NeurIPS 2025 论文列表

While Generative AI rapidly advances in various domains, generating truly creative, aesthetic, and counter-intuitive outputs remains a challenge. This paper presents an approach to tackle these difficulties in the domain of chess puzzles. We start by benchmarking Generative AI architectures, and then introduce an RL framework with novel rewards based on chess engine search statistics to overcome some of those shortcomings. The rewards are designed to enhance a puzzle's uniqueness, counter-intuitiveness, diversity, and realism. Our RL approach dramatically increases counter-intuitive puzzle generation by 10x, from 0.22\% (supervised) to 2.5\%, surpassing existing dataset rates (2.1\%) and the best Lichess-trained model (0.4\%). Our puzzles meet novelty and diversity benchmarks, retain aesthetic themes, and are rated by human experts as more creative, enjoyable, and counter-intuitive than composed book puzzles, even approaching classic compositions. Our final outcome is a curated booklet of these novel AI-generated puzzles, which is acknowledged for creativity by three world-renowned experts.

Light field microscopy (LFM) has become an emerging tool in neuroscience for large-scale neural imaging in vivo, with XLFM (eXtended Light Field Microscopy) notable for its single-exposure volumetric imaging, broad field of view, and high temporal resolution. However, learning-based 3D reconstruction in XLFM remains underdeveloped due to two core challenges: the absence of standardized datasets and the lack of methods that can efficiently model its angular–spatial structure while remaining physically grounded. We address these challenges by introducing three key contributions. First, we construct the XLFM-Zebrafish benchmark, a large-scale dataset and evaluation suite for XLFM reconstruction. Second, we propose Masked View Modeling for Light Fields (MVM-LF), a self-supervised task that learns angular priors by predicting occluded views, improving data efficiency. Third, we formulate the Optical Rendering Consistency Loss (ORC Loss), a differentiable rendering constraint that enforces alignment between predicted volumes and their PSF-based forward projections. On the XLFM-Zebrafish benchmark, our method improves PSNR by 7.7\% over state-of-the-art baselines. Code and datasets are publicly available at: https://github.com/hefengcs/XLFM-Former.

Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring heuristic MSA subsampling approaches for generating alternative states. In parallel, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for imaging near-native structural heterogeneity, but is challenged by arduous pipelines to transform raw experimental data into atomic models. Here, we bridge the gap between these modalities, combining cryo-EM density maps with the rich sequence and biophysical priors learned by protein structure prediction models. Our method, CryoBoltz, guides the sampling trajectory of a pretrained biomolecular structure prediction model using both global and local structural constraints derived from density maps, driving predictions towards conformational states consistent with the experimental data. We demonstrate that this flexible yet powerful inference-time approach allows us to build atomic models into heterogeneous cryo-EM maps across a variety of dynamic biomolecular systems including transporters and antibodies.

We consider random instances of non-convex perceptron problems in the high-dimensional limit of a large number of examples $M$ and weights $N$, with finite load $\alpha = M/N$. We develop a formalism based on replica theory to predict the fundamental limits of efficiently sampling the solution space using generative diffusion algorithms, conjectured to be saturated when the score function is provided by Approximate Message Passing. For the spherical perceptron with negative margin $\kappa$, we find that the uniform distribution over solutions can be efficiently sampled in most of the Replica Symmetric region of the $\alpha$–$\kappa$ plane. In contrast, for binary weights, sampling from the uniform distribution remains intractable. A theoretical analysis of this obstruction leads us to identify a potential $U(s) = -\log(s)$, under which the corresponding tilted distribution becomes efficiently samplable via diffusion. Moreover, we show numerically that an annealing procedure over the shape of this potential yields a fast and robust Markov Chain Monte Carlo algorithm for sampling the solution space of the binary perceptron.

