NeurIPS 2025 论文列表

As large language models (LLMs) are increasingly deployed in high-stakes settings, the risk of generating harmful or toxic content remains a central challenge. Post-hoc alignment methods are brittle: once unsafe patterns are learned during pretraining, they are hard to remove. In this work, we present a data-centric pretraining framework that builds safety into the model from the start. Our framework consists of four key steps: (i) Safety Filtering: building a safety classifier to classify webdata into safe and unsafe categories; (ii) Safety Rephrasing: we recontextualize unsafe webdata into safer narratives; (iii) Native Refusal: we synthetically generate pretraining datasets that actively teach models to refuse on unsafe content and the moral reasoning behind it, and (iv) Harmfulness-Tag annotated pretraining: we flag unsafe content during pretraining using a special token, and use it to steer models away from unsafe generations at inference-time. Our safety-pretrained models reduce attack success rates from 38.8% to 8.4% on standard LLM safety benchmarks with no performance degradation on general tasks.

Vision Transformers (ViTs) have become a universal backbone for both image recognition and image generation. Yet their Multi–Head Self–Attention (MHSA) layer still performs a quadratic query–key interaction for \emph{every} token pair, spending the bulk of computation on visually weak or redundant correlations. We introduce \emph{Visual–Contrast Attention} (VCA), a drop-in replacement for MHSA that injects an explicit notion of discrimination while reducing the theoretical complexity from $\mathcal{O}(N^{2}C)$ to $\mathcal{O}(N n C)$ with $n\!\ll\!N$. VCA first distils each head’s dense query field into a handful of spatially pooled \emph{visual–contrast tokens}, then splits them into a learnable \emph{positive} and \emph{negative} stream whose differential interaction highlights what truly separates one region from another. The module adds fewer than $0.3$\,M parameters to a DeiT-Tiny backbone, requires no extra FLOPs, and is wholly architecture-agnostic. Empirically, VCA lifts DeiT-Tiny top-1 accuracy on ImageNet-1K from $72.2\%$ to \textbf{$75.6\%$} (+$3.4$) and improves three strong hierarchical ViTs by up to $3.1$\%, while in class-conditional ImageNet generation it lowers FID-50K by $2.1$ to $5.2$ points across both diffusion (DiT) and flow (SiT) models. Extensive ablations confirm that (i) spatial pooling supplies low-variance global cues, (ii) dual positional embeddings are indispensable for contrastive reasoning, and (iii) combining the two in both stages yields the strongest synergy. VCA therefore offers a simple path towards faster and sharper Vision Transformers. The source code is available at \href{https://github.com/LeapLabTHU/LinearDiff}{https://github.com/LeapLabTHU/LinearDiff}.

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single‑cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling. 28 chemicals, each acting on distinct biological pathways or mechanisms of action (MoAs), were applied to U2-OS cells in two experimental data generation rounds, creating paired sets of replicates that were then profiled independently by scRNA‑seq or Cell Painting. Using scGeneScope, we derive a replicate- and experiment-split treatment identification benchmark simulating MoA discovery under realistic laboratory variability conditions and evaluate unimodal, multimodal, and multiprofile models ranging in complexity from linear approaches to recent foundation models. Multiprofile integration improved performance in both the unimodal and multimodal settings, with gains more consistent in the former. Evaluation of unimodal models for MoA identification demonstrated that recent scRNA-seq foundation models deployed zero-shot were consistently outperformed by classic fit-to-data methods, underscoring the need for careful, realistic benchmarking in machine learning for biology. We release the scGeneScope dataset and benchmarking code to support further research.

