NeurIPS 2025 Papers

Graph neural networks have shown promising results in weather forecasting, which is critical for human activity such as agriculture planning and extreme weather preparation. However, most studies focus on finite and local areas for training, overlooking the influence of broader areas and limiting their ability to generalize effectively. Thus, in this work, we study global weather forecasting that is irregularly distributed and dynamically varying in practice, requiring the model to generalize to unobserved locations. To address such challenges, we propose a general Mesh Interpolation Graph Network (MIGN) that models the irregular weather station forecasting, consisting of two key designs: (1) learning spatially irregular data with regular mesh interpolation network to align the data; (2) leveraging parametric spherical harmonics location embedding to further enhance spatial generalization ability. Extensive experiments on an up-to-date observation dataset show that MIGN significantly outperforms existing data-driven models. Besides, we show that MIGN has spatial generalization ability, and is capable of generalizing to previously unseen stations.

In recent years, large language models with Transformer architecture as the core have made breakthrough progress in many fields. At the same time, there are also some weaknesses in the large language model that have prompted people to reflect, among which the most fundamental one is the reflection on the Transformer architecture. The Transformer architecture has high parallelism and can fully utilize the computing power of GPUs, thus replacing models such as LSTM in the past few years. However, high parallelism is not a free lunch, as it fundamentally limits the performance of models. Especially, the problems that logarithmic precision Transformer architecture can solve are strictly limited to the $TC^0$. And there are many important issues that are usually considered out of $TC^0$, such as Python code evaluation, entity tracking, chess, and other state tracking tasks. Meanwhile, some recent state space methods based on Delta Rule have been able to break through the $TC^0$ architecture, but they are limited by fixed size state spaces and perform poorly on many tasks. To this end, we have re-examined the Transformer from the perspective of a state space with kernel functions and propose an improved Transformer called DeltaFormer. We have theoretically and practically demonstrated that the proposed new architecture can break through the limitation of the inherent $TC^0$ expressivity of Transformers and verified that it is not weaker than standard Transformer in language modeling tasks. We hope our work can provide inspiration for designing more expressive models.

Recent results show that modern Large Language Models (LLM) are indeed capable of understanding and answering questions about structured data such as graphs. This new paradigm can lead to solutions that require less supervision while, at the same time, providing a model that can generalize and answer questions beyond the training labels. Existing proposals often use some description of the graph to create an ``augmented'' prompt fed to the LLM. For a chosen class of graphs, if a well-tailored graph encoder is deployed to play together with a pre-trained LLM, the model can answer graph-related questions well. Existing solutions to graph-based prompts range from graph serialization to graph transformers. In this work, we show that the use of a parameter-free graph encoder based on Fock space representations, a concept borrowed from mathematical physics, is remarkably versatile in this problem setting. The simple construction, inherited directly from the theory with a few small adjustments, can provide rich and informative graph encodings, for a wide range of different graphs. We investigate the use of this idea for prefix-tuned prompts leveraging the capabilities of a pre-trained, frozen LLM. The modifications lead to a model that can answer graph-related questions -- from simple graphs to proteins to hypergraphs -- effectively and with minimal, if any, adjustments to the architecture. Our work significantly simplifies existing solutions and generalizes well to multiple different graph-based structures effortlessly.

Reinforcement learning (RL) is increasingly applied to real-world problems involving complex and structured decisions, such as routing, scheduling, and assortment planning. These settings challenge standard RL algorithms, which struggle to scale, generalize, and exploit structure in the presence of combinatorial action spaces. We propose Structured Reinforcement Learning (SRL), a novel actor-critic paradigm that embeds combinatorial optimization-layers into the actor neural network. We enable end-to-end learning of the actor via Fenchel-Young losses and provide a geometric interpretation of SRL as a primal-dual algorithm in the dual of the moment polytope. Across six environments with exogenous and endogenous uncertainty, SRL matches or surpasses the performance of unstructured RL and imitation learning on static tasks and improves over these baselines by up to 92\% on dynamic problems, with improved stability and convergence speed.

