NeurIPS 2025 Papers

Understanding the dynamic behavior of proteins is critical to elucidating their functional mechanisms, yet generating realistic, temporally coherent trajectories of protein ensembles remains a significant challenge. In this work, we introduce a novel hierarchical autoregressive framework for modeling protein dynamics that leverages the intrinsic multi-scale organization of molecular motions. Unlike existing methods that focus on generating static conformational ensembles or treat dynamic sampling as an independent process, our approach characterizes protein dynamics as a Markovian process. The framework employs a two-scale architecture: a low-resolution model captures slow, collective motions driving major conformational transitions, while a high-resolution model generates detailed local fluctuations conditioned on these large-scale movements. This hierarchical design ensures that the causal dependencies inherent in protein dynamics are preserved, enabling the generation of temporally coherent and physically realistic trajectories. By bridging high-level biophysical principles with state-of-the-art generative modeling, our approach provides an efficient framework for simulating protein dynamics that balances computational efficiency with physical accuracy.

Recent advances in generative models trained on large-scale datasets have enabled high-quality 3D synthesis across various domains. However, these models also raise critical privacy concerns. Unlike 2D image synthesis, where risks typically involve the leakage of visual features or identifiable patterns, 3D generation introduces additional challenges, as reconstructed shapes, textures, and spatial structures may inadvertently expose proprietary designs, biometric data, or other sensitive geometric information. This paper presents the first exploration of machine unlearning in 3D generation tasks. We investigate different unlearning objectives, including re-targeting and partial unlearning, and propose a novel framework that does not require full supervision of the unlearning target. To enable a more efficient unlearning process, we introduce a skip-acceleration mechanism, which leverages the similarity between multi-view generated images to bypass redundant computations. By establishing coherence across viewpoints during acceleration, our framework not only reduces computation but also enhances unlearning effectiveness, outperforming the non-accelerated baseline in both accuracy and efficiency. We conduct extensive experiments on the typical 3D generation models (Zero123 and Zero123XL), demonstrating that our approach achieves a 30\% speedup, while effectively unlearning target concepts without compromising generation quality. Our framework provides a scalable and practical solution for privacy-preserving 3D generation, ensuring responsible AI deployment in real-world applications. The code is available at: https://github.com/sxxsxw/Fast-3D-Unlearn-with-Skip-acceleration

Agent systems based on large language models (LLMs) have shown great potential in complex reasoning tasks, but building efficient and generalizable workflows remains a major challenge. Most existing approaches rely on manually designed processes, which limits their adaptability across different tasks. While a few methods attempt automated workflow generation, they are often tied to specific datasets or query types and make limited use of intermediate feedback, reducing system robustness and reasoning depth. Moreover, their operations are typically predefined and inflexible. To address these limitations, we propose **DyFlow**, a dynamic workflow generation framework that adaptively constructs and adjusts reasoning procedures based on task requirements and real-time intermediate feedback, thereby enhancing cross-task generalization. DyFlow consists of two core components: a designer and an executor. The designer decomposes complex problems into a sequence of sub-goals defined by high-level objectives and dynamically plans the next steps based on intermediate outputs and feedback. These plans are then carried out by the executor, which executes each operation using dynamic operators with context-aware parameterization, enabling flexible and semantically grounded reasoning. We systematically evaluate DyFlow across diverse domains, including social reasoning, biomedical tasks, mathematical problem solving, and code generation. Results demonstrate that DyFlow significantly outperforms existing baselines, achieving substantial Pass@k improvements and exhibiting robust generalization across diverse domains.

It is common to reject undesired outputs of Large Language Models (LLMs); however, current methods to do so require an excessive amount of computation to re-sample after a rejection, or distort the distribution of outputs by constraining the output to highly improbable tokens. We present a method, Approximately Aligned Decoding (AprAD), to balance the distortion of the output distribution with computational efficiency, inspired by algorithms from the speculative decoding literature. AprAD allows for the generation of long sequences of text with difficult-to-satisfy constraints, while amplifying low probability outputs much less compared to existing methods. We show through a series of experiments that the task-specific performance of AprAD is comparable to methods that do not distort the output distribution, while being much more computationally efficient.

We introduce PartCrafter, the first structured 3D generative model that jointly synthesizes multiple semantically meaningful and geometrically distinct 3D meshes from a single RGB image. Unlike existing methods that either produce monolithic 3D shapes or follow two-stage pipelines, i.e. first segmenting an image and then reconstructing each segment, PartCrafter adopts a unified, compositional generation architecture that does not rely on pre-segmented inputs. Conditioned on a single image, it simultaneously denoises multiple 3D parts, enabling end-to-end part-aware generation of both individual objects and complex multi-object scenes. PartCrafter builds upon a pretrained 3D mesh diffusion transformer (DiT) trained on whole objects, inheriting the pretrained weights, encoder, and decoder, and introduces two key innovations: (1) A compositional latent space, where each 3D part is represented by a set of disentangled latent tokens; (2) A hierarchical attention mechanism that enables structured information flow both within individual parts and across all parts, ensuring global coherence while preserving part-level detail during generation. To support part-level supervision, we curate a new dataset by mining part-level annotations from large-scale 3D object datasets. Experiments show that PartCrafter outperforms existing approaches in generating decomposable 3D meshes, including parts that are not directly visible in input images, demonstrating the strength of part-aware generative priors for 3D understanding and synthesis. Code and training data are released.

