimensions of multimodal semantics: intent, emotion, dialogue act, sentiment, speaking style, and communication behavior. We evaluate eight mainstream branches of LLMs and MLLMs using three methods: zero-shot inference, supervised fine-tuning, and instruction tuning. Extensive experiments reveal that even fine-tuned models achieve only about 60~70% accuracy, underscoring the limitations of current MLLMs in understanding complex human language. We believe that MMLA will serve as a solid foundation for exploring the potential of large language models in multimodal language analysis and provide valuable resources to advance this field. The datasets and code are open-sourced at https://github.com/thuiar/MMLA.

Adding entropic regularization to Optimal Transport (OT) problems has become a standard approach for designing efficient and scalable solvers. However, regularization introduces a bias from the true solution. To mitigate this bias while still benefiting from the acceleration provided by regularization, a natural solver would adaptively decrease the regularization as it approaches the solution. Although some algorithms heuristically implement this idea, their theoretical guarantees and the extent of their acceleration compared to using a fixed regularization remain largely open. In the setting of semi-discrete OT, where the source measure is continuous and the target is discrete, we prove that decreasing the regularization can indeed accelerate convergence. To this end, we introduce DRAG: Decreasing (entropic) Regularization Averaged Gradient, a stochastic gradient descent algorithm where the regularization decreases with the number of optimization steps. We provide a theoretical analysis showing that DRAG benefits from decreasing regularization compared to a fixed scheme, achieving an unbiased $\mathcal{O}(1/t)$ sample and iteration complexity for both the OT cost and the potential estimation, and a $\mathcal{O}(1/\sqrt{t})$ rate for the OT map. Our theoretical findings are supported by numerical experiments that validate the effectiveness of DRAG and highlight its practical advantages.

Diffusion models have achieved remarkable success in image generation and editing tasks. Inversion within these models aims to recover the latent noise representation for a real or generated image, enabling reconstruction, editing, and other downstream tasks. However, to date, most inversion approaches suffer from an intrinsic trade-off between reconstruction accuracy and editing flexibility. This limitation arises from the difficulty of maintaining both semantic alignment and structural consistency during the inversion process. In this work, we introduce **Dual-Conditional Inversion (DCI)**, a novel framework that jointly conditions on the source prompt and reference image to guide the inversion process. Specifically, DCI formulates the inversion process as a dual-condition fixed-point optimization problem, minimizing both the latent noise gap and the reconstruction error under the joint guidance. This design anchors the inversion trajectory in both semantic and visual space, leading to more accurate and editable latent representations. Our novel setup brings new understanding to the inversion process. Extensive experiments demonstrate that DCI achieves state-of-the-art performance across multiple editing tasks, significantly improving both reconstruction quality and editing precision. Furthermore, we also demonstrate that our method achieves strong results in reconstruction tasks, implying a degree of robustness and generalizability approaching the ultimate goal of the inversion process. Our codes are available at: [https://github.com/Lzxhh/Dual-Conditional-Inversion](https://github.com/Lzxhh/Dual-Conditional-Inversion)

Exploration is crucial in Reinforcement Learning (RL) as it enables the agent to understand the environment for better decision-making. Existing exploration methods fall into two paradigms: active exploration, which injects stochasticity into the policy but struggles in high-dimensional environments, and passive exploration, which manages the replay buffer to prioritize under-explored regions but lacks sample diversity. To address the limitation in passive exploration, we propose Modelic Generative Exploration (MoGE), which augments exploration through the generation of under-explored critical states and synthesis of dynamics-consistent experiences. MoGE consists of two components: (1) a diffusion generator for critical states under the guidance of entropy and TD error, and (2) a one-step imagination world model for constructing critical transitions for agent learning. Our method is simple to implement and seamlessly integrates with mainstream off-policy RL algorithms without structural modifications. Experiments on OpenAI Gym and DeepMind Control Suite demonstrate that MoGE, as an exploration augmentation, significantly enhances efficiency and performance in complex tasks.

Transformer-based large language models (LLMs) cache context as key-value (KV) pairs during inference. As context length grows, KV cache sizes expand, leading to substantial memory overhead and increased attention latency. This paper introduces \textit{KVzip}, a query-agnostic KV cache eviction method enabling effective reuse of compressed KV caches across diverse queries. KVzip quantifies the importance of a KV pair using the underlying LLM to reconstruct original contexts from cached KV pairs, subsequently evicting pairs with lower importance. Extensive empirical evaluations demonstrate that KVzip reduces KV cache size by $3$-$4\times$ and FlashAttention decoding latency by approximately $2\times$, with negligible performance loss in question-answering, retrieval, reasoning, and code comprehension tasks. Evaluations include various models such as LLaMA3.1, Qwen2.5, and Gemma3, with context lengths reaching up to 170K tokens. KVzip significantly outperforms existing query-aware KV eviction methods, which suffer from performance degradation even at a 90\% cache budget ratio under multi-query scenarios.

Prompt engineering is crucial for leveraging the full potential of large language models (LLMs). While automatic prompt optimization offers a scalable alternative to costly manual design, generating effective prompts remains challenging. Existing methods often struggle to stably generate improved prompts, leading to low efficiency, and overlook that prompt optimization easily gets trapped in local optima. Addressing this, we propose GRACE, a framework that integrates two synergistic strategies: Gated Refinement and Adaptive Compression, achieving Efficient prompt optimization. The gated refinement strategy introduces a feedback regulation gate and an update rejection gate, which refine update signals to produce stable and effective prompt improvements. When optimization stagnates, the adaptive compression strategy distills the prompt’s core concepts, restructuring the optimization trace and opening new paths. By strategically introducing information loss through refinement and compression, GRACE delivers substantial gains in performance and efficiency. In extensive experiments on 11 tasks across three practical domains, including BIG-Bench Hard (BBH), domain-specific, and general NLP tasks, GRACE achieves significant average relative performance improvements of 4.7\%, 4.4\% and 2.7\% over state-of-the-art methods, respectively. Further analysis shows that GRACE achieves these gains using only 25\% of the prompt generation budget required by prior methods, highlighting its high optimization efficiency and low computational overhead. Our code is available at https://github.com/Eric8932/GRACE.

