NeurIPS 2025 Papers

Petrography is a branch of geology that analyzes the mineralogical composition of rocks from microscopical thin section samples. It is essential for understanding rock properties across geology, archaeology, engineering, mineral exploration, and the oil industry. However, petrography is a labor-intensive task requiring experts to conduct detailed visual examinations of thin section samples through optical polarization microscopes, thus hampering scalability and highlighting the need for automated techniques. To address this challenge, we introduce the Large-scale Imaging and Thin section Optical-polarization Set (LITHOS), the largest and most diverse publicly available experimental framework for automated petrography. LITHOS includes 211,604 high-resolution RGB patches of polarized light and 105,802 expert-annotated grains across 25 mineral categories. Each annotation consists of the mineral class, spatial coordinates, and expert-defined major and minor axes represented as intersecting vector paths, capturing grain geometry and orientation. We evaluate multiple deep learning techniques for mineral classification in LITHOS and propose a dual-encoder transformer architecture that integrates both polarization modalities as a strong baseline for future reference. Our method consistently outperforms single-polarization models, demonstrating the value of polarization synergy in mineral classification. We have made the LITHOS Benchmark publicly available, comprising our dataset, code, and pretrained models, to foster reproducibility and further research in automated petrographic analysis.

Forest ecosystems play a critical role in the Earth system as major carbon sinks that are essential for carbon neutralization and climate change mitigation. However, the Earth has undergone significant deforestation and forest degradation, and the remaining forested areas are also facing increasing pressures from socioeconomic factors and climate change, potentially pushing them towards tipping points. Responding to the grand challenge, a theory-based Ecosystem Demography (ED) model has been continuously developed over the past two decades and serves as a key component in major initiatives, including the Global Carbon Budget, NASA Carbon Monitoring System, and US Greenhouse Gas Center. Despite its growing importance in combating climate change and shaping carbon policies, ED's expensive computation significantly limits its ability to estimate carbon dynamics at the global scale with high spatial resolution. Recently, machine learning (ML) models have shown promising potential in approximating theory-based models with interesting success in various domains including weather forecasting, thanks to the open-source benchmark datasets made available. However, there are currently no publicly available ML-ready datasets for global carbon dynamics forecasting in forest ecosystems. The limited data availability hinders the development of corresponding ML emulators. Furthermore, the inputs needed for running ED are highly complex with over a hundred variables from various remote sensing products. To bridge the gap, we develop a new ML-ready benchmark dataset, \textit{CarbonGlobe}, for carbon dynamics forecasting, featuring that: (1) the data has a global-scale coverage at 0.5$^\circ$ resolution; (2) the temporal range spans 40 years; (3) the inputs integrate extensive multi-source data from different sensing products, with calibrated outputs from ED; (4) the data is formatted in ML-ready forms and split into different evaluation scenarios based on climate conditions, etc.; (5) a set of problem-driven metrics is designed to develop benchmarks using various ML models to best align with the needs of downstream applications. Our dataset and code are publicly available on Kaggle and GitHub: https://www.kaggle.com/datasets/zhihaow/carbonglobe and https://github.com/zhwang0/carbon-globe.

In dance performances, choreographers define the visual expression of movement, while cinematographers shape its final presentation through camera work. Consequently, the synthesis of camera movements informed by both music and dance has garnered increasing research interest. While recent advancements have led to notable progress in this area, existing methods predominantly operate in an offline manner—that is, they require access to the entire dance sequence before generating corresponding camera motions. This constraint renders them impractical for real-time applications, particularly in live stage performances, where immediate responsiveness is essential. To address this limitation, we introduce a more practical yet challenging task: online camera movement synthesis, in which camera trajectories must be generated using only the current and preceding segments of dance and music. In this paper, we propose TemMEGA (Temporal Masked Generative Modeling), a unified framework capable of handling both online and offline camera movement generation. TemMEGA consists of three key components. First, a discrete camera tokenizer encodes camera motions as discrete tokens via a discrete quantization scheme. Second, a consecutive memory encoder captures historical context by jointly modeling long- and short-term temporal dependencies across dance and music sequences. Finally, a temporal conditional masked transformer is employed to predict future camera motions by leveraging masked token prediction. Extensive experimental evaluations demonstrate the effectiveness of our TemMEGA, highlighting its superiority in both online and offline camera movement synthesis.

