NeurIPS 2025 Papers

Modeling and reconstructing multidimensional physical dynamics from sparse and off-grid observations presents a fundamental challenge in scientific research. Recently, diffusion-based generative modeling shows promising potential for physical simulation. However, current approaches typically operate on on-grid data with preset spatiotemporal resolution, but struggle with the sparsely observed and continuous nature of real-world physical dynamics. To fill the gaps, we present SDIFT, Sequential DIffusion in Functional Tucker space, a novel framework that generates full-field evolution of physical dynamics from irregular sparse observations. SDIFT leverages the functional Tucker model as the latent space representer with proven universal approximation property, and represents sparse observations as latent functions and Tucker core sequences. We then construct a sequential diffusion model with temporally augmented UNet in the functional Tucker space, denoising noise drawn from a Gaussian process to generate the sequence of core tensors. At the posterior sampling stage, we propose a Message-Passing Posterior Sampling mechanism, enabling conditional generation of the entire sequence guided by observations at limited time steps. We validate SDIFT on three physical systems spanning astronomical (supernova explosions, light-year scale), environmental (ocean sound speed fields, kilometer scale), and molecular (organic liquid, millimeter scale) domains, demonstrating significant improvements in both reconstruction accuracy and computational efficiency compared to state-of-the-art approaches.

Graph anomaly detection (GAD) has become a critical research area, with successful applications in financial fraud and telecommunications. Traditional Graph Neural Networks (GNNs) face significant challenges: at the topology level, they suffer from over-smoothing that averages out anomalous signals; at the feature level, discriminative models struggle when fraudulent nodes obfuscate their features to evade detection. In this paper, we propose a Conditional Graph Anomaly Diffusion Model (CGADM) that addresses these issues through the iterative refinement and denoising reconstruction properties of diffusion models. Our approach incorporates a prior-guided diffusion process that injects a pre-trained conditional anomaly estimator into both forward and reverse diffusion chains, enabling more accurate anomaly detection. For computational efficiency on large-scale graphs, we introduce a prior confidence-aware mechanism that adaptively determines the number of reverse denoising steps based on prior confidence. Experimental results on benchmark datasets demonstrate that CGADM achieves state-of-the-art performance while maintaining significant computational advantages for large-scale graph applications.

We propose LiteReality, a novel pipeline that converts RGB-D scans of indoor environments into compact, realistic, and interactive 3D virtual replicas. LiteReality not only reconstructs scenes that visually resemble reality but also supports key features essential for graphics pipelines, such as object individuality, articulation, and high-quality physically based rendering (PBR) materials. At its core, LiteReality first performs scene understanding and parses the results into a coherent 3D layout and object set with the help of a structured scene graph. It then reconstructs the scene by retrieving the most visually similar artist-crafted 3D models from a curated asset database. The Material Painting module further enhances realism by recovering high-quality, spatially varying materials from observed images. Finally, the reconstructed scene is integrated into a simulation engine, where basic physical properties are assigned to enable interactive behavior. The resulting scenes are compact, editable, and fully compatible with standard graphics pipelines, making them suitable for applications in AR/VR, gaming, robotics, and digital-twin systems. In addition, LiteReality introduces a training-free object-retrieval module that achieves state-of-the-art similarity performance on the Scan2CAD dataset, along with a robust Material Painting module capable of transferring appearances from images of any style to 3D assets—even under severe misalignment, occlusion, and poor lighting. We demonstrate the effectiveness of LiteReality on both real-world scans and standard public datasets.