Human–AI conversation frequently relies on quoting earlier text—“check it with the formula I just highlighted”—yet today’s large language models (LLMs) lack an explicit mechanism for locating and exploiting such spans. We formalize the challenge as span-conditioned generation, decomposing each turn into the dialogue history, a set of token-offset quotation spans, and an intent utterance. Building on this abstraction, we introduce a quotation-centric data pipeline that automatically synthesizes task-specific dialogues, verifies answer correctness through multi-stage consistency checks, and yields both a heterogeneous training corpus and the first benchmark covering five representative scenarios. To meet the benchmark’s zero-overhead and parameter-efficiency requirements, we propose QuAda, a lightweight training-based method that attaches two bottleneck projections to every attention head, dynamically amplifying or suppressing attention to quoted spans at inference time while leaving the prompt unchanged and updating < 2.8% of backbone weights. Experiments across models show that QuAda is suitable for all scenarios and generalizes to unseen topics, offering an effective, plug-and-play solution for quotation-aware dialogue.

In this work, we address the task of table image to LaTeX code generation, with the goal of automating the reconstruction of high-quality, publication-ready tables from visual inputs. A central challenge of this task lies in accurately handling complex tables—those with large sizes, deeply nested structures, and semantically rich or irregular cell content—where existing methods often fail. We begin with a comprehensive analysis, identifying key challenges and highlighting the limitations of current evaluation protocols. To overcome these issues, we propose a reinforced multimodal large language model (MLLM) framework, where a pre-trained MLLM is fine-tuned on a large-scale table-to-LaTeX dataset. To further improve generation quality, we introduce a dual-reward reinforcement learning strategy based on Group Relative Policy Optimization (GRPO). Unlike standard approaches that optimize purely over text outputs, our method incorporates both a structure-level reward on LaTeX code and a visual fidelity reward computed from rendered outputs, enabling direct optimization of the visual output quality. We adopt a hybrid evaluation protocol combining TEDS-Structure and CW-SSIM, and show that our method achieves state-of-the-art performance, particularly on structurally complex tables, demonstrating the effectiveness and robustness of our approach.

Large language models (LLMs) have demonstrated remarkable progress in generating functional code, leading to numerous AI-based coding program tools. However, their reliance on the perplexity objective during both training and inference primarily emphasizes functionality, often at the expense of efficiency—an essential consideration for real-world coding tasks. Perhaps interestingly, we observed that well-trained LLMs inherently possess knowledge about code efficiency, but this potential remains underutilized with standard decoding approaches. To address this, we design strategic prompts to activate the model’s embedded efficiency understanding, effectively using LLMs as \textit{efficiency critiques} to guide code generation toward higher efficiency without sacrificing—and sometimes even improving—functionality, all without the need for costly real code execution. Extensive experiments on benchmark datasets (EffiBench, HumanEval+) across multiple representative code models demonstrate up to a 70.6\% reduction in average execution time and a 13.6\% decrease in maximum memory usage, highlighting the computational efficiency and practicality of our approach compared to existing alternatives.

Instance-dependent Partial Label Learning (ID-PLL) aims to learn a multi-class predictive model given training instances annotated with candidate labels related to features, among which correct labels are hidden fixed but unknown. The previous works involve leveraging the identification capability of the training model itself to iteratively refine supervision information. However, these methods overlook a critical aspect of ID-PLL: within the original label space, the model may fail to distinguish some incorrect candidate labels that are strongly correlated with features from correct labels. This leads to poor-quality supervision signals and creates a bottleneck in the training process. In this paper, we propose to leverage reduction-based pseudo-labels to alleviate the influence of incorrect candidate labels and train our predictive model to overcome this bottleneck. Specifically, reduction-based pseudo-labels are generated by performing weighted aggregation on the outputs of a multi-branch auxiliary model, with each branch trained in a label subspace that excludes certain labels. This approach ensures that each branch explicitly avoids the disturbance of the excluded labels, allowing the pseudo-labels provided for instances troubled by these excluded labels to benefit from the unaffected branches. Theoretically, we demonstrate that reduction-based pseudo-labels exhibit greater consistency with the Bayes optimal classifier compared to pseudo-labels directly generated from the training predictive model.