Securing software supply chains is a growing challenge due to the inadequacy of existing datasets in capturing the complexity of next-gen attacks, such as multiphase malware execution, remote access activation, and dynamic payload generation. Existing datasets, which rely on metadata inspection and static code analysis, are inadequate for detecting such attacks. This creates a critical gap because these datasets do not capture what happens during and after a package is installed. To address this gap, we present QUT-DV25, a dynamic analysis dataset specifically designed to support and advance research on detecting and mitigating supply chain attacks within the Python Package Index (PyPI) ecosystem. This dataset captures install and post-install-time traces from 14,271 Python packages, of which 7,127 are malicious. The packages are executed in an isolated sandbox environment using an extended Berkeley Packet Filter (eBPF) kernel and user-level probes. It captures 36 real-time features, that includes system calls, network traffic, resource usages, directory access patterns, dependency logs, and installation behaviors, enabling the study of next-gen attack vectors. ML analysis using the QUT-DV25 dataset identified four malicious PyPI packages previously labeled as benign, each with thousands of downloads. These packages deployed covert remote access and multi-phase payloads, were reported to PyPI maintainers, and subsequently removed. This highlights the practical value of QUT-DV25, as it outperforms reactive, metadata, and static datasets, offering a robust foundation for developing and benchmarking advanced threat detection within the evolving software supply chain ecosystem.

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation---a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates promising improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

Pose-free Neural Radiance Field (NeRF) aims at novel view synthesis (NVS) without relying on accurate poses, exhibiting significant practical value. Image and LiDAR point cloud are two pivotal modalities in autonomous driving scenarios. While demonstrating impressive performance, single-modality pose-free NeRFs often suffer from local optima due to the limited geometric information provided by dense image textures or the sparse, textureless nature of point clouds. Although prior methods have explored the complementary strengths of both modalities, they have only leveraged inherently sparse point clouds for discrete, non-pixel-wise depth supervision, and are limited to NVS of images. As a result, a Multimodal Unified Pose-free framework remains notably absent. In light of this, we propose MUP, a pose-free framework for LiDAR-Camera joint NVS in large-scale scenes. This unified framework enables continuous depth supervision for image reconstruction using LiDAR-Fields rather than discrete point clouds. By leveraging multimodal inputs, pose optimization receives gradients from the rendering loss of point cloud geometry and image texture, thereby alleviating the issue of local optima commonly encountered in single-modality pose-free tasks. Moreover, to further guide pose optimization of NeRF, we propose a multimodal geometric optimizer that leverages geometric relations from point clouds and photometric regularization from adjacent image frames. Besides, to alleviate the domain gap between modalities, we propose a multimodal-specific coarse-to-fine training approach for unified, compact reconstruction. Extensive experiments on KITTI-360 and NuScenes datasets demonstrate MUP's superiority in accomplishing geometry-aware, modality-consistent, and pose-free 3D reconstruction.

Image generation requires intensive computations and faces challenges due to long latency. Exploiting redundancy in the input images and intermediate representations throughout the neural network pipeline is an effective way to accelerate image generation. Token merging (ToMe) exploits similarities among input tokens by clustering them and merges similar tokens into one, thus significantly reducing the number of tokens that are fed into the transformer block. This work introduces Fourier Token Merging, a new method for understanding and capitalizing frequency domain for efficient image generation. By introducing frequency token merging, we find that transforming the token into the frequency domain representation for clustering can better exert the ability of clustering based on the underlying redundancy after de-correlation. Through analytical and empirical studies, we demonstrate the benefits of using Fourier clustering over the original time domain clustering. We experimented fourier token merging on the stable diffusion model, and the results show up to 25\% reduction in latency without impairing image quality. The code is available at https://github.com/Fred1031/Fourier-Token-Merging.

3D reconstruction of indoor and urban environments is a prominent research topic with various downstream applications. However, existing geometric priors for addressing low-texture regions in indoor and urban settings often lack global consistency. Moreover, Gaussian Splatting and implicit SDF fields often suffer from discontinuities or exhibit computational inefficiencies, resulting in a loss of detail. To address these issues, we propose an Atlanta-world guided implicit-structured Gaussian Splatting that achieves smooth indoor and urban scene reconstruction while preserving high-frequency details and rendering efficiency. By leveraging the Atlanta-world model, we ensure the accurate surface reconstruction for low-texture regions, while the proposed novel implicit-structured GS representations provide smoothness without sacrificing efficiency and high-frequency details. Specifically, we propose a semantic GS representation to predict the probability of all semantic regions and deploy a structure plane regularization with learnable plane indicators for global accurate surface reconstruction. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches in both indoor and urban scenes, delivering superior surface reconstruction quality.