Neural PDE solvers offer a powerful tool for modeling complex dynamical systems, but often struggle with error accumulation over long time horizons and maintaining stability and physical consistency. We introduce a multiscale implicit neural emulator that enhances long-term prediction accuracy by conditioning on a hierarchy of lower-dimensional future state representations. Drawing inspiration from the stability properties of numerical implicit time-stepping methods, our approach leverages predictions several steps ahead in time at increasing compression rates for next-timestep refinements. By actively adjusting the temporal downsampling ratios, our design enables the model to capture dynamics across multiple granularities and enforce long-range temporal coherence. Experiments on turbulent fluid dynamics show that our method achieves high short-term accuracy and produces long-term stable forecasts, significantly outperforming autoregressive baselines while adding minimal computational overhead.

Transformer-based Large Language Models (LLMs) have become increasingly important. However, scaling LLMs to longer contexts incurs slow inference speed and high GPU memory consumption for caching key-value (KV) vectors. This paper presents RetrievalAttention, a training-free approach to both accelerate the decoding phase and reduce GPU memory consumption by pre-building KV vector indexes for fixed contexts and maintaining them in CPU memory for efficient retrieval. Unlike conventional KV cache methods, RetrievalAttention integrate approximate nearest neighbor search (ANNS) indexes into attention computation. We observe that off-the-shelf ANNS techniques often fail due to the out-of-distribution (OOD) nature of query and key vectors in attention mechanisms. RetrievalAttention overcomes this with an attention-aware vector index. Our evaluation shows RetrievalAttention achieves near full attention accuracy while accessing only 1-3\% of the data, significantly reducing inference costs. Remarkably, RetrievalAttention enables LLMs with 8B parameters to handle 128K tokens on a single NVIDIA RTX4090 (24GB), achieving a decoding speed of 0.107 seconds per token.

While Classifier-Free Guidance (CFG) has become standard for improving sample fidelity in conditional diffusion models, it can harm diversity and induce memorization by applying constant guidance regardless of whether a particular sample needs correction. We propose **F**eed**B**ack **G**uidance (FBG), which uses a state-dependent coefficient to self-regulate guidance amounts based on need. Our approach is derived from first principles by assuming the learned conditional distribution is linearly corrupted by the unconditional distribution, contrasting with CFG's implicit multiplicative assumption. Our scheme relies on feedback of its own predictions about the conditional signal informativeness to adapt guidance dynamically during inference, challenging the view of guidance as a fixed hyperparameter. The approach is benchmarked on ImageNet512x512, where it significantly outperforms Classifier-Free Guidance and is competitive to Limited Interval Guidance (LIG) while benefitting from a strong mathematical framework. On Text-To-Image generation, we demonstrate that, as anticipated, our approach automatically applies higher guidance scales for complex prompts than for simpler ones and that it can be easily combined with existing guidance schemes such as CFG or LIG.

The success of DeepSeek-R1 demonstrates the immense potential of using reinforcement learning (RL) to enhance LLMs' reasoning capabilities. This paper introduces Retrv-R1, the first R1-style MLLM specifically designed for multimodal universal retrieval, achieving higher performance by employing step-by-step reasoning to produce more accurate retrieval results. We find that directly applying the methods of DeepSeek-R1 to retrieval tasks is not feasible, mainly due to (1) the high computational cost caused by the large token consumption required for multiple candidates with reasoning processes, and (2) the instability and suboptimal results when directly applying RL to train for retrieval tasks. To address these issues, Retrv-R1 introduces an information compression module with a details inspection mechanism, which enhances computational efficiency by reducing the number of tokens while ensuring that critical information for challenging candidates is preserved. Additionally, a new training paradigm is proposed, including an activation stage using a retrieval-tailored synthetic CoT dataset for more effective optimization, followed by RL with a novel curriculum reward to improve both performance and efficiency. Incorporating these novel designs, Retrv-R1 achieves SOTA performance, high efficiency, and strong generalization ability, as demonstrated by extensive experiments across multiple benchmarks and tasks.

