NeurIPS 2025 Papers

Geometric molecule generative models have found expanding applications across various scientific domains, but their generation inefficiency has become a critical bottleneck. Through a systematic investigation of the generative trajectory, we discover a unique challenge for molecule geometric graph generation: generative models require determining the permutation order of atoms in the molecule before refining its atomic feature values. Based on this insight, we decompose the generation process into permutation phase and adjustment phase, and propose a geometric-informed prior and consistency parameter objective to accelerate each phase. Extensive experiments demonstrate that our approach achieves competitive performance with approximately 10 sampling steps, 7.5 × faster than previous state-of-the-art models and approximately 100 × faster than diffusion-based models, offering a significant step towards scalable molecular generation.

Existing video generation models excel at producing photo-realistic videos from text or images, but often lack physical plausibility and 3D controllability. To overcome these limitations, we introduce PhysCtrl, a novel framework for physics-grounded image-to-video generation with physical parameters and force control. At its core is a generative physics network that learns the distribution of physical dynamics across four materials (elastic, sand, plasticine, and rigid) via a diffusion model conditioned on physics parameters and applied forces. We represent physical dynamics as 3D point trajectories and train on a large-scale synthetic dataset of 550K animations generated by physics simulators. We enhance the diffusion model with a novel spatiotemporal attention block that emulates particle interactions and incorporates physics-based constraints during training to enforce physical plausibility. Experiments show that PhysCtrl generates realistic, physics-grounded motion trajectories which, when used to drive image-to-video models, yield high-fidelity, controllable videos that outperform existing methods in both visual quality and physical plausibility. Our code, model and data will be made publicly available upon publication.

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks whose CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single path without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS/tree/main/OpenMol/TDN).

Recent work shows that features from Stable Diffusion (SD) and contrastively pretrained models like DINO can be directly used for zero-shot semantic correspondence via naive feature concatenation. In this paper, we explore the stronger potential of Stable Diffusion 3 (SD3), a rectified flow-based model with a multimodal transformer backbone (MM-DiT). We show that semantic signals in SD3 are scattered across multiple timesteps and transformer layers, and propose a multi-level fusion scheme to extract discriminative features. Moreover, we identify that naive fusion across models suffers from inconsistent distributions, thus leading to suboptimal performance. To address this, we propose a simple yet effective confidence-aware feature fusion strategy that re-weights each model’s contribution based on prediction confidence scores derived from their matching uncertainties. Notably, this fusion approach is not only training-free but also enables per-pixel adaptive integration of heterogeneous features. The resulting representation, Fuse2Match, significantly outperforms strong baselines on SPair-71k, PF-Pascal, and PSC6K, validating the benefit of combining SD3, SD, and DINO through our proposed confidence-aware feature fusion. Code is available at https://github.com/panda7777777/fuse2match

Trajectory modeling, which includes research on trajectory data pattern mining and future prediction, has widespread applications in areas such as life services, urban transportation, and public administration. Numerous methods have been proposed to address specific problems within trajectory modeling. However, the heterogeneity of data and the diversity of trajectory tasks make effective and reliable trajectory modeling an important yet highly challenging endeavor, even for domain experts. In this paper, we propose TrajAgent, a agent framework powered by large language models (LLMs), designed to facilitate robust and efficient trajectory modeling through automation modeling. This framework leverages and optimizes diverse specialized models to address various trajectory modeling tasks across different datasets effectively. In TrajAgent, we first develop UniEnv, an execution environment with a unified data and model interface, to support the execution and training of various models. Building on UniEnv, we introduce an agentic workflow designed for automatic trajectory modeling across various trajectory tasks and data. Furthermore, we introduce collaborative learning schema between LLM-based agents and small speciallized models, to enhance the performance of the whole framework effectively. Extensive experiments on four tasks using four real-world datasets demonstrate the effectiveness of TrajAgent in automated trajectory modeling, achieving a performance improvement of 2.38%-69.91% over baseline methods. The codes and data can be accessed via https://github.com/tsinghua-fib-lab/TrajAgent.

We study fundamental connections between coalition formation games and clustering, illustrating the cross-disciplinary relevance of these concepts. We focus on graphical hedonic games where agents' preferences are compactly represented by a friendship graph and an enemy graph. In the context of clustering, friendship relations naturally align with data point similarities, whereas enmity corresponds to dissimilarities. We consider two stability notions based on single-agent deviations: local popularity and local stability. Exploring these concepts from an algorithmic viewpoint, we design efficient mechanisms for finding locally stable or locally popular partitions. Besides gaining theoretical insight into the computational complexity of these problems, we perform simulations that demonstrate how our algorithms can be successfully applied in clustering and community detection. Our findings highlight the interplay between coalition formation games and data-driven clustering techniques, offering fresh perspectives and applications in both areas.