We consider the Schrödinger bridge problem which, given ensemble measurements of the initial and final configurations of a stochastic dynamical system and some prior knowledge on the dynamics, aims to reconstruct the "most likely" evolution of the system compatible with the data. Most existing literature assume Brownian reference dynamics, and are implicitly limited to modelling systems driven by the gradient of a potential energy. We depart from this regime and consider reference processes described by a multivariate Ornstein-Uhlenbeck process with generic drift matrix $\mathbf{A} \in \mathbb{R}^{d \times d}$. When $\mathbf{A}$ is asymmetric, this corresponds to a non-equilibrium system in which non-gradient forces are at play: this is important for applications to biological systems, which naturally exist out-of-equilibrium. In the case of Gaussian marginals, we derive explicit expressions that characterise exactly the solution of both the static and dynamic Schrödinger bridge. For general marginals, we propose mvOU-OTFM, a simulation-free algorithm based on flow and score matching for learning an approximation to the Schrödinger bridge. In application to a range of problems based on synthetic and real single cell data, we demonstrate that mvOU-OTFM achieves higher accuracy compared to competing methods, whilst being significantly faster to train.

The creation of photorealistic dynamic hair remains a major challenge in digital human modeling because of the complex motions, occlusions, and light scattering. Existing methods often resort to static capture and physics-based models that do not scale as they require manual parameter fine-tuning to handle the diversity of hairstyles and motions, and heavy computation to obtain high-quality appearance. In this paper, we present Dynamic Gaussian Hair (DGH), a novel framework that efficiently learns hair dynamics and appearance. We propose: (1) a coarse-to-fine model that learns temporally coherent hair motion dynamics across diverse hairstyles; (2) a strand-guided optimization module that learns a dynamic 3D Gaussian representation for hair appearance with support for differentiable rendering, enabling gradient-based learning of view-consistent appearance under motion. Unlike prior simulation-based pipelines, our approach is fully data-driven, scales with training data, and generalizes across various hairstyles and head motion sequences. Additionally, DGH can be seamlessly integrated into a 3D Gaussian avatar framework, enabling realistic, animatable hair for high-fidelity avatar representation. DGH achieves promising geometry and appearance results, providing a scalable, data-driven alternative to physics-based simulation and rendering.

Offline Goal-Conditioned Reinforcement Learning (GCRL) holds great promise for domains such as autonomous navigation and locomotion, where collecting interactive data is costly and unsafe. However, it remains challenging in practice due to the need to learn from datasets with limited coverage of the state-action space and to generalize across long-horizon tasks. To improve on these challenges, we propose a Physics-informed (Pi) regularized loss for value learning, derived from the Eikonal Partial Differential Equation (PDE) and which induces a geometric inductive bias in the learned value function. Unlike generic gradient penalties that are primarily used to stabilize training, our formulation is grounded in continuous-time optimal control and encourages value functions to align with cost-to-go structures. The proposed regularizer is broadly compatible with temporal-difference-based value learning and can be integrated into existing Offline GCRL algorithms. When combined with Hierarchical Implicit Q-Learning (HIQL), the resulting method, Eikonal-regularized HIQL (Eik-HIQL), yields significant improvements in both performance and generalization, with pronounced gains in stitching regimes and large-scale navigation tasks. Code is available at https://github.com/VittorioGiammarino/Eik-HIQL.

Humanoid robots are promising to acquire various skills by imitating human behaviors. However, existing algorithms are only capable of tracking smooth, low-speed human motions, even with delicate reward and curriculum design. This paper presents a physics-based humanoid control framework, aiming to master highly-dynamic human behaviors such as Kungfu and dancing through multi-steps motion processing and adaptive motion tracking. For motion processing, we design a pipeline to extract, filter out, correct, and retarget motions, while ensuring compliance with physical constraints to the maximum extent. For motion imitation, we formulate a bi-level optimization problem to dynamically adjust the tracking accuracy tolerance based on the current tracking error, creating an adaptive curriculum mechanism. We further construct an asymmetric actor-critic framework for policy training. In experiments, we train whole-body control policies to imitate a set of highly dynamic motions. Our method achieves significantly lower tracking errors than existing approaches and is successfully deployed on the Unitree G1 robot, demonstrating stable and expressive behaviors. The project page is https://kungfubot.github.io.