Diffusion transformers (DiTs) struggle to generate images at resolutions higher than their training resolutions. The primary obstacle is that the explicit positional encodings (PE), such as RoPE, need extrapolating to unseen positions which degrades performance when the inference resolution differs from training. In this paper, We propose a Length-Extrapolatable Diffusion Transformer (LEDiT) to overcome this limitation. LEDiT needs no explicit PEs, thereby avoiding PE extrapolation. The key innovation of LEDiT lies in the use of causal attention. We demonstrate that causal attention can implicitly encode global positional information and show that such information facilitates extrapolation. We further introduce a locality enhancement module, which captures fine-grained local information to complement the global coarse-grained position information encoded by causal attention. Experimental results on both conditional and text-to-image generation tasks demonstrate that LEDiT supports up to 4× resolution scaling (e.g., from 256$\times$256 to 512$\times$512), achieving better image quality compared to the state-of-the-art length extrapolation methods. We believe that LEDiT marks a departure from the standard RoPE-based methods and offers a promising insight into length extrapolation. Project page: https://shenzhang2145.github.io/ledit/

AI agents today are mostly siloed — they either retrieve and reason over vast amount of digital information and knowledge obtained online; or interact with the physical world through embodied perception, planning and action — but rarely both. This separation limits their ability to solve tasks that require integrated physical and digital intelligence, such as cooking from online recipes, navigating with dynamic map data, or interpreting real-world landmarks using web knowledge. We introduce \textsc{Embodied Web Agents}, a novel paradigm for AI agents that fluidly bridge embodiment and web-scale reasoning. To operationalize this concept, we first develop the \textsc{Embodied Web Agents} task environments, a unified simulation platform that integrates realistic 3D indoor and outdoor environments with functional web interfaces. Building upon this platform, we construct and release the \textsc{Embodied Web Agents} Benchmark, which encompasses a diverse suite of tasks including cooking, navigation, shopping, tourism, and geolocation — all requiring coordinated reasoning across physical and digital realms for systematic assessment of cross-domain intelligence. Experimental results reveal significant performance gaps between state-of-the-art AI systems and human capabilities, establishing both challenges and opportunities at the intersection of embodied cognition and web-scale knowledge access.

Low-Rank Adaptation (LoRA) is a popular method for parameter-efficient fine-tuning (PEFT) of generative models, valued for its simplicity and effectiveness. Despite recent enhancements, LoRA still suffers from a fundamental limitation: overfitting when the bottleneck is widened. It performs best at ranks 32–64, yet its accuracy stagnates or declines at higher ranks, still falling short of full fine-tuning (FFT) performance. We identify the root cause as LoRA’s structural bottleneck, which introduces gradient entanglement to the unrelated input channels and distorts gradient propagation. To address this, we introduce a novel structure, Granular Low-Rank Adaptation (GraLoRA) that partitions weight matrices into sub-blocks, each with its own low-rank adapter. With negligible computational or storage cost, GraLoRA overcomes LoRA’s limitations, effectively increases the representational capacity, and more closely approximates FFT behavior. Experiments on code generation, commonsense reasoning, mathematical reasoning, general language understanding, and image generation benchmarks show that GraLoRA consistently outperforms LoRA and other baselines, achieving up to +8.5\% absolute gain in Pass@1 on HumanEval+. These improvements hold across model sizes and rank settings, making GraLoRA a scalable and robust solution for PEFT.

Multi-view clustering aims to enhance clustering performance by leveraging information from diverse sources. However, its practical application is often hindered by a barrier: the lack of correspondences across views. This paper focuses on the understudied problem of fully incomplete multi-view clustering (FIMC), a scenario where existing methods fail due to their reliance on partial alignment. To address this problem, we introduce the Contrastive Prototype Matching Network (CPMN), a novel framework that establishes a new paradigm for cross-view alignment based on matching high-level categorical structures. Instead of aligning individual instances, CPMN performs a more robust cluster prototype alignment. CPMN first employs a correspondence-free graph contrastive learning approach, leveraging mutual $k$-nearest neighbors (MNN) to uncover intrinsic data structures and establish initial prototypes from entirely unpaired views. Building on the prototypes, we introduce a cross-view prototype graph matching stage to resolve category misalignment and forge a unified clustering structure. Finally, guided by this alignment, we devise a prototype-aware contrastive learning mechanism to promote semantic consistency, replacing the reliance on the initial MNN-based structural similarity. Extensive experiments on benchmark datasets demonstrate that our method significantly outperforms various baselines and ablation variants, validating its effectiveness.

