NeurIPS 2025 Papers

How to integrate and verify spatial intelligence in foundation models remains an open challenge. Current practice often proxies Visual-Spatial Intelligence (VSI) with purely textual prompts and VQA-style scoring, which obscures geometry, invites linguistic shortcuts, and weakens attribution to genuinely spatial skills. We introduce Spatial Intelligence Grid (SIG): a structured, grid-based schema that explicitly encodes object layouts, inter-object relations, and physically grounded priors. As a complementary channel to text, SIG provides a faithful, compositional representation of scene structure for foundation-model reasoning. Building on SIG, we derive SIG-informed evaluation metrics that quantify a model’s intrinsic VSI, which separates spatial capability from language priors. In few-shot in-context learning with state-of-the-art multimodal LLMs (e.g. GPT- and Gemini-family models), SIG yields consistently larger, more stable, and more comprehensive gains across all VSI metrics compared to VQA-only representations, indicating its promise as a data-labeling and training schema for learning VSI. We also release SIGBench, a benchmark of 1.4K driving frames annotated with ground-truth SIG labels and human gaze traces, supporting both grid-based machine VSI tasks and attention-driven, human-like VSI tasks in autonomous-driving scenarios.

Neural rendering techniques, including NeRF and Gaussian Splatting (GS), rely on photometric consistency to produce high-quality reconstructions. However, in real-world driving scenarios, it is challenging to guarantee perfect photometric consistency in acquired images. Appearance codes have been widely used to address this issue, but their modeling capability is limited, as a single code is applied to the entire image. Recently, the bilateral grid was introduced to perform pixel-wise color mapping, but it is difficult to optimize and constrain effectively. In this paper, we propose a novel multi-scale bilateral grid that unifies appearance codes and bilateral grids. We demonstrate that this approach significantly improves geometric accuracy in dynamic, decoupled autonomous driving scene reconstruction, outperforming both appearance codes and bilateral grids. This is crucial for autonomous driving, where accurate geometry is important for obstacle avoidance and control. Our method shows strong results across four datasets: Waymo, NuScenes, Argoverse, and PandaSet. We further demonstrate that the improvement in geometry is driven by the multi-scale bilateral grid, which effectively reduces floaters caused by photometric inconsistency.

Text-to-SQL systems translate natural language (NL) questions into SQL queries, enabling non-technical users to interact with structured data. While large language models (LLMs) have shown promising results on the text-to-SQL task, they often produce semantically incorrect yet syntactically valid queries, with limited insight into their reliability. We propose SQLens, an end-to-end framework for fine-grained detection and correction of semantic errors in LLM-generated SQL. SQLens integrates error signals from both the underlying database and the LLM to identify potential semantic errors within SQL clauses. It further leverages these signals to guide query correction. Empirical results on two public benchmarks show that SQLens outperforms the best LLM-based self-evaluation method by 25.78% in F1 for error detection, and improves execution accuracy of out-of-the-box text-to-SQL systems by up to 20%.

Mask-based pretraining has become a cornerstone of modern large-scale models across language, vision, and recently biology. Despite its empirical success, its role and limits in learning data representations have been unclear. In this work, we show that the behavior of mask-based pretraining can be directly characterized by test risk in high-dimensional minimum-norm ("ridge-less") linear regression, without relying on further model specifications. Further analysis of linear models uncovers several novel aspects of mask-based pretraining. The theoretical framework and its implications have been validated across diverse neural architectures (including MLPs, CNNs, and Transformers) applied to both vision and language tasks. Guided by our theory, we propose an embarrassingly simple yet overlooked pretraining scheme named *Randomly Random Mask AutoEncoding* (**R²MAE**), which enforces capturing multi-scale features from data and is able to outperform optimal fixed mask ratio settings in our linear model framework. We implement R²MAE in vision, language, DNA sequence, and single-cell models, where it consistently outperforms standard and more complicated masking schemes, leading to improvements for state-of-the-art models. Our code is available at [this URL](https://github.com/MingzeDong/r2mae).