Recent advancements in foundation models for 2D vision have substantially improved the analysis of dynamic scenes from monocular videos. However, despite their strong generalization capabilities, these models often lack 3D consistency, a fundamental requirement for understanding scene geometry and motion, thereby causing severe spatial misalignment and temporal flickering in complex 3D environments. In this paper, we present Motion4D, a novel framework that addresses these challenges by integrating 2D priors from foundation models into a unified 4D Gaussian Splatting representation. Our method features a two-part iterative optimization framework: 1) Sequential optimization, which updates motion and semantic fields in consecutive stages to maintain local consistency, and 2) Global optimization, which jointly refines all attributes for long-term coherence. To enhance motion accuracy, we introduce a 3D confidence map that dynamically adjusts the motion priors, and an adaptive resampling process that inserts new Gaussians into under-represented regions based on per-pixel RGB and semantic errors. Furthermore, we enhance semantic coherence through an iterative refinement process that resolves semantic inconsistencies by alternately optimizing the semantic fields and updating prompts of SAM2. Extensive evaluations demonstrate that our Motion4D significantly outperforms both 2D foundation models and existing 3D-based approaches across diverse scene understanding tasks, including point-based tracking, video object segmentation, and novel view synthesis. Our code is available at https://hrzhou2.github.io/motion4d-web/.

Latent Gaussian variables have been popularised in probabilistic machine learning. In turn, gradient estimators are the machinery that facilitates gradient-based optimisation for models with latent Gaussian variables. The reparameterisation trick is often used as the default estimator as it is simple to implement and yields low-variance gradients for variational inference. In this work, we propose the R2-G2 estimator as the Rao-Blackwellisation of the reparameterisation gradient estimator. Interestingly, we show that the local reparameterisation gradient estimator for Bayesian MLPs is an instance of the R2-G2 estimator and Rao-Blackwellisation. This lets us extend benefits of Rao-Blackwellised gradients to a suite of probabilistic models. We show that initial training with R2-G2 consistently yields better performance in models with multiple applications of the reparameterisation trick.

Recent advances in feed-forward 3D Gaussian Splatting have led to rapid improvements in efficient scene reconstruction from sparse views. However, most existing approaches construct Gaussian primitives directly aligned with the pixels in one or more of the input images. This leads to redundancies in the representation when input views overlap and constrains the position of the primitives to lie along the input rays without full flexibility in 3D space. Moreover, these pixel-aligned approaches do not naturally generalize to dynamic scenes, where effectively leveraging temporal information requires resolving both redundant and newly appearing content across frames. To address these limitations, we introduce a novel Fuse-and-Refine module that enhances existing feed-forward models by merging and refining the primitives in a canonical 3D space. At the core of our method is an efficient hybrid Splat-Voxel representation – from an initial set of pixel-aligned Gaussian primitives, we aggregate local features into a coarse-to-fine voxel hierarchy, and then use a sparse voxel transformer to process these voxel features and generate refined Gaussian primitives. By fusing and refining an arbitrary number of inputs into a consistent set of primitives, our representation effectively reduces redundancy and naturally adapts to temporal frames, enabling history-aware online reconstruction of dynamic scenes. Trained on large-scale static scene datasets, our model learns an effective global strategy to process around 200k primitives within 15ms and significantly enhances reconstruction quality compared to pixel-aligned reconstruction approaches. Without additional training, our model generalizes to video by fusing primitives across time, yielding a more temporally coherent result compared to baseline methods with graceful handling of occluded content. Our approach achieves state-of-the-art performance in both static and streaming scene reconstructions while running at interactive rates (15 fps with 350ms delay) on a single H100 GPU.

Conditional diffusion models provide a natural framework for probabilistic prediction of dynamical systems and have been successfully applied to fluid dynamics and weather prediction. However, in many settings, the available information at a given time represents only a small fraction of what is needed to predict future states, either due to measurement uncertainty or because only a small fraction of the state can be observed. This is true for example in solar physics, where we can observe the Sun’s surface and atmosphere, but its evolution is driven by internal processes for which we lack direct measurements. In this paper, we tackle the probabilistic prediction of partially observable, long-memory dynamical systems, with applications to solar dynamics and the evolution of active regions. We show that standard inference schemes, such as autoregressive rollouts, fail to capture long-range dependencies in the data, largely because they do not integrate past information effectively. To overcome this, we propose a multiscale inference scheme for diffusion models, tailored to physical processes. Our method generates trajectories that are temporally fine-grained near the present and coarser as we move farther away, which enables capturing long-range temporal dependencies without increasing computational cost. When integrated into a diffusion model, we show that our inference scheme significantly reduces the bias of the predicted distributions and improves rollout stability.