Transformer models have become the dominant backbone for sequence modeling, leveraging self-attention to produce contextualized token representations. These are typically aggregated into fixed-size vectors via pooling operations for downstream tasks. While much of the literature has focused on attention mechanisms, the role of pooling remains underexplored despite its critical impact on model behavior. In this paper, we introduce a theoretical framework that rigorously characterizes the expressivity of Transformer-based models equipped with widely used pooling methods by deriving closed-form bounds on their representational capacity and the ability to distinguish similar inputs. Our analysis extends to different variations of attention formulations, demonstrating that these bounds hold across diverse architectural variants. We empirically evaluate pooling strategies across tasks requiring both global and local contextual understanding, spanning three major modalities: computer vision, natural language processing, and time-series analysis. Results reveal consistent trends in how pooling choices affect accuracy, sensitivity, and optimization behavior. Our findings unify theoretical and empirical perspectives, providing practical guidance for selecting or designing pooling mechanisms suited to specific tasks. This work positions pooling as a key architectural component in Transformer models and lays the foundation for more principled model design beyond attention alone.

Large Multimodal Models (LMMs) have made significant breakthroughs with the advancement of instruction tuning. However, while existing models can understand images and videos at a holistic level, they still struggle with instance-level understanding that requires a more fine-grained comprehension and alignment. Instance-level understanding is crucial for LMMs, as it focuses on the specific elements that we are most interested in. Excitingly, existing works find that the state-of-the-art LMMs exhibit strong instance understanding capabilities when provided with explicit visual cues. Motivated by this, we proposed Inst-IT, a solution to enhance LMMs in Instance understanding via explicit visual prompt Instruction Tuning for instance guidance. Inst-IT consists of a benchmark to diagnose multimodal instance-level understanding, a large-scale instruction-tuning dataset, and a continuous instruction-tuning training paradigm to effectively enhance spatial-temporal instance understanding capabilities of existing LMMs. Experimental results show that, enhanced by Inst-IT, our models not only achieve outstanding performance on Inst-IT-Bench and other instance understanding benchmarks, but also demonstrate significant improvements across various generic image and video understanding benchmarks. This highlights that our method not only boosts instance-level understanding but also strengthens the overall capabilities of generic image and video comprehension.

We propose RoPECraft, a training-free video motion transfer method for diffusion transformers that operates solely by modifying their rotary positional embeddings (RoPE). We first extract dense optical flow from a reference video, and utilize the resulting motion offsets to warp the complex-exponential tensors of RoPE, effectively encoding motion into the generation process. These embeddings are then further optimized during denoising time steps via trajectory alignment between the predicted and target velocities using a flow-matching objective. To keep the output faithful to the text prompt and prevent duplicate generations, we incorporate a regularization term based on the phase components of the reference video’s Fourier transform, projecting the phase angles onto a smooth manifold to suppress high-frequency artifacts. Experiments on benchmarks reveal that RoPECraft outperforms all recently published methods, both qualitatively and quantitatively.

Fine-tuning foundation models has emerged as a powerful approach for generating objects with specific desired properties. Reinforcement learning (RL) provides an effective framework for this purpose, enabling models to generate outputs that maximize a given reward function. However, in many applications such as text generation and drug discovery, it can be suboptimal to optimize using a single reward signal, as multiple evaluation criteria are often necessary. This paper proposes a novel reinforcement learning-based method for fine-tuning foundation models using multiple reward signals. By employing an iterative fine-tuning strategy across these rewards, our approach generalizes state-of-the-art RL-based methods. We further provide a theoretical analysis that offers insights into the performance of multi-reward RL fine-tuning. Experimental results across diverse domains including text, biological sequence, and small molecule generation, demonstrate the effectiveness of the proposed algorithm compared to state-of-the-art baselines.