Predicting the bioactivity of candidate ligands remains a central challenge in drug discovery. Ligands and endogenous substrates often compete for the same binding sites on target proteins, and the extent to which a ligand can modulate protein function depends not only on its binding but also on how effectively it occupies the relevant pocket. However, most existing methods focus narrowly on local interactions within protein–ligand complexes and neglect spatial emptiness—the unoccupied regions within the binding site that may permit endogenous molecules to engage or interfere. Such unfilled space can diminish the ligand’s functional impact, regardless of binding affinity. To overcome this key limitation in protein–ligand modeling, we propose LigoSpace, a novel method integrating three core components. LigoSpace introduces GeoREC (Geometric Representation of Spatial Emptiness in Complexes) to quantify atomic-level empty space and Union-Pocket to unify multiple protein pockets, providing a global view of binding sites. Additionally, LigoSpace employs a pairwise loss instead of commonly used MSE loss, to better capture relative relationships critical for drug discovery. Extensive experiments on multiple datasets with diverse bioactivity types demonstrate that LigoSpace significantly improves performance when integrated into state-of-the-art models, highlighting the effectiveness of its novel components.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, we present a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only $\sim$50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to build increasingly capable AI models.

Text-to-image diffusion models often exhibit degraded performance when generating images beyond their training resolution. Recent training-free methods can mitigate this limitation, but they often require substantial computation or are incompatible with recent Diffusion Transformer models. In this paper, we propose ScaleDiff, a model-agnostic and highly efficient framework for extending the resolution of pretrained diffusion models without any additional training. A core component of our framework is Neighborhood Patch Attention (NPA), an efficient mechanism that reduces computational redundancy in the self-attention layer with non-overlapping patches. We integrate NPA into an SDEdit pipeline and introduce Latent Frequency Mixing (LFM) to better generate fine details. Furthermore, we apply Structure Guidance to enhance global structure during the denoising process. Experimental results demonstrate that ScaleDiff achieves state-of-the-art performance among training-free methods in terms of both image quality and inference speed on both U-Net and Diffusion Transformer architectures.

Nuclear fusion plays a pivotal role in the quest for reliable and sustainable energy production. A major roadblock to viable fusion power is understanding plasma turbulence, which significantly impairs plasma confinement, and is vital for next generation reactor design. Plasma turbulence is governed by the nonlinear gyrokinetic equation, which evolves a 5D distribution function over time. Due to its high computational cost, reduced-order models are often employed in practice to approximate turbulent transport of energy. However, they omit nonlinear effects unique to the full 5D dynamics. To tackle this, we introduce GyroSwin, the first scalable 5D neural surrogate that can model 5D nonlinear gyrokinetic simulations, thereby capturing the physical phenomena neglected by reduced models, while providing accurate estimates of turbulent heat transport. GyroSwin (i) extends hierarchical Vision Transformers to 5D, (ii) introduces cross-attention and integration modules for latent 3D$\leftrightarrow$5D interactions between electrostatic potential fields and the distribution function, and (iii) performs channelwise mode separation inspired by nonlinear physics. We demonstrate that GyroSwin outperforms widely used reduced numerics on heat flux prediction, captures the turbulent energy cascade, and reduces the cost of fully resolved nonlinear gyrokinetics by three orders of magnitude while remaining physically verifiable. GyroSwin shows promising scaling laws, tested up to one billion parameters, paving the way for scalable neural surrogates for gyrokinetic simulations of plasma turbulence.

Nuclear Magnetic Resonance (NMR) spectroscopy is a cornerstone technique for determining the structures of small molecules and is especially critical in the discovery of novel natural products and clinical therapeutics. Yet, interpreting NMR spectra remains a time-consuming, manual process requiring extensive domain expertise. We introduce ChefNMR (CHemical Elucidation From NMR), an end-to-end framework that directly predicts an unknown molecule's structure solely from its 1D NMR spectra and chemical formula. We frame structure elucidation as conditional generation from an atomic diffusion model built on a non-equivariant transformer architecture. To model the complex chemical groups found in natural products, we generated a dataset of simulated 1D NMR spectra for over 111,000 natural products. ChefNMR predicts the structures of challenging natural product compounds with an unsurpassed accuracy of over 65%. This work takes a significant step toward solving the grand challenge of automating small-molecule structure elucidation and highlights the potential of deep learning in accelerating molecular discovery.