Advancements in AI for science unlocks capabilities for critical drug discovery tasks such as protein-ligand binding affinity prediction. However, current models overfit to existing oversimplified datasets that does not represent naturally occurring and biologically relevant proteins with modifications. In this work, we curate a complete and modification-aware version of the widely used DAVIS dataset by incorporating 4,032 kinase–ligand pairs involving substitutions, insertions, deletions, and phosphorylation events. This enriched dataset enables benchmarking of predictive models under biologically realistic conditions. Based on this new dataset, we propose three benchmark settings—Augmented Dataset Prediction, Wild-Type to Modification Generalization, and Few-Shot Modification Generalization—designed to assess model robustness in the presence of protein modifications. Through extensive evaluation of both docking-free and docking-based methods, we find that docking-based model generalize better in zero-shot settings. In contrast, docking-free models tend to overfit to wild-type proteins and struggle with unseen modifications but show notable improvement when fine-tuned on a small set of modified examples. We anticipate that the curated dataset and benchmarks offer a valuable foundation for developing models that better generalize to protein modifications, ultimately advancing precision medicine in drug discovery. The benchmark is available at: https://github.com/ZhiGroup/DAVIS-complete

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained molecular annotations across multiple levels, bridging the gap between molecules and textual descriptions. Additionally, we propose chemically-informative molecular representation, effectively addressing limitations in existing molecular representation strategies. Building upon these innovations, we develop KnowMol, a state-of-the-art multi-modal molecular large language model. Extensive experiments demonstrate that KnowMol achieves superior performance across molecular understanding and generation tasks.

Recent advancements in static feed-forward scene reconstruction have demonstrated significant progress in high-quality novel view synthesis. However, these models often struggle with generalizability across diverse environments and fail to effectively handle dynamic content. We present BTimer (short for Bullet Timer), the first motion-aware feed-forward model for real-time reconstruction and novel view synthesis of dynamic scenes. Our approach reconstructs the full scene in a 3D Gaussian Splatting representation at a given target (‘bullet’) timestamp by aggregating information from all the context frames. Such a formulation allows BTimer to gain scalability and generalization by leveraging both static and dynamic scene datasets. Given a casual monocular dynamic video, BTimer reconstructs a bullet-time scene within 150ms while reaching state-of-the-art performance on both static and dynamic scene datasets, even compared with optimization-based approaches.

In this work, we address the task of 3D reconstruction in dynamic scenes, where object motions frequently degrade the quality of previous 3D pointmap regression methods, such as DUSt3R, that are originally designed for static 3D scene reconstruction. Although these methods provide an elegant and powerful solution in static settings, they struggle in the presence of dynamic motions that disrupt alignment based solely on camera poses. To overcome this, we propose D$^2$USt3R that directly regresses Static-Dynamic Aligned Pointmaps (SDAP) that simultaneiously capture both static and dynamic 3D scene geometry. By explicitly incorporating both spatial and temporal aspects, our approach successfully encapsulates 3D dense correspondence to the proposed pointmaps, enhancing downstream tasks. Extensive experimental evaluations demonstrate that our proposed approach consistently achieves superior 3D reconstruction performance across various datasets featuring complex motions.

We introduce MusclePose as an end-to-end learnable physics-infused 3D human pose estimator that incorporates muscle-dynamics modeling to infer human dynamics from monocular video. Current physics pose estimators aim to predict physically plausible poses by enforcing the underlying dynamics equations that govern motion. Since this is an underconstrained problem without force-annotated data, methods often estimate kinetics with external physics optimizers that may not be compatible with existing learning frameworks, or are too slow for real-time inference. While more recent methods use a regression-based approach to overcome these issues, the estimated kinetics can be seen as auxiliary predictions, and may not be physically plausible. To this end, we build on existing regression-based approaches, and aim to improve the biofidelity of kinetic inference with a multihypothesis approach --- by inferring joint torques via Lagrange’s equations and via muscle dynamics modeling with muscle torque generators. Furthermore, MusclePose predicts detailed human anthropometrics based on values from biomechanics studies, in contrast to existing physics pose estimators that construct their human models with shape primitives. We show that MusclePose is competitive with existing 3D pose estimators in positional accuracy, while also able to infer plausible human kinetics and muscle signals consistent with values from biomechanics studies, without requiring an external physics engine.

