NeurIPS 2025 论文列表

Recent advances in radiance fields and novel view synthesis enable creation of realistic digital twins from photographs. However, current methods struggle with flat, texture-less surfaces, creating uneven and semi-transparent reconstructions, due to an ill-conditioned photometric reconstruction objective. Surface reconstruction methods solve this issue but sacrifice visual quality. We propose a novel hybrid 2D/3D representation that jointly optimizes constrained planar (2D) Gaussians for modeling flat surfaces and freeform (3D) Gaussians for the rest of the scene. Our end-to-end approach dynamically detects and refines planar regions, improving both visual fidelity and geometric accuracy. It achieves state-of-the-art depth estimation on ScanNet++ and ScanNetv2, and excels at mesh extraction without overfitting to a specific camera model, showing its effectiveness in producing high-quality reconstruction of indoor scenes.

Hitting times provide a fundamental measure of distance in random processes, quantifying the expected number of steps for a random walk starting at node $u$ to reach node $v$. They have broad applications across domains such as network centrality analysis, ranking and recommendation systems, and epidemiology. In this work, we develop local algorithms for estimating hitting times between a pair of vertices $u,v$ without accessing the full graph, overcoming scalability issues of prior global methods. Our first algorithm uses the key insight that hitting time computations can be truncated at the meeting time of two independent random walks from $u$ and $v$. This leads to an efficient estimator analyzed via the Kronecker product graph and Markov Chain Chernoff bounds. We also present an algorithm extending the work of Peng et al. [2021] that introduces a novel adaptation of the spectral cutoff technique to account for the asymmetry of hitting times. This adaptation captures the directionality of the underlying random walk and requires non-trivial modifications to ensure accuracy and efficiency. In addition to the algorithmic upper bounds, we also provide tight asymptotic lower bounds. Finally, we reveal a connection between hitting time estimation and distribution testing, and we validate our algorithms using experiments on both real and synthetic data.

Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods, though effective for small molecules, only model the single unit of polymers and fail to produce consistent vector representations for the true polymer structure with varying numbers of units. To address this challenge, we introduce Graph Repetition Invariance (GRIN), a novel method to learn polymer representations that are invariant to the number of repeating units in their graph representations. GRIN integrates a graph-based maximum spanning tree alignment with repeat-unit augmentation to ensure structural consistency. We provide theoretical guarantees for repetition‐invariance from both model and data perspectives, demonstrating that three repeating units are the minimal augmentation required for optimal invariant representation learning. GRIN outperforms state-of-the-art baselines on both homopolymer and copolymer benchmarks, learning stable, repetition-invariant representations that generalize effectively to polymer chains of unseen sizes.

Augmented Large Language Models (LLMs) enhance standalone LLMs by integrating external data sources through API calls. In interactive applications, efficient scheduling is crucial for maintaining low request completion times, directly impacting user engagement. However, these augmentations introduce new scheduling challenges: the size of augmented requests (in tokens) no longer correlates proportionally with execution time, making traditional size-based scheduling algorithms like Shortest Job First less effective. Additionally, requests may require different handling during API calls, which must be incorporated into scheduling. This paper presents MARS, a novel inference framework that optimizes augmented LLM latency by explicitly incorporating system- and application-level considerations into scheduling. MARS introduces a predictive, memory-aware scheduling approach that integrates API handling and request prioritization to minimize completion time. We implement MARS on top of vLLM and evaluate its performance against baseline LLM inference systems, demonstrating improvements in end-to-end latency by 27%-85% and reductions in TTFT by 4%-96% compared to the existing augmented-LLM system, with even greater gains over vLLM. Our implementation is available online.

Masked Graph Autoencoders (MGAEs) have gained significant attention recently. Their proxy tasks typically involve random corruption of input graphs followed by reconstruction. However, in the molecular domain, two main issues arise: the predetermined mask ratio and reconstruction objectives can lead to suboptimal performance or negative transfer due to overly simplified or complex tasks, and these tasks may deviate from chemical priors. To tackle these challenges, we propose Dynamic and Chemical Constraints (DyCC) for MGAEs. This includes a masking strategy called GIBMS, which preserves essential semantic information during graph masking while adaptively adjusting the mask ratio and content for each molecule. Additionally, we introduce a Soft Label Generator (SLG) that reconstructs masked tokens as learnable prototypes (soft labels) rather than hard labels. These components adhere to chemical constraints and allow dynamic variation of proxy tasks during training. We integrate the model-agnostic DyCC into various MGAEs and conduct comprehensive experiments, demonstrating significant performance improvements. Our code is available at \url{https://github.com/forever-ly/DyCC}.