Recent work has shown that the attention maps of the widely popular DINOv2 model exhibit artifacts, which hurt both model interpretability and performance on dense image tasks. These artifacts emerge due to the model repurposing patch tokens with redundant local information for the storage of global image information. To address this problem, additional register tokens have been incorporated in which the model can store such information instead. We carefully examine the influence of these register tokens on the relationship between global and local image features, showing that while register tokens yield cleaner attention maps, these maps do not accurately reflect the integration of local image information in large models. Instead, global information is dominated by information extracted from register tokens, leading to a disconnect between local and global features. Inspired by these findings, we show that the [CLS] token itself leads to a very similar phenomenon in models without explicit register tokens. Our work shows that care must be taken when interpreting attention maps of large ViTs. Further, by clearly attributing the faulty behavior to register and [CLS] tokens, we show a path towards more interpretable vision models.

Physics-informed neural networks (PINN) have achieved notable success in solving partial differential equations (PDE), yet solving the Navier-Stokes equations (NSE) with complex boundary conditions remains a challenging task. In this paper, we introduce a novel Hybrid Boundary PINN (HB-PINN) method that combines a pretrained network for efficient initialization with a boundary-constrained mechanism. The HB-PINN method features a primary network focused on inner domain points and a distance metric network that enhances predictions at the boundaries, ensuring accurate solutions for both boundary and interior regions. Comprehensive experiments have been conducted on the NSE under complex boundary conditions, including the 2D cylinder wake flow and the 2D blocked cavity flow with a segmented inlet. The proposed method achieves state-of-the-art (SOTA) performance on these benchmark scenarios, demonstrating significantly improved accuracy over existing PINN-based approaches.

Machine learning models increasingly map biological sequence-fitness landscapes to predict mutational effects. Effective evaluation of these models requires benchmarks curated from empirical data. Despite their impressive scales, existing benchmarks lack topographical information regarding the underlying fitness landscapes, which hampers interpretation and comparison of model performance beyond averaged scores. Here, we introduce GraphFLA, a Python framework that constructs and analyzes fitness landscapes from diverse modalities (DNA, RNA, protein, and beyond.), accommodating datasets up to millions of mutants. GraphFLA calculates 20 biologically relevant features that characterize 4 fundamental aspects of landscape topography. By applying GraphFLA to over 5,300 landscapes from ProteinGym, RNAGym, and CIS-BP, we demonstrate its utility in interpreting and comparing the performance of dozens of fitness prediction models, highlighting factors influencing model accuracy and respective advantages of different models. Additionally, we release 155 combinatorially complete empirical fitness landscapes, encompassing over 2.2 million sequences across various modalities. All the codes and datasets are available at https://github.com/COLA-Laboratory/GraphFLA.

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biology. In the zero-shot setting, variant impact is estimated by comparing the likelihoods of sequences, under the assumption that likelihood serves as a proxy for fitness. However, this assumption often breaks down in practice: sequence likelihood reflects not only evolutionary fitness constraints, but also phylogenetic structure and sampling biases, especially as model capacity increases. We introduce Likelihood-Fitness Bridging (LFB), a simple and general strategy that improves variant effect prediction by averaging model scores across sequences subject to similar selective pressures. Assuming an Ornstein-Uhlenbeck model of evolution, LFB can be viewed as a way to marginalize the effects of genetic drift, although its benefits appear to extend more broadly. LFB applies to existing protein and genomic language models without requiring retraining, and incurs only modest computational overhead. Evaluated on large-scale deep mutational scans and clinical benchmarks, LFB consistently improves predictive performance across model families and sizes. Notably, it reverses the performance plateau observed in larger protein language models, making the largest models the most accurate when combined with LFB. These results suggest that accounting for phylogenetic and sampling biases is essential to realizing the full potential of large sequence models in variant effect prediction.