Cosmological simulations provide a wealth of data in the form of point clouds and directed trees. A crucial goal is to extract insights from this data that shed light on the nature and composition of the Universe. In this paper we introduce CosmoBench, a benchmark dataset curated from state-of-the-art cosmological simulations whose runs required more than 41 million core-hours and generated over two petabytes of data. CosmoBench is the largest dataset of its kind: it contains 34 thousand point clouds from simulations of dark matter halos and galaxies at three different length scales, as well as 25 thousand directed trees that record the formation history of halos on two different time scales. The data in CosmoBench can be used for multiple tasks---to predict cosmological parameters from point clouds and merger trees, to predict the velocities of individual halos and galaxies from their collective positions, and to reconstruct merger trees on finer time scales from those on coarser time scales. We provide multiple baselines on these tasks, some based on established approaches from cosmological modeling and others rooted in machine learning. For the latter, we study different approaches---from simple linear models that are minimally constrained by symmetries to much larger and more computationally-demanding models in deep learning, such as graph neural networks. We find that least-squares fits with a handful of invariant features sometimes outperform deep architectures with many more parameters and far longer training times. Still there remains tremendous potential to improve these baselines by combining machine learning and cosmological modeling in a more principled way, one that fully exploits the structure in the data. CosmoBench sets the stage for bridging cosmology and geometric deep learning at scale. We invite the community to push the frontier of scientific discovery by engaging with this challenging, high-impact dataset. The data and code are available at [this URL](https://cosmobench.streamlit.app/).

Spatiotemporal trajectory data is crucial for various traffic-related applications. However, issues such as device malfunctions and network instability often result in sparse trajectories that lose detailed movement information compared to their dense counterparts. Recovering missing points in sparse trajectories is thus essential. Despite recent progress, three challenges remain. First, the lack of large-scale dense trajectory datasets hinders the training of a trajectory recovery model. Second, the varying spatiotemporal correlations in sparse trajectories make it hard to generalize across different sampling intervals. Third, extracting road conditions for missing points is non-trivial. To address these challenges, we propose $\textit{PLMTrajRec}$, a novel trajectory recovery model. It leverages the scalability of a pre-trained language model (PLM) and can effectively recover trajectories by fine-tuning with small-scale dense trajectory datasets. To handle different sampling intervals in sparse trajectories, we first convert sampling intervals and movement features into prompts for the PLM to understand. We then introduce a trajectory encoder to unify trajectories of varying intervals into a single interval. To extract road conditions for missing points, we propose an area flow-guided implicit trajectory prompt that represents traffic conditions in each region, and a road condition passing mechanism that infers the road conditions of missing points using the observed ones. Experiments on four public trajectory datasets with three sampling intervals demonstrate the effectiveness, scalability, and generalization ability of PLMTrajRec. Code is available at https://github.com/wtl52656/PLMTrajRec.

Machine learning interatomic potentials (MLIPs) have revolutionized molecular and materials modeling, but existing benchmarks suffer from data leakage, limited transferability, and an over-reliance on error-based metrics tied to specific density functional theory (DFT) references. We introduce MLIP Arena, a benchmark platform that evaluates force field performance based on physics awareness, chemical reactivity, stability under extreme conditions, and predictive capabilities for thermodynamic properties and physical phenomena. By moving beyond static DFT references and revealing the important failure modes of current foundation MLIPs in real-world settings, MLIP Arena provides a reproducible framework to guide the next-generation MLIP development toward improved predictive accuracy and runtime efficiency while maintaining physical consistency. The Python package and online leaderboard are available at https://github.com/atomind-ai/mlip-arena.