Detecting structural change in dynamic network data has wide-ranging applications. Existing approaches typically divide the data into time bins, extract network features within each bin, and then compare these features over time. This introduces an inherent tradeoff between temporal resolution and the statistical stability of the extracted features. Despite this tradeoff, reminiscent of time–frequency tradeoffs in signal processing, most methods rely on a \emph{fixed temporal resolution}. Choosing an appropriate resolution parameter is typically difficult, and can be especially problematic in domains like cybersecurity, where anomalous behavior may emerge at multiple time scales. We address this challenge by proposing ANIE ($\textbf{A}$daptive $\textbf{N}$etwork $\textbf{I}$ntensity $\textbf{E}$stimation), a multi-resolution framework designed to automatically identify the time scales at which network structure evolves, enabling the joint detection of both rapid and gradual changes. Modeling interactions as Poisson processes, our method proceeds in two steps: (1) estimating a low-dimensional subspace of node behavior, and (2) deriving a set of novel *empirical affinity coefficients* that measure change in interaction intensity between latent factors and support statistical testing for structural change across time scales. We provide theoretical guarantees for subspace estimation and the asymptotic behavior of the affinity coefficients, enabling model-based change detection. Experiments on synthetic networks show that ANIE adapts to the appropriate time resolution, and is able to capture sharp structural changes while remaining robust to noise. Furthermore, applications to real-world data showcase the practical benefits of ANIE’s multiresolution approach to detecting structural change over fixed resolution methods. An open-source implementation of the method is available at [https://github.com/aida-ugent/anie].

The optimal transport (OT) map is a geometry-driven transformation between high-dimensional probability distributions which underpins a wide range of tasks in statistics, applied probability, and machine learning. However, existing statistical theory for OT map estimation is quite restricted, hinging on Brenier's theorem (quadratic cost, absolutely continuous source) to guarantee existence and uniqueness of a deterministic OT map, on which various additional regularity assumptions are imposed to obtain quantitative error bounds. In many real‐world problems these conditions fail or cannot be certified, in which case optimal transportation is possible only via stochastic maps that can split mass. To broaden the scope of map estimation theory to such settings, this work introduces a novel metric for evaluating the transportation quality of stochastic maps. Under this metric, we develop computationally efficient map estimators with near-optimal finite-sample risk bounds, subject to easy-to-verify minimal assumptions. Our analysis further accommodates common forms of adversarial sample contamination, yielding estimators with robust estimation guarantees. Empirical experiments are provided which validate our theory and demonstrate the utility of the proposed framework in settings where existing theory fails. These contributions constitute the first general-purpose theory for map estimation, compatible with a wide spectrum of real-world applications where optimal transport may be intrinsically stochastic.

Over the past decades, pansharpening has contributed greatly to numerous remote sensing applications, with methods evolving from theoretically grounded models to deep learning approaches and their hybrids. Though promising, existing methods rarely address pansharpening through the lens of underlying physical imaging processes. In this work, we revisit the spectral imaging mechanism and propose a novel physics‐informed neural operator framework for pansharpening, termed PINO, which faithfully models the end‐to‐end electro‐optical sensor process. Specifically, PINO operates as: (1) First, a spatial-spectral encoder pair is introduced to aggregate multi-granularity high-resolution panchromatic (PAN) and low-resolution multispectral (LRMS) features. (2) Subsequently, an iterative neural integral process utilizes these fused spatial-spectral characteristics to learn a continuous radiance field $L_i(x, y, \lambda)$ over spatial coordinates and wavelength, effectively emulating band-wise spectral integration. (3) Finally, the learned radiance field is modulated by the sensor’s spectral responsivity $R_b(\lambda)$ to produce physically consistent spatial–spectral fusion products. This physics-grounded fusion paradigm offers a principled solution for reconstructing high-resolution multispectral and hyperspectral images in accordance with sensor imaging physics, effectively harnessing the unique advantages of spectral data to better uncover real-world characteristics. Experiments on multiple benchmark datasets show that our method surpasses state-of-the-art fusion algorithms, achieving reduced spectral aberrations and finer spatial textures. Furthermore, extension to hyperspectral (HS) data demonstrates its generalizability and universality. The code will be available upon potential acceptance.