Diffusion Transformers (DiT) have become the de-facto model for generating high-quality visual content like videos and images. A huge bottleneck is the attention mechanism where complexity scales quadratically with resolution and video length. One logical way to lessen this burden is sparse attention, where only a subset of tokens or patches are included in the calculation. However, existing techniques fail to preserve visual quality at extremely high sparsity levels and might even incur non-negligible compute overheads. To address this concern, we propose Re-ttention, which implements very high sparse attention for visual generation models by leveraging the temporal redundancy of Diffusion Models to overcome the probabilistic normalization shift within the attention mechanism. Specifically, Re-ttention reshapes attention scores based on the prior softmax distribution history in order to preserve the visual quality of the full quadratic attention at very high sparsity levels. Experimental results on T2V/T2I models such as CogVideoX and the PixArt DiTs demonstrate that Re-ttention requires as few as 3.1% of the tokens during inference, outperforming contemporary methods like FastDiTAttn, Sparse VideoGen and MInference.

3D Gaussian Splatting (3DGS) has emerged as a powerful representation for real-time, high-performance rendering, enabling a wide range of applications. However, representing 3D scenes with numerous explicit Gaussian primitives imposes significant storage and memory overhead. Recent studies have shown that high-quality rendering can be achieved with a substantially reduced number of Gaussians when represented with high-precision attributes. Nevertheless, existing 3DGS compression methods still rely on a relatively large number of Gaussians, focusing primarily on attribute compression. This is because a smaller set of Gaussians becomes increasingly sensitive to lossy attribute compression, leading to severe quality degradation. Since the number of Gaussians is directly tied to computational costs, it is essential to reduce the number of Gaussians effectively rather than only optimizing storage. In this paper, we propose Optimized Minimal Gaussians representation (OMG), which significantly reduces storage while using a minimal number of primitives. First, we determine the distinct Gaussian from the near ones, minimizing redundancy without sacrificing quality. Second, we propose a compact and precise attribute representation that efficiently captures both continuity and irregularity among primitives. Additionally, we propose a sub-vector quantization technique for improved irregularity representation, maintaining fast training with a negligible codebook size. Extensive experiments demonstrate that OMG reduces storage requirements by nearly 50% compared to the previous state-of-the-art and enables 600+ FPS rendering while maintaining high rendering quality. Our source code is available at https://maincold2.github.io/omg/.

Despite their superior performance on a wide range of domains, large language models (LLMs) remain vulnerable to misuse for generating harmful content, a risk that has been further amplified by various jailbreak attacks. Existing jailbreak attacks mainly follow sequential logic, where LLMs understand and answer each given task one by one. However, concurrency, a natural extension of the sequential scenario, has been largely overlooked. In this work, we first propose a word-level method to enable task concurrency in LLMs, where adjacent words encode divergent intents. Although LLMs maintain strong utility in answering concurrent tasks, which is demonstrated by our evaluations on mathematical and general question-answering benchmarks, we notably observe that combining a harmful task with a benign one significantly reduces the probability of it being filtered by the guardrail, showing the potential risks associated with concurrency in LLMs. Based on these findings, we introduce $\texttt{JAIL-CON}$, an iterative attack framework that $\underline{\text{JAIL}}$breaks LLMs via task $\underline{\text{CON}}$currency. Experiments on widely-used LLMs demonstrate the strong jailbreak capabilities of $\texttt{JAIL-CON}$ compared to existing attacks. Furthermore, when the guardrail is applied as a defense, compared to the sequential answers generated by previous attacks, the concurrent answers in our $\texttt{JAIL-CON}$ exhibit greater stealthiness and are less detectable by the guardrail, highlighting the unique feature of task concurrency in jailbreaking LLMs.