Large language models (LLMs) have shown that generative pretraining can distill vast world knowledge into compact token representations. While LLMs encapsulate extensive world knowledge, they remain limited in modeling the behavioral knowledge contained within user interaction histories. User behavior forms a distinct modality, where each action—defined by multi-dimensional attributes such as time, context, and transaction type—constitutes a behavioral token. Modeling these high-cardinality, sparse, and irregular sequences is challenging, and discriminative models often falter under limited supervision. To bridge this gap, we extend generative pretraining to user behavior, learning transferable representations from unlabeled behavioral data analogous to how LLMs learn from text. We present PANTHER, a hybrid generative–discriminative framework that unifies user behavior pretraining and downstream adaptation, enabling large-scale sequential user representation learning and real-time inference. PANTHER introduces: (1) Structured Tokenization to compress multi-dimensional transaction attributes into an interpretable vocabulary; (2) Sequence Pattern Recognition Module (SPRM) for modeling periodic transaction motifs; (3) a Unified User-Profile Embedding that fuses static demographics with dynamic transaction histories, enabling both personalized predictions and population-level knowledge transfer; and (4) Real-time scalability enabled by offline caching of pre-trained embeddings for millisecond-level inference.Fully deployed and operational online at WeChat Pay, PANTHER delivers a 25.6\% boost in next-transaction prediction HitRate@1 and a 38.6\% relative improvement in fraud detection recall over baselines. Cross-domain evaluations on public benchmarks (CCT, MBD, MovieLens-1M, Yelp) show strong generalization, achieving up to 21\% HitRate@1 gains over transformer baselines, establishing PANTHER as a scalable, high-performance framework for industrial user sequential behavior modeling.

Accurately modeling complex dynamic spatio-temporal systems requires capturing flow-mediated interdependencies and context-sensitive interaction dynamics. Existing methods, predominantly graph-based or attention-driven, rely on similarity-driven connectivity assumptions, neglecting asymmetric flow exchanges that govern system evolution. We propose Spatio-Temporal Flow, a physics-inspired paradigm that explicitly models dynamic node couplings through quantifiable flow transfers governed by conservation principles. Building on this, we design FlowNet, a novel architecture leveraging flow tokens as information carriers to simulate source-to-destination transfers via Flow Allocation Modules, ensuring state redistribution aligns with physical laws. FlowNet dynamically adjusts the interaction radius through an Adaptive Spatial Masking module, suppressing irrelevant noise while enabling context-aware propagation. A cascaded architecture enhances scalability and nonlinear representation capacity. Experiments demonstrate that FlowNet significantly outperforms existing SOTA approaches on seven metrics in the modeling of three real-world systems, validating its efficiency and physical interpretability. We establish a principled methodology for modeling complex systems through spatio-temporal flow interactions.

Recent progress in panoramic image generation has underscored two critical limitations in existing approaches. First, most methods are built upon diffusion models, which are inherently ill-suited for equirectangular projection (ERP) panoramas due to the violation of the identically and independently distributed (i.i.d.) Gaussian noise assumption caused by their spherical mapping. Second, these methods often treat text-conditioned generation (text-to-panorama) and image-conditioned generation (panorama outpainting) as separate tasks, relying on distinct architectures and task-specific data. In this work, we propose a unified framework, Panoramic AutoRegressive model (PAR), which leverages masked autoregressive modeling to address these challenges. PAR avoids the i.i.d. assumption constraint and integrates text and image conditioning into a cohesive architecture, enabling seamless generation across tasks. To address the inherent discontinuity in existing generative models, we introduce circular padding to enhance spatial coherence and propose a consistency alignment strategy to improve the generation quality. Extensive experiments demonstrate competitive performance in text-to-image generation and panorama outpainting tasks while showcasing promising scalability and generalization capabilities.

Multi-compartment Hodgkin-Huxley models are biophysical models of how electrical signals propagate throughout a neuron, and they form the basis of our knowledge of neural computation at the cellular level. However, these models have many free parameters that must be estimated for each cell, and existing fitting methods rely on intracellular voltage measurements that are highly challenging to obtain in-vivo. Recent advances in neural recording technology with high-density probes and arrays enable dense sampling of extracellular voltage from many sites surrounding a neuron, allowing indirect measurement of many compartments of a cell simultaneously. Here, we propose a method for inferring the underlying membrane voltage, biophysical parameters, and the neuron's position relative to the probe, using extracellular measurements alone. We use an Extended Kalman Filter to infer membrane voltage and channel states using efficient, differentiable simulators. Then, we learn the model parameters by maximizing the marginal likelihood using gradient-based methods. We demonstrate the performance of this approach using simulated data and real neuron morphologies.