Kernel ridge regression (KRR) is a foundational tool in machine learning, with recent work emphasizing its connections to neural networks. However, existing theory primarily addresses the i.i.d. setting, while real-world data often exhibits structured dependencies - particularly in applications like denoising score learning where multiple noisy observations derive from shared underlying signals. We present the first systematic study of KRR generalization for non-i.i.d. data with signal-noise causal structure, where observations represent different noisy views of common signals. Under standard spectral decay assumptions, we develop a novel blockwise decomposition method that enables precise concentration analysis for dependent data. Using this technique, we derive excess risk bounds for KRR that explicitly depend on: (1) the kernel spectrum, (2) causal structure parameters, and (3) sampling mechanisms (including relative sample sizes for signals and noises). We further apply our results to denoising score learning, establishing generalization guarantees and providing principled guidance for sampling noisy data points. This work advances KRR theory while providing practical tools for analyzing dependent data in modern machine learning applications.

Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising methods rely on oversimplied molecular dynamics that assume atomic motions to be isotropic and homoscedastic. To address these limitations, we propose a novel denoising framework AniDS: Anisotropic Variational Autoencoder for 3D Molecular Denoising. AniDS introduces a structure-aware anisotropic noise generator that can produce atom-specific, full covariance matrices for Gaussian noise distributions to better reflect directional and structural variability in molecular systems. These covariances are derived from pairwise atomic interactions as anisotropic corrections to an isotropic base. Our design ensures that the resulting covariance matrices are symmetric, positive semi-definite, and SO(3)-equivariant, while providing greater capacity to model complex molecular dynamics. Extensive experiments show that AniDS outperforms prior isotropic and homoscedastic denoising models and other leading methods on the MD17 and OC22 benchmarks, achieving average relative improvements of 8.9% and 6.2% in force prediction accuracy. Our case study on a crystal and molecule structure shows that AniDS adaptively suppresses noise along the bonding direction, consistent with physicochemical principles. Our code is available at https://github.com/ZeroKnighting/AniDS.

Advances in single-cell sequencing have enabled high-resolution profiling of diverse molecular modalities, while integrating unpaired multi-omics single-cell data remains challenging. Existing approaches either rely on pair information or prior correspondences, or require computing a global pairwise coupling matrix, limiting their scalability and flexibility. In this paper, we introduce a scalable and flexible generative framework called single-cell Multi-omics Regularized Disentangled Representations (scMRDR) for unpaired multi-omics integration. Specifically, we disentangle each cell’s latent representations into modality-shared and modality-specific components using a well-designed $\beta$-VAE architecture, which are augmented with isometric regularization to preserve intra-omics biological heterogeneity, adversarial objective to encourage cross-modal alignment, and masked reconstruction loss strategy to address the issue of missing features across modalities. Our method achieves excellent performance on benchmark datasets in terms of batch correction, modality alignment, and biological signal preservation. Crucially, it scales effectively to large-level datasets and supports integration of more than two omics, offering a powerful and flexible solution for large-scale multi-omics data integration and downstream biological discovery.

We consider the problem of preprocessing an $n\times n$ matrix $\mathbf{M}$, and supporting queries that, for any vector $v$, returns the matrix-vector product $\mathbf{M} v$. This problem has been extensively studied in both theory and practice: on one side, practitioners have developed algorithms that are highly efficient in practice, whereas on the other side, theoreticians have proven that the problem cannot be solved faster than naive multiplication in the worst-case. This lower bound holds even in the average-case, implying that existing average-case analyses cannot explain this gap between theory and practice. Hence, we study the problem for \emph{structured} matrices. We show that for $n\times n$ Boolean matrices of VC-dimension $d$, the matrix-vector multiplication problem can be solved with $\smash{\tilde{O}(n^2)}$ preprocessing and $\smash{\tilde O(n^{2-1/d})}$ query time. Given the low constant VC-dimensions observed in most real-world data, our results posit an explanation for why the problem can be solved so much faster in practice. Furthermore, we show how to extend this result to the non-Boolean setting with the Pollard pseudodimension. Our results yield the first non-trivial upper bounds for many applications. In previous works, the online matrix-vector (OMv) hypothesis (conjecturing that quadratic time is needed per query, even over the boolean semi-ring) was used to prove many conditional lower bounds, showing that it is impossible to compute and maintain high-accuracy estimates for effective resistance, Laplacian solvers, shortest paths, and triangle detection in graphs subject to node insertions and deletions in subquadratic time. Yet, via a reduction to our matrix-vector-multiplication result, we show we can maintain these problems efficiently if the input is structured, providing the first subquadratic upper bounds in the high-accuracy regime.