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.

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/

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.

Developing improved predictive models for multi-molecular systems is crucial, as nearly every chemical product used results from a mixture of chemicals. While being a vital part of the industry pipeline, the chemical mixture space remains relatively unexplored by the Machine Learning (ML) community. In this paper, we introduce CheMixHub, a holistic benchmark for molecular mixtures spanning a corpus of 11 chemical mixtures property prediction tasks. With applications ranging from drug delivery formulations to battery electrolytes, CheMixHub currently totals approximately 500k data points gathered and curated from 7 publicly available datasets. We devise various data splitting techniques to assess context-specific generalization and model robustness, providing a foundation for the development of predictive models for chemical mixture properties. Furthermore, we map out the modelling space of deep learning models for chemical mixtures, establishing initial benchmarks for the community. This dataset has the potential to accelerate chemical mixture development, encompassing reformulation, optimization, and discovery. The dataset and code for the benchmarks can be found at: https://github.com/chemcognition-lab/chemixhub

Recent advances in 3D scene reconstruction enable real-time viewing in virtual and augmented reality. To support interactive operations for better immersiveness, such as moving or editing objects, 3D scene inpainting methods are proposed to repair or complete the altered geometry. To support users in interacting (such as moving or editing objects) with the scene for the next level of immersiveness, 3D scene inpainting methods are developed to repair the altered geometry. However, current approaches rely on lengthy and computationally intensive optimization, making them impractical for real-time or online applications. We propose InstaInpaint, a reference-based feed-forward framework that produces 3D-scene inpainting from a 2D inpainting proposal within 0.4 seconds. We develop a self-supervised masked-finetuning strategy to enable training of our custom large reconstruction model (LRM) on the large-scale dataset. Through extensive experiments, we analyze and identify several key designs that improve generalization, textural consistency, and geometric correctness. InstaInpaint achieves a 1000$\times$ speed-up from prior methods while maintaining a state-of-the-art performance across two standard benchmarks. Moreover, we show that InstaInpaint generalizes well to flexible downstream applications such as object insertion and multi-region inpainting.

This work proposes the Lattice Boltzmann Model (LBM) to learn real-world pixel dynamicity for visual tracking. LBM decomposes visual representations into dynamic pixel lattices and solves pixel motion states through collision-streaming processes. Specifically, the high-dimensional distribution of the target pixels is acquired through a multilayer predict-update network to estimate the pixel positions and visibility. The predict stage formulates lattice collisions among the spatial neighborhood of target pixels and develops lattice streaming within the temporal visual context. The update stage rectifies the pixel distributions with online visual representations. Compared with existing methods, LBM demonstrates practical applicability in an online and real-time manner, which can efficiently adapt to real-world visual tracking tasks. Comprehensive evaluations of real-world point tracking benchmarks such as TAP-Vid and RoboTAP validate LBM's efficiency. A general evaluation of large-scale open-world object tracking benchmarks such as TAO, BFT, and OVT-B further demonstrates LBM's real-world practicality.

Accurate video forecasting enables autonomous vehicles to anticipate hazards, robotics and surveillance systems to predict human intent, and environmental models to issue timely warnings for extreme weather events. However, existing methods remain limited: transformers rely on global attention with quadratic complexity, making them impractical for high-resolution, long-horizon video prediction, while convolutional and recurrent networks suffer from short-range receptive fields and vanishing gradients, losing key information over extended sequences. To overcome these challenges, we introduce VideoTitans, the first architecture to adapt the gradient-driven Titans memory—originally designed for language modelling to video prediction. VideoTitans integrates three core ideas: (i) a sliding-window attention core that scales linearly with sequence length and spatial resolution, (ii) an episodic memory that dynamically retains only informative tokens based on a gradient-based surprise signal, and (iii) a small set of persistent tokens encoding task-specific priors that stabilize training and enhance generalization. Extensive experiments on Moving-MNIST, Human3.6M, TrafficBJ and WeatherBench benchmarks show that VideoTitans consistently reduces computation (FLOPs) and achieves competitive visual fidelity compared to state-of-the-art recurrent, convolutional, and efficient-transformer methods. Comprehensive ablations confirm that each proposed component contributes significantly.