Joint-embedding self-supervised learning (SSL) commonly relies on transformations such as data augmentation and masking to learn visual representations, a task achieved by enforcing invariance or equivariance with respect to these transformations applied to two views of an image. This dominant two-view paradigm in SSL often limits the flexibility of learned representations for downstream adaptation by creating performance trade-offs between high-level invariance-demanding tasks such as image classification and more fine-grained equivariance-related tasks. In this work, we propose $\textit{seq-JEPA}$, a world modeling framework that introduces architectural inductive biases into joint-embedding predictive architectures to resolve this trade-off. Without relying on dual equivariance predictors or loss terms, seq-JEPA simultaneously learns two architecturally segregated representations: one equivariant to specified transformations and another invariant to them. To do so, our model processes short sequences of different views (observations) of inputs. Each encoded view is concatenated with an embedding of the relative transformation (action) that produces the next observation in the sequence. These view-action pairs are passed through a transformer encoder that outputs an aggregate representation. A predictor head then conditions this aggregate representation on the upcoming action to predict the representation of the next observation. Empirically, seq-JEPA demonstrates strong performance on both equivariant and invariant benchmarks without sacrificing one for the other. Furthermore, it excels at tasks that inherently require aggregating a sequence of observations, such as path integration across actions and predictive learning across eye movements.

Network traffic classification is essential for network management and security. In recent years, deep learning (DL) algorithms have emerged as essential tools for classifying complex traffic. However, they rely heavily on high-quality labeled training data. In practice, traffic data is often noisy due to human error or inaccurate automated labeling, which could render classification unreliable and lead to severe consequences. Although some studies have alleviated the label noise issue in specific scenarios, they are difficult to generalize to general traffic classification tasks due to the inherent semantic complexity of traffic data. In this paper, we propose FlowRefiner, a robust and general traffic classification framework against label noise. FlowRefiner consists of three core components: a traffic semantics-driven noise detector, a confidence-guided label correction mechanism, and a cross-granularity robust classifier. First, the noise detector utilizes traffic semantics extracted from a pre-trained encoder to identify mislabeled flows. Next, the confidence-guided label correction module fine-tunes a label predictor to correct noisy labels and construct refined flows. Finally, the cross-granularity robust classifier learns generalized patterns of both flow-level and packet-level, improving classification robustness against noisy labels. We evaluate our method on four traffic datasets with various classification scenarios across varying noise ratios. Experimental results demonstrate that FlowRefiner mitigates the impact of label noise and consistently outperforms state-of-the-art baselines by a large margin. The code is available at https://github.com/NSSL-SJTU/FlowRefiner.

The theoretical understanding of self-attention (SA) has been steadily progressing. A prominent line of work studies a class of SA layers that admit an energy function decreased by state updates. While it provides valuable insights into inherent biases in signal propagation, it often relies on idealized assumptions or additional constraints not necessarily present in standard SA. Thus, to broaden our understanding, this work aims to relax these energy constraints and provide an energy-agnostic characterization of inference dynamics by dynamical systems analysis. In more detail, we first consider relaxing the symmetry and single-head constraints traditionally required in energy-based formulations. Next, we show that analyzing the Jacobian matrix of the state is highly valuable when investigating more general SA architectures without necessarily admitting an energy function. It reveals that the normalization layer plays an essential role in suppressing the Lipschitzness of SA and the Jacobian's complex eigenvalues, which correspond to the oscillatory components of the dynamics. In addition, the Lyapunov exponents computed from the Jacobians demonstrate that the normalized dynamics lie close to a critical state, and this criticality serves as a strong indicator of high inference performance. Furthermore, the Jacobian perspective also enables us to develop regularization methods for training and a pseudo-energy for monitoring inference dynamics.

We study a relaxation of the problem of coupling probability distributions — a list of samples is generated from one distribution and an *accept* is declared if any one of these samples is identical to the sample generated from the other distribution. We propose a novel method for generating samples, which extends the Gumbel-max sampling suggested in Daliri et al. (2025) for coupling probability distributions. We also establish a corresponding lower bound on the acceptance probability, which we call the \emph{list matching lemma}. We next discuss two applications of our setup. First, we develop a new mechanism for multi-draft speculative sampling that is simple to implement and achieves performance competitive with baselines such as SpecTr and SpecInfer across a range of language tasks. Our method also guarantees a certain degree of *drafter invariance* with respect to the output tokens which is not supported by existing schemes. We also provide a theoretical lower bound on the token level acceptance probability. As our second application, we consider distributed lossy compression with side information in a setting where a source sample is compressed and available to multiple decoders, each with independent side information. We propose a compression technique that is based on our generalization of Gumbel-max sampling and show that it provides significant gains in experiments involving synthetic Gaussian sources and the MNIST image dataset.