Accurate prediction of ionic conductivity in electrolyte systems is crucial for advancing numerous scientific and technological applications. While significant progress has been made, current research faces two fundamental challenges: (1) the lack of high-quality standardized benchmarks, and (2) inadequate modeling of geometric structure and intermolecular interactions in mixture systems. To address these limitations, we first reorganize and enhance the CALiSol and DiffMix electrolyte datasets by incorporating geometric graph representations of molecules. We then propose GeoMix, a novel geometry-aware framework that preserves Set-SE(3) equivariance—an essential but challenging property for mixture systems. At the heart of GeoMix lies the Geometric Interaction Network (GIN), an equivariant module specifically designed for intermolecular geometric message passing. Comprehensive experiments demonstrate that GeoMix consistently outperforms diverse baselines (including MLPs, GNNs, and geometric GNNs) across both datasets, validating the importance of cross-molecular geometric interactions and equivariant message passing for accurate property prediction. This work not only establishes new benchmarks for electrolyte research but also provides a general geometric learning framework that advances modeling of mixture systems in energy materials, pharmaceutical development, and beyond.

We present WUKONG, a novel training-free framework for high-fidelity textured 3D morphing that takes a pair of source and target prompts (text or images) as input. Unlike conventional methods -- which rely on manual correspondence matching and deformation trajectory estimation (limiting generalization and requiring costly preprocessing) -- WUKONG leverages the generative prior of flow-based transformers to produce high-fidelity 3D transitions with rich texture details. To ensure smooth shape transitions, we exploit the inherent continuity of flow-based generative processes and formulate morphing as an optimal transport barycenter problem. We further introduce a sequential initialization strategy to prevent abrupt geometric distortions and preserve identity coherence. For faithful texture preservation, we propose a similarity-guided semantic consistency mechanism that selectively retains high-frequency details and enables precise control over blending dynamics. This avoids common artifacts like oversmoothing while maintaining semantic fidelity. Through extensive quantitative and qualitative evaluations, we demonstrate that WUKONG significantly outperforms state-of-the-art methods, achieving superior results across diverse geometry and texture variations.

We introduce Neural Green’s Function, a neural solution operator for linear partial differential equations (PDEs) whose differential operators admit eigendecompositions. Inspired by Green’s functions, the solution operators of linear PDEs that depend exclusively on the domain geometry, we design Neural Green’s Function to imitate their behavior, achieving superior generalization across diverse irregular geometries and source and boundary functions. Specifically, Neural Green’s Function extracts per-point features from a volumetric point cloud representing the problem domain and uses them to predict a decomposition of the solution operator, which is subsequently applied to evaluate solutions via numerical integration. Unlike recent learning-based solution operators, which often struggle to generalize to unseen source or boundary functions, our framework is, by design, agnostic to the specific functions used during training, enabling robust and efficient generalization. In the steady-state thermal analysis of mechanical part geometries from the MCB dataset, Neural Green’s Function outperforms state-of-the-art neural operators, achieving an average error reduction of 13.9% across five shape categories, while being up to 350 times faster than a numerical solver that requires computationally expensive meshing.

Graph Neural Networks (GNNs) have achieved impressive results across diverse network modeling tasks, but accurately estimating uncertainty on graphs remains difficult—especially under distributional shifts. Unlike traditional uncertainty estimation, graph-based uncertainty must account for randomness arising from both the graph’s structure and its label distribution, which adds complexity. In this paper, making an analogy between the evolution of a stochastic partial differential equation (SPDE) driven by Mat\'ern Gaussian Process and message passing using GNN layers, we present a principled way to design a novel message passing scheme that incorporates spatial-temporal noises motivated by the Gaussian Process approach to SPDE. Our method simultaneously captures uncertainty across space and time and allows explicit control over the covariance kernel’s smoothness, thereby enhancing uncertainty estimates on graphs with both low and high label informativeness. Our extensive experiments on Out-of-Distribution (OOD) detection on graph datasets with varying label informativeness demonstrate the soundness and superiority of our model to existing approaches.