We present the Electronic Tensor Reconstruction Algorithm (ELECTRA) - an equivariant model for predicting electronic charge densities using floating orbitals. Floating orbitals are a long-standing concept in the quantum chemistry community that promises more compact and accurate representations by placing orbitals freely in space, as opposed to centering all orbitals at the position of atoms. Finding the ideal placement of these orbitals requires extensive domain knowledge, though, which thus far has prevented widespread adoption. We solve this in a data-driven manner by training a Cartesian tensor network to predict the orbital positions along with orbital coefficients. This is made possible through a symmetry-breaking mechanism that is used to learn position displacements with lower symmetry than the input molecule while preserving the rotation equivariance of the charge density itself. Inspired by recent successes of Gaussian Splatting in representing densities in space, we are using Gaussian orbitals and predicting their weights and covariance matrices. Our method achieves a state-of-the-art balance between computational efficiency and predictive accuracy on established benchmarks. Furthermore, ELECTRA is able to lower the compute time required to arrive at converged DFT solutions - initializing calculations using our predicted densities yields an average 50.72 % reduction in self-consistent field (SCF) iterations on unseen molecules.

This paper introduces Codified Profiles for role-playing, a novel approach that represents character logic as structured, executable functions for behavioral decision-making. Converted by large language model (LLM) from textual profiles, each codified profile defines a set of functions parse_by_scene(scene) that output multiple logic-grounded assertions according to scene, using both explicit control structures (e.g., if-then-else) and flexible check_condition(scene, question) functions where each question is a semantically meaningful prompt about the scene (e.g., "Is the character in danger?") discriminated by the role-playing LLM as true, false, or unknown. This explicit representation offers three key advantages over traditional prompt-based textual profiles, which append character descriptions directly into text prompts: (1) Persistence, by enforcing complete and consistent execution of character logic, rather than relying on the model's implicit reasoning; (2) Updatability, through systematic inspection and revision of behavioral logic, which is difficult to track or debug in prompt-only approaches; (3) Controllable Randomness, by supporting stochastic behavior directly within the logic, enabling fine-grained variability that prompting alone struggles to achieve. To validate these advantages, we introduce a new benchmark constructed from 83 characters and 5,141 scenes curated from Fandom, using natural language inference (NLI)-based scoring to compare character responses against ground-truths. Our experiments demonstrate the significant benefits of codified profiles in improving persistence, updatability, and behavioral diversity. Notably, by offloading a significant portion of reasoning to preprocessing, codified profiles enable even 1B-parameter models to perform high-quality role-playing, providing an efficient, lightweight foundation for local deployment of role-play agents.

Towards intelligent image editing, object removal should eliminate both the target object and its causal visual artifacts, such as shadows and reflections. However, existing image appearance-based methods either follow strictly mask-aligned training and fail to remove these casual effects which are not explicitly masked, or adopt loosely mask-aligned strategies that lack controllability and may unintentionally over-erase other objects. We identify that these limitations stem from ignoring the causal relationship between an object’s geometry presence and its visual effects. To address this limitation, we propose a geometry-aware two-stage framework that decouples object removal into (1) geometry removal and (2) appearance rendering. In the first stage, we remove the object directly from the geometry (e.g., depth) using strictly mask-aligned supervision, enabling structure-aware editing with strong geometric constraints. In the second stage, we render a photorealistic RGB image conditioned on the updated geometry, where causal visual effects are considered implicitly as a result of the modified 3D geometry. To guide learning in the geometry removal stage, we introduce a preference-driven objective based on positive and negative sample pairs, encouraging the model to remove objects as well as their causal visual artifacts while avoiding new structural insertions. Extensive experiments demonstrate that our method achieves state-of-the-art performance in removing both objects and their associated artifacts on two popular benchmarks. The project page is available at https://buxiangzhiren.github.io/GeoRemover.