Inferring synaptic connectivity from neural population activity is a fundamental challenge in computational neuroscience, complicated by partial observability and mismatches between inference models and true circuit dynamics. In this study, we propose a graph-based neural inference model that simultaneously predicts neural activity and infers latent connectivity by modeling neurons as interacting nodes in a graph. The architecture features two distinct modules: one for learning structural connectivity and another for predicting future spiking activity via a graph neural network (GNN). Our model accommodates unobserved neurons through auxiliary nodes, allowing for inference in partially observed circuits. We evaluate this approach using synthetic data generated from ring attractor network models and real spike recordings from head direction cells in mice. Across a wide range of conditions, including varying recurrent connectivity, external inputs, and incomplete observations, our model reliably resolves spurious correlations and recovers accurate weight profiles. When applied to real data, the inferred connectivity aligns with theoretical predictions of continuous attractor models. These results highlight the potential of GNN-based models to infer latent neural circuitry through self-supervised structure learning, while leveraging the spike prediction task to flexibly link connectivity and dynamics across both simulated and biological neural systems.

Egocentric hand-object motion generation is crucial for immersive AR/VR and robotic imitation but remains challenging due to unstable viewpoints, self-occlusions, perspective distortion, and noisy ego-motion. Existing methods rely on predefined 3D object priors, limiting generalization to novel objects, which restricts their generalizability to novel objects. Meanwhile, recent multimodal approaches suffer from ambiguous generation from abstract textual cues, intricate pipelines for modeling 3D hand-object correlation, and compounding errors in open-loop prediction. We propose **MEgoHand**, a multimodal framework that synthesizes physically plausible hand-object interactions from egocentric RGB, text, and initial hand pose. MEgoHand introduces a bi-level architecture: a high-level “cerebrum” leverages a vision language model (VLM) to infer motion priors from visual-textual context and a monocular depth estimator for object-agnostic spatial reasoning, while a low-level DiT-based flow-matching policy generates fine-grained trajectories with temporal orthogonal filtering to enhance stability. To address dataset inconsistency, we design a dataset curation paradigm with an Inverse MANO Retargeting Network and Virtual RGB-D Renderer, curating a unified dataset of **3.35M** RGB-D frames, **24K** interactions, and **1.2K** objects. Extensive experiments across **five** in-domain and **two** cross-domain datasets demonstrate the effectiveness of MEgoHand, achieving substantial reductions in wrist translation error (**86.9%**) and joint rotation error (**34.1%**), highlighting its capacity to accurately model fine-grained hand joint structures and generalize robustly across diverse scenarios.

In real-world scenarios, providing user queries with visually enhanced responses can considerably benefit understanding and memory, underscoring the great value of interleaved image-text generation. Despite recent progress, like the visual autoregressive model that unifies text and image processing in a single transformer architecture, generating high-quality interleaved content remains challenging. Moreover, evaluations of these interleaved sequences largely remain underexplored, with existing benchmarks often limited by unimodal metrics that inadequately assess the intricacies of combined image-text outputs. To address these issues, we present RAG-IGBench, a thorough benchmark designed specifically to evaluate the task of Interleaved Generation based on Retrieval-Augmented Generation (RAG-IG) in open-domain question answering. RAG-IG integrates multimodal large language models (MLLMs) with retrieval mechanisms, enabling the models to access external image-text information for generating coherent multimodal content. Distinct from previous datasets, RAG-IGBench draws on the latest publicly available content from social platforms and introduces innovative evaluation metrics that measure the quality of text and images, as well as their consistency. Through extensive experiments with state-of-the-art MLLMs (both open-source and proprietary) on RAG-IGBench, we provide an in-depth analysis examining the capabilities and limitations of these models. Additionally, we validate our evaluation metrics by demonstrating their high correlation with human assessments. Models fine-tuned on RAG-IGBench's training set exhibit improved performance across multiple benchmarks, confirming both the quality and practical utility of our dataset. Our benchmark is available at https://github.com/zry13/RAG-IGBench.