Large vision-language models (VLMs) have made great achievements in Earth vision. However, complex disaster scenes with diverse disaster types, geographic regions, and satellite sensors have posed new challenges for VLM applications. To fill this gap, we curate the first remote sensing vision-language dataset (DisasterM3) for global-scale disaster assessment and response. DisasterM3 includes 26,988 bi-temporal satellite images and 123k instruction pairs across 5 continents, with three characteristics: **1) Multi-hazard**: DisasterM3 involves 36 historical disaster events with significant impacts, which are categorized into 10 common natural and man-made disasters. **2) Multi-sensor**: Extreme weather during disasters often hinders optical sensor imaging, making it necessary to combine Synthetic Aperture Radar (SAR) imagery for post-disaster scenes. **3) Multi-task**: Based on real-world scenarios, DisasterM3 includes 9 disaster-related visual perception and reasoning tasks, harnessing the full potential of VLM's reasoning ability with progressing from disaster-bearing body recognition to structural damage assessment and object relational reasoning, culminating in the generation of long-form disaster reports. We extensively evaluated 14 generic and remote sensing VLMs on our benchmark, revealing that state-of-the-art models struggle with the disaster tasks, largely due to the lack of a disaster-specific corpus, cross-sensor gap, and damage object counting insensitivity. Focusing on these issues, we fine-tune four VLMs using our dataset and achieve stable improvements (up to 10.4\%$\uparrow$QA, 2.1$\uparrow$Report, 40.8\%$\uparrow$Referring Seg.) with robust cross-sensor and cross-disaster generalization capabilities. Project: https://github.com/Junjue-Wang/DisasterM3.

Quantum many-body problems are central to various scientific disciplines, yet their ground-state properties are intrinsically challenging to estimate. Recent advances in deep learning (DL) offer potential solutions in this field, complementing prior purely classical and quantum approaches. However, existing DL-based models typically assume access to a large-scale and noiseless labeled dataset collected by infinite sampling. This idealization raises fundamental concerns about their practical utility, especially given the limited availability of quantum hardware in the near term. To unleash the power of these DL-based models, we propose AiDE-Q (\underline{a}utomat\underline{i}c \underline{d}ata \underline{e}ngine for \underline{q}uantum property estimation), an effective framework that addresses this challenge by iteratively generating high-quality synthetic labeled datasets. Specifically, AiDE-Q utilizes a confidence-check method to assess the quality of synthetic labels and continuously improves the employed DL models with the identified high-quality synthetic dataset. To verify the effectiveness of AiDE-Q, we conduct extensive numerical simulations on a diverse set of quantum many-body and molecular systems, with up to 50 qubits. The results show that AiDE-Q enhances prediction performance for various reference learning models, with improvements of up to $14.2\\%$. Moreover, we exhibit that a basic supervised learning model integrated with AiDE-Q outperforms advanced reference models, highlighting the importance of a synthetic dataset. Our work paves the way for more efficient and practical applications of DL for quantum property estimation.

When simulating partial differential equations, hybrid solvers combine coarse numerical solvers with learned correctors. They promise accelerated simulations while adhering to physical constraints. However, as shown in our theoretical framework, directly applying learned corrections to solver outputs leads to significant autoregressive errors, which originate from amplified perturbations that accumulate during long-term rollouts, especially in chaotic regimes. To overcome this, we propose the Indirect Neural Corrector ($\mathrm{INC}$), which integrates learned corrections into the governing equations rather than applying direct state updates. Our key insight is that $\mathrm{INC}$ reduces the error amplification on the order of $\Delta t^{-1} + L$, where $\Delta t$ is the timestep and $L$ the Lipschitz constant. At the same time, our framework poses no architectural requirements and integrates seamlessly with arbitrary neural networks and solvers. We test $\mathrm{INC}$ in extensive benchmarks, covering numerous differentiable solvers, neural backbones, and test cases ranging from a 1D chaotic system to 3D turbulence. INC improves the long-term trajectory performance ($R^2$) by up to 158.7\%, stabilizes blowups under aggressive coarsening, and for complex 3D turbulence cases yields speed-ups of several orders of magnitude. INC thus enables stable, efficient PDE emulation with formal error reduction, paving the way for faster scientific and engineering simulations with reliable physics guarantees.