The pursuit of efficient and controllable high-quality content generation stands as a pivotal challenge in artificial intelligence-generated content (AIGC). While one-step generators, refined through diffusion distillation techniques, offer excellent generation quality and computational efficiency, adapting them to new control conditions—such as structural constraints, semantic guidelines, or external inputs—poses a significant challenge. Conventional approaches often necessitate computationally expensive modifications to the base model and subsequent diffusion distillation. This paper introduces Noise Consistency Training (NCT), a novel and lightweight approach to directly integrate new control signals into pre-trained one-step generators without requiring access to original training images or retraining the base diffusion model. NCT operates by introducing an adapter module and employs a noise consistency loss in the noise space of the generator. This loss aligns the adapted model's generation behavior across noises that are conditionally dependent to varying degrees, implicitly guiding it to adhere to the new control. This training objective can be interpreted as aligning the adapted generator with the intractable conditional distribution defined by a discriminative model and the one-step generator from moment-matching perspectives. NCT is modular, data-efficient, and easily deployable, relying only on the pre-trained one-step generator and a control signal model. Extensive experiments demonstrate that NCT achieves state-of-the-art controllable generation in a single forward pass, surpassing existing multi-step and distillation-based methods in both generation quality and computational efficiency.

How well do AI systems perform in algorithm engineering for hard optimization problems in domains such as package-delivery routing, crew scheduling, factory production planning, and power-grid balancing? We introduce $\textit{ALE-Bench}$, a new benchmark for evaluating AI systems on score-based algorithmic programming contests. Drawing on real tasks from the AtCoder Heuristic Contests, ALE-Bench presents optimization problems that are computationally hard and admit no known exact solution. Unlike short-duration, pass/fail coding benchmarks, ALE-Bench encourages iterative solution refinement over long time horizons. Our software framework supports interactive agent architectures that leverage test-run feedback and visualizations. Our evaluation of frontier LLMs revealed that while they demonstrate high performance on specific problems, a notable gap remains compared to humans in terms of consistency across problems and long-horizon problem-solving capabilities. This highlights the need for this benchmark to foster future AI advancements.

The increasing demand for long-context generation has made the KV cache in large language models a bottleneck in memory consumption. Quantizing the cache to lower bit widths is an effective way to reduce memory costs; however, previous methods struggle with key cache quantization due to outliers, resulting in suboptimal performance. We propose a novel quantization approach PolarQuant, which provides a new perspective for key cache quantization and efficiently addresses the outlier dilemma. We observe that the distribution of the key states reveals well-structured patterns under polar transformation. Outliers generally appear in only one of the two dimensions, which are rotated together by a specific angle when rotary position embeddings are applied. When represented as two-dimensional vectors, these dimensions exhibit well-organized patterns, with radii and angles smoothly distributed in polar space. This alleviates the channel-wise outliers, making them well-suited for key cache quantization. PolarQuant divides key vectors into groups of two-dimensional sub-vectors, encoding them as the quantized radius and the polar angle, rather than quantizing original key vectors directly. PolarQuant achieves the superior efficiency in KV cache quantization and accelerates the decoding process by turning the query-key inner product into a table lookup, all while maintaining the downstream performance of full-precision models. Our code is available at https://github.com/ericshwu/PolarQuant.

We present a neural network structure, FramePack, to train next-frame (or next-frame-section) prediction models for video generation. FramePack compresses input frame contexts with frame-wise importance so that more frames can be encoded within a fixed context length, with more important frames having longer contexts. The frame importance can be measured using time proximity, feature similarity, or hybrid metrics. The packing method allows for inference with thousands of frames and training with relatively large batch sizes. We also present drift prevention methods to address observation bias (error accumulation), including early-established endpoints, adjusted sampling orders, and discrete history representation. Ablation studies validate the effectiveness of the anti-drifting methods in both single-directional video streaming and bi-directional video generation. Finally, we show that existing video diffusion models can be finetuned with FramePack, and analyze the differences between different packing schedules.

While large language models (LLMs) demonstrate strong reasoning capabilities utilizing reinforcement learning (RL) with verifiable reward, whether large vision-language models (VLMs) can directly inherit such capabilities through similar post-training strategies remains underexplored. In this work, we conduct a systematic compositional probing study to evaluate whether current VLMs trained with RL or other post-training strategies can compose capabilities across modalities or tasks under out-of-distribution conditions. We design a suite of diagnostic tasks that train models on unimodal tasks or isolated reasoning skills, and evaluate them on multimodal, compositional variants requiring skill integration. Through comparisons between supervised fine-tuning (SFT) and RL-trained models, we identify three key findings: (1) RL-trained models consistently outperform SFT on compositional generalization, demonstrating better integration of learned skills; (2) although VLMs achieve strong performance on individual tasks, they struggle to generalize compositionally under cross-modal and cross-task scenarios, revealing a significant gap in current training strategies; (3) enforcing models to explicitly describe visual content before reasoning (e.g., caption-before-thinking), along with rewarding progressive vision-to-text grounding, yields notable gains. It highlights two essential ingredients for improving compositionality in VLMs: visual-to-text alignment and accurate visual grounding. Our findings shed light on the current limitations of RL-based reasoning VLM training and provide actionable insights toward building models that reason compositionally across modalities and tasks.