Recent developments in DNN-based image watermarking techniques have achieved impressive results in protecting digital content. However, most existing methods are constrained to low-resolution images as they need to encode the entire image, leading to prohibitive memory and computational costs when applied to high-resolution images. Moreover, they lack robustness to distortions prevalent in large-image transmission, such as extreme scaling and random cropping. To address these issues, we propose a novel watermarking method based on implicit neural representations (INRs). Leveraging the properties of INRs, our method employs resolution-independent coordinate sampling mechanism to generate watermarks pixel-wise, achieving ultra-high resolution watermark generation with fixed and limited memory and computational resources. This design ensures strong robustness in watermark extraction, even under extreme cropping and scaling distortions. Additionally, we introduce a hierarchical multi-scale coordinate embedding and a low-rank watermark injection strategy to ensure high-quality watermark generation and robust decoding. Experimental results demonstrate that our method significantly outperforms existing schemes in terms of both robustness and computational efficiency while preserving high image quality. Our approach achieves an accuracy greater than 98\% in watermark extraction with only 0.4\% of the image area in 2K images. These results highlight the effectiveness of our method, making it a promising solution for large-scale and high-resolution image watermarking applications.

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in-full for each system of interest. The widespread success of generative models has inspired interest into overcoming this limitation through learning sampling algorithms. Despite performing on par with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We prove that deep learning enables the design of scalable and transferable samplers by introducing Ensemble, a 200 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Ensemble draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Ensemble as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based finetuning procedure to achieve superior performance to established methods such as sequential Monte Carlo. We open-source the Ensemble codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and finetuning objectives.

Symbolic regression (SR) seeks interpretable analytical expressions that uncover the governing relationships within data, providing mechanistic insight beyond 'black-box' models. However, existing SR methods often suffer from two key limitations: (1) *redundant representations* that fail to capture mathematical equivalences and higher-order operand relations, breaking permutation invariance and hindering efficient learning; and (2) *sparse rewards* caused by incomplete incorporation of constraints that can only be evaluated on full expressions, such as constant fitting or physical-law verification. To address these challenges, we propose a unified framework, **Graph-based Symbolic Regression (GSR)**, which compresses the search space through a permutation-invariant representation, Expression Graphs (EGs), that intrinsically encode expression equivalences via a term-rewriting system (TRS) and a directed acyclic graph (DAG) structure; and mitigates reward sparsity via employing hybrid neural-guided Monte-Carlo tree search (hnMCTS) on EGs, where the constraint-informed neural guidance enables direct incorporation of expression-level constraint priors, and an adaptive $\epsilon$-UCB policy balances exploration and exploitation. Theoretical analyses establish the uniqueness of our proposed EG representation and the convergence of the hnMCTS algorithm. Experiments on synthetic and real-world scientific datasets demonstrate the efficiency and accuracy of GSR in discovering underlying expressions and adhering to physical laws, offering practical solutions for scientific discovery.

Patent examination remains an ongoing challenge in the NLP literature even after the advent of large language models (LLMs), as it requires an extensive yet nuanced human judgment on whether a submitted $\textit{claim}$ meets the statutory standards of $\textit{novelty}$ and $\textit{non-obviousness}$ against previously granted claims—$\textit{prior art}$—in expert domains. Previous NLP studies have approached this challenge as a prediction task (e.g., forecasting grant outcomes) with high-level proxies such as similarity metrics or classifiers trained on historical labels. However, this approach often overlooks the step-by-step evaluations that examiners must make with profound information, including rationales for the decisions provided in $\textit{office actions}$ documents, which also makes it harder to measure the current state of techniques in patent review processes. To fill this gap, we construct PANORAMA, a dataset of 8,143 U.S. patent examination records that preserves the full decision trails, including original applications, all cited references, $\textit{Non-Final Rejections}$, and $\textit{Notices of Allowance}$. Also, PANORAMA decomposes the trails into sequential benchmarks that emulate patent professionals' patent review processes and allow researchers to examine large language models' capabilities at each step of them. Our findings indicate that, although LLMs are relatively effective at retrieving relevant prior art and pinpointing the pertinent paragraphs, they struggle to assess the novelty and non-obviousness of patent claims. We discuss these results and argue that advancing NLP, including LLMs, in the patent domain requires a deeper understanding of real-world patent examination. Our dataset is openly available at https://huggingface.co/datasets/LG-AI-Research/PANORAMA.