We present BrainODE, a neural ordinary differential equation (ODE)-based framework for modeling continuous longitudinal deformations of brain shapes. BrainODE learns a deformation space over anatomically meaningful brain regions to facilitate early prediction of neurodegenerative disease progression. Addressing inherent challenges of longitudinal neuroimaging data-such as limited sample sizes, irregular temporal sampling, and substantial inter-subject variability-we propose a conditional neural ODE architecture that models shape dynamics with subject-specific age and cognitive status. To enable autoregressive forecasting of brain morphology from a single observation, we propose a pseudo-cognitive status embedding that allows progressive shape prediction across intermediate time points with predicted cognitive decline. Experiments show that BrainODE outperforms time-aware baselines in predicting future brain shapes, demonstrating strong generalization across longitudinal datasets with both regular and irregular time intervals.

Modeling the transport dynamics of natural processes from population-level observations is a ubiquitous problem in the natural sciences. Such models rely on key assumptions about the underlying process in order to enable faithful learning of governing dynamics that mimic the actual system behavior. The de facto assumption in current approaches relies on the principle of least action that results in gradient field dynamics and leads to trajectories minimizing an energy functional between two probability measures. However, many real-world systems, such as cell cycles in single-cell RNA, are known to exhibit non-gradient, periodic behavior, which fundamentally cannot be captured by current state-of-the-art methods such as flow and bridge matching. In this paper, we introduce Curly Flow Matching (Curly-FM), a novel approach that is capable of learning non-gradient field dynamics by designing and solving a Schrödinger bridge problem with a non-zero drift reference process---in stark contrast to typical zero-drift reference processes---which is constructed using inferred velocities in addition to population snapshot data. We showcase Curly-FM by solving the trajectory inference problems for single cells, computational fluid dynamics, and ocean currents with approximate velocities. We demonstrate that Curly-FM can learn trajectories that better match both the reference process and population marginals. Curly-FM expands flow matching models beyond the modeling of populations and towards the modeling of known periodic behavior in physical systems. Our code repository is accessible at: https://github.com/kpetrovicc/curly-flow-matching.git

Adverse weather severely impairs real-world visual perception, while existing vision models trained on synthetic data with fixed parameters struggle to generalize to complex degradations. To address this, we first construct HFLS-Weather, a physics-driven, high-fidelity dataset that simulates diverse weather phenomena, and then design a dual-level reinforcement learning framework initialized with HFLS-Weather for cold-start training. Within this framework, at the local level, weather-specific restoration models are refined through perturbation-driven image quality optimization, enabling reward-based learning without paired supervision; at the global level, a meta-controller dynamically orchestrates model selection and execution order according to scene degradation. This framework enables continuous adaptation to real-world conditions and achieves state-of-the-art performance across a wide range of adverse weather scenarios. Code is available at https://github.com/xxclfy/AgentRL-Real-Weather

Subgraph matching in logic circuits is foundational for numerous Electronic Design Automation (EDA) applications, including datapath optimization, arithmetic verification, and hardware trojan detection. However, existing techniques rely primarily on structural graph isomorphism and thus fail to identify function-related subgraphs when synthesis transformations substantially alter circuit topology. To overcome this critical limitation, we introduce the concept of functional subgraph matching, a novel approach that identifies whether a given logic function is implicitly present within a larger circuit, irrespective of structural variations induced by synthesis or technology mapping. Specifically, we propose a two-stage multi-modal framework: (1) learning robust functional embeddings across AIG and post-mapping netlists for functional subgraph detection, and (2) identifying fuzzy boundaries using a graph segmentation approach. Evaluations on standard benchmarks (ITC99, OpenABCD, ForgeEDA) demonstrate significant performance improvements over existing structural methods, with average 93.8% accuracy in functional subgraph detection and a dice score of 91.3% in fuzzy boundary identification.

Retrieval-Augmented Generation (RAG) provides additional contextual knowledge to complement the parametric knowledge in Large Language Models (LLMs). These two knowledge interweave to enhance the accuracy and timeliness of LLM responses. However, the internal mechanisms by which LLMs utilize these knowledge remain unclear. We propose modeling the forward propagation of knowledge as an entity flow, employing this framework to trace LLMs' internal behaviors when processing mixed-source knowledge. Linear probing utilizes a trainable linear classifier to detect specific attributes in hidden layers. However, once trained, a probe cannot adapt to dynamically specified entities. To address this challenge, we construct an entity-aware probe, which introduces special tokens to mark probing targets and employs a small trainable rank-8 lora update to process these special markers. We first verify this approach through an attribution experiment, demonstrating that it can accurately detect information about ad-hoc entities from complex hidden states. Next, we trace entity flows across layers to understand how LLMs reconcile conflicting knowledge internally. Our probing results reveal that contextual and parametric knowledge are routed between tokens through distinct sets of attention heads, supporting attention competition only within knowledge types. While conflicting knowledge maintains a residual presence across layers, aligned knowledge from multiple sources gradually accumulates, with the magnitude of this accumulation directly determining its influence on final outputs.