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising five large-scale, labeled datasets, four of which were generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16), and one curated for new Protein Data Bank (PDB) entries deposited between July 2024 and August 2025. PSBench includes over 1.4 million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench’s utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods. These results highlight PSBench as a valuable resource for advancing EMA research in protein complex modeling. PSBench is publicly available at: https://github.com/BioinfoMachineLearning/PSBench.

People continuously perceive and interact with their surroundings based on underlying intentions that drive their exploration and behaviors. While research in egocentric user and scene understanding has focused primarily on motion and contact-based interaction, forecasting human visual perception itself remains less explored despite its fundamental role in guiding human actions and its implications for AR/VR and assistive technologies. We address the challenge of egocentric 3D visual span forecasting, predicting where a person's visual perception will focus next within their three-dimensional environment. To this end, we propose EgoSpanLift, a novel method that transforms egocentric visual span forecasting from 2D image planes to 3D scenes. EgoSpanLift converts SLAM-derived keypoints into gaze-compatible geometry and extracts volumetric visual span regions. We further combine EgoSpanLift with 3D U-Net and unidirectional transformers, enabling spatio-temporal fusion to efficiently predict future visual span in the 3D grid. In addition, we curate a comprehensive benchmark from raw egocentric multisensory data, creating a testbed with 364.6K samples for 3D visual span forecasting. Our approach outperforms competitive baselines for egocentric gaze anticipation and 3D localization, while achieving comparable results even when projected back onto 2D image planes without additional 2D-specific training.

The Mamba-type neural networks have gained significant popularity recently. To effectively and efficiently establish model architectures of Mamba, it is natural to introduce Neural Architecture Search (NAS) methods into Mamba. However, existing NAS methods tailored for Mamba are training-based, leading to substantial time and computational resource expenditure. To address this issue, and considering that Mamba2 is an improved version of the original Mamba, we propose a training-free NAS method specifically designed for Mamba2. Based on rank collapse in stacked State Space Duality (SSD) blocks, we design a proxy that only requires the computation of the transformation matrix and its gradient between two tensors within the network. Additionally, we develop a corresponding search space and introduce a novel approach for determining adjustable hyperparameter ranges. Experimental results show that our method outperforms all existing training-free NAS approaches in terms of both ranking correlation and the performance of search results for Mamba2 architecture. To the best of our knowledge, this is the first training-free NAS method designed for Mamba-type architectures. Our codes are available at https://github.com/fanyi-plus/tf-nas.

Private large language model (LLM) inference based on cryptographic primitives offers a promising path towards privacy-preserving deep learning. However, existing frameworks only support dense LLMs like LLaMA-1 and struggle to scale to mixture-of-experts (MoE) architectures. The key challenge comes from securely evaluating the dynamic routing mechanism in MoE layers, which may reveal sensitive input information if not fully protected. In this paper, we propose CryptoMoE, the first framework that enables private, efficient, and accurate inference for MoE-based models. CryptoMoE balances expert loads to protect expert routing information and proposes novel protocols for secure expert dispatch and combine. CryptoMoE also develops a confidence-aware token selection strategy and a batch matrix multiplication protocol to improve accuracy and efficiency further. Extensive experiments on DeepSeekMoE-16.4B, OLMoE-6.9B, and QWenMoE-14.3B show that CryptoMoE achieves $2.8\sim3.5\times$ end-to-end latency reduction and $3\sim6\times$ communication reduction over a dense baseline with minimum accuracy loss. We also adapt CipherPrune (ICLR'25) for MoE inference and demonstrate CryptoMoE can reduce the communication by up to $4.3 \times$.