Current 3D gaze estimation methods struggle to generalize across diverse data domains, primarily due to $\textbf{i)}$ $\textit{the scarcity of annotated datasets}$, and $\textbf{ii)}$ $\textit{the insufficient diversity of labeled data}$. In this work, we present OmniGaze, a semi-supervised framework for 3D gaze estimation, which utilizes large-scale unlabeled data collected from diverse and unconstrained real-world environments to mitigate domain bias and generalize gaze estimation in the wild. First, we build a diverse collection of unlabeled facial images, varying in facial appearances, background environments, illumination conditions, head poses, and eye occlusions. In order to leverage unlabeled data spanning a broader distribution, OmniGaze adopts a standard pseudo-labeling strategy and devises a reward model to assess the reliability of pseudo labels. Beyond pseudo labels as 3D direction vectors, the reward model also incorporates visual embeddings extracted by an off-the-shelf visual encoder and semantic cues from gaze perspective generated by prompting a Multimodal Large Language Model to compute confidence scores. Then, these scores are utilized to select high-quality pseudo labels and weight them for loss computation. Extensive experiments demonstrate that OmniGaze achieves state-of-the-art performance on five datasets under both in-domain and cross-domain settings. Furthermore, we also evaluate the efficacy of OmniGaze as a scalable data engine for gaze estimation, which exhibits robust zero-shot generalization on four unseen datasets.

Reduced-order modeling (ROM) of time-dependent and parameterized differential equations aims to accelerate the simulation of complex high-dimensional systems by learning a compact latent manifold representation that captures the characteristics of the solution fields and their time-dependent dynamics. Although high-fidelity numerical solvers generate the training datasets, they have thus far been excluded from the training process, causing the learned latent dynamics to drift away from the discretized governing physics. This mismatch often limits generalization and forecasting capabilities. In this work, we propose **Ph**ysics-**i**nformed **ROM** ($\Phi$-ROM) by incorporating differentiable PDE solvers into the training procedure. Specifically, the latent space dynamics and its dependence on PDE parameters are shaped directly by the governing physics encoded in the solver, ensuring a strong correspondence between the full and reduced systems. Our model outperforms state-of-the-art data-driven ROMs and other physics-informed strategies by accurately generalizing to new dynamics arising from unseen parameters, enabling long-term forecasting beyond the training horizon, maintaining continuity in both time and space, and reducing the data cost. Furthermore, $\Phi$-ROM learns to recover and forecast the solution fields even when trained or evaluated with sparse and irregular observations of the fields, providing a flexible framework for field reconstruction and data assimilation. We demonstrate the framework’s robustness across various PDE solvers and highlight its broad applicability by providing an open-source JAX implementation that is readily extensible to other PDE systems and differentiable solvers, available at https://phi-rom.github.io.

Gradient boosting has become a cornerstone of machine learning, enabling base learners such as decision trees to achieve exceptional predictive performance. While existing algorithms primarily handle scalar or Euclidean outputs, increasingly prevalent complex-structured data, such as distributions, networks, and manifold-valued outputs, present challenges for traditional methods. Such non-Euclidean data lack algebraic structures such as addition, subtraction, or scalar multiplication required by standard gradient boosting frameworks. To address these challenges, we introduce Fréchet geodesic boosting (FGBoost), a novel approach tailored for outputs residing in geodesic metric spaces. FGBoost leverages geodesics as proxies for residuals and constructs ensembles in a way that respects the intrinsic geometry of the output space. Through theoretical analysis, extensive simulations, and real-world applications, we demonstrate the strong performance and adaptability of FGBoost, showcasing its potential for modeling complex data.

Watermarking is a promising defense against the misuse of large language models (LLMs), yet it remains vulnerable to scrubbing and spoofing attacks. This vulnerability stems from an inherent trade-off governed by watermark window size: smaller windows resist scrubbing better but are easier to reverse-engineer, enabling low-cost statistics-based spoofing attacks. This work expands the trade-off boundary by introducing a novel mechanism, equivalent texture keys, where multiple tokens within a watermark window can independently support the detection. Based on the redundancy, we propose a watermark scheme with **S**ub-vocabulary decomposed **E**quivalent t**E**xture **K**ey (**SEEK**). It achieves a Pareto improvement, increasing the resilience against scrubbing attacks without compromising robustness to spoofing. Our code will be available at [https://github.com/Hearum/SeekWM](https://github.com/Hearum/SeekWM).