Deep generative models have recently been proposed for sampling protein conformations from the Boltzmann distribution, as an alternative to often prohibitively expensive Molecular Dynamics simulations. However, current state-of-the-art approaches rely on fine-tuning pre-trained folding models and evolutionary sequence information, limiting their applicability and efficiency, and introducing potential biases. In this work, we propose a flow matching model for sampling protein conformations based solely on backbone geometry - BBFlow. We introduce a geometric encoding of the backbone equilibrium structure as input and propose to condition not only the flow but also the prior distribution on the respective equilibrium structure, eliminating the need for evolutionary information. The resulting model is orders of magnitudes faster than current state-of-the-art approaches at comparable accuracy, is transferable to multi-chain proteins, and can be trained from scratch in a few GPU days. In our experiments, we demonstrate that the proposed model achieves competitive performance with reduced inference time, across not only an established benchmark of naturally occurring proteins but also de novo proteins, for which evolutionary information is scarce or absent. BBFlow is available at https://github.com/graeter-group/bbflow.

This paper presents PartCAD, a novel framework for reconstructing CAD modeling sequences directly from point clouds by projection-guided, part-aware geometry reasoning. It consists of (1) an autoregressive approach that decomposes point clouds into part-aware latent representations, serving as interpretable anchors for CAD generation; (2) a projection guidance module that provides explicit cues about underlying design intent via triplane projections; and (3) a non-autoregressive decoder to generate sketch-extrusion parameters in a single forward pass, enabling efficient and structurally coherent CAD instruction synthesis. By bridging geometric signals and semantic understanding, PartCAD tackles the challenge of reconstructing editable CAD models—capturing underlying design processes—from 3D point clouds. Extensive experiments show that PartCAD significantly outperforms existing methods for CAD instruction generation in both accuracy and robustness. The work sheds light on part-driven reconstruction of interpretable CAD models, opening new avenues in reverse engineering and CAD automation.

Solving time-dependent Partial Differential Equations (PDEs) using a densely discretized spatial domain is a fundamental problem in various scientific and engineering disciplines, including modeling climate phenomena and fluid dynamics. However, performing these computations directly in the physical space often incurs significant computational costs. To address this issue, several neural surrogate models have been developed that operate in a compressed latent space to solve the PDE. While these approaches reduce computational complexity, they often use Transformer-based attention mechanisms to handle irregularly sampled domains, resulting in increased memory consumption. In contrast, convolutional neural networks allow memory-efficient encoding and decoding but are limited to regular discretizations. Motivated by these considerations, we propose CALM-PDE, a model class that efficiently solves arbitrarily discretized PDEs in a compressed latent space. We introduce a novel continuous convolution-based encoder-decoder architecture that uses an epsilon-neighborhood-constrained kernel and learns to apply the convolution operator to adaptive and optimized query points. We demonstrate the effectiveness of CALM-PDE on a diverse set of PDEs with both regularly and irregularly sampled spatial domains. CALM-PDE is competitive with or outperforms existing baseline methods while offering significant improvements in memory and inference time efficiency compared to Transformer-based methods.

A fundamental challenge in probabilistic modeling is to balance expressivity and inference efficiency. Tractable probabilistic models (TPMs) aim to directly address this tradeoff by imposing constraints that guarantee efficient inference of certain queries while maintaining expressivity. In particular, probabilistic circuits (PCs) provide a unifying framework for many TPMs, by characterizing families of models as circuits satisfying different structural properties. Because the complexity of inference on PCs is a function of the circuit size, understanding the size requirements of different families of PCs is fundamental in mapping the trade-off between tractability and expressive efficiency. However, the study of expressive efficiency of circuits are often concerned with exact representations, which may not align with model learning, where we look to approximate the underlying data distribution closely by some distance measure. Moreover, due to hardness of inference tasks, exactly representing distributions while supporting tractable inference often incurs exponential size blow-ups. In this paper, we consider a natural, yet so far underexplored, question: can we avoid such size blow-up by allowing for some small approximation error? We study approximating distributions with probabilistic circuits with guarantees based on $f$-divergences, and analyze which inference queries remain well-approximated under this framework. We show that approximating an arbitrary distribution with bounded $f$-divergence is NP-hard for any model that can tractably compute marginals. In addition, we prove an exponential size gap for approximation between the class of decomposable PCs and that of decomposable and deterministic PCs.