We propose a general framework for conditional sampling in PDE-based inverse problems, targeting the recovery of whole solutions from extremely sparse or noisy measurements. This is accomplished by a function-space diffusion model and plug-and-play guidance for conditioning. Our method first trains an unconditional discretization-agnostic denoising model using neural operator architectures. At inference, we refine the samples to satisfy sparse observation data via a gradient-based guidance mechanism. Through rigorous mathematical analysis, we extend Tweedie's formula to infinite-dimensional Hilbert spaces, providing the theoretical foundation for our posterior sampling approach. Our method (FunDPS) accurately captures posterior distribution in function spaces under minimal supervision and severe data scarcity. Across five PDE tasks with only 3\% observation, our method achieves an average 32\% accuracy improvement over state-of-the-art fixed-resolution diffusion baselines while reducing sampling steps by 4x. Furthermore, multi-resolution fine-tuning ensures strong cross-resolution generalizability and speedup. To the best of our knowledge, this is the first diffusion-based framework to operate independently of discretization, offering a practical and flexible solution for forward and inverse problems in the context of PDEs. Code is available at https://github.com/neuraloperator/FunDPS.

Operator eigenvalue problems play a critical role in various scientific fields and engineering applications, yet numerical methods are hindered by the curse of dimensionality. Recent deep learning methods provide an efficient approach to address this challenge by iteratively updating neural networks. These methods' performance relies heavily on the spectral distribution of the given operator: larger gaps between the operator's eigenvalues will improve precision, thus tailored spectral transformations that leverage the spectral distribution can enhance their performance. Based on this observation, we propose the **S**pectral **T**ransformation **Net**work (**STNet**). During each iteration, STNet uses approximate eigenvalues and eigenfunctions to perform spectral transformations on the original operator, turning it into an equivalent but easier problem. Specifically, we employ deflation projection to exclude the subspace corresponding to already solved eigenfunctions, thereby reducing the search space and avoiding converging to existing eigenfunctions. Additionally, our filter transform magnifies eigenvalues in the desired region and suppresses those outside, further improving performance. Extensive experiments demonstrate that STNet consistently outperforms existing learning-based methods, achieving state-of-the-art performance in accuracy.

Misinformation detectors often rely on superficial cues (i.e., shortcuts) that correlate with misinformation in training data but fail to generalize to the diverse and evolving nature of real-world misinformation. This issue is exacerbated by large language models (LLMs), which can easily generate convincing misinformation using simple prompts. We introduce TruthOverTricks, a unified evaluation paradigm for measuring shortcut learning in misinformation detection. TruthOverTricks categorizes shortcut behaviors into intrinsic shortcut induction and extrinsic shortcut injection, and evaluates seven representative detectors across 14 popular benchmarks, along with two new factual misinformation datasets, NQ-Misinfo and Streaming-Misinfo. Empirical results reveal that existing detectors suffer severe performance degradation when exposed to both naturally occurring and adversarially crafted shortcuts. To address this, we propose the Shortcut Mitigation Framework (SMF), an LLM-augmented data augmentation framework that mitigates shortcut reliance through paraphrasing, factual summarization, and sentiment normalization. SMF consistently enhances robustness across 16 benchmarks, forcing models to rely on deeper semantic understanding rather than shortcut cues.

We propose Sparta Alignment, an algorithm to collectively align multiple LLMs through competition and combat. To complement a single model's lack of diversity in generation and biases in evaluation, multiple LLMs form a 'sparta tribe' to compete against each other in fulfilling instructions while serving as judges for the competition of others. For each iteration, one instruction and two models are selected for a duel, the other models evaluate the two responses, and their evaluation scores are aggregated through a adapted elo-ranking based reputation system, where winners/losers of combat gain/lose weight in evaluating others. The peer-evaluated combat results then become preference pairs where the winning response is preferred over the losing one, and all models learn from these preferences at the end of each iteration. Sparta Alignment enables the self-evolution of multiple LLMs in an iterative and collective competition process. Extensive experiments demonstrate that Sparta Alignment outperforms initial models and 4 self-alignment baselines across 10 out of 12 tasks and datasets with 7.0\% average improvement. Further analysis reveals that Sparta Alignment generalizes more effectively to unseen tasks and leverages the expertise diversity of participating models to produce more logical, direct and informative outputs.

**Diffusion models** achieve remarkable generative performance but are hampered by slow, iterative inference. Model distillation seeks to train a fast student generator. **Variational Score Distillation (VSD)** offers a principled KL-divergence minimization framework for this task. This method cleverly avoids computing the teacher model's Jacobian, but its student gradient relies on the score of the student's own noisy marginal distribution, $\nabla\_{\mathbf{x}\_t} \log p\_{\phi,t}(\mathbf{x}\_t)$. VSD thus requires approximations, such as training an auxiliary network to estimate this score. These approximations can introduce biases, cause training instability, or lead to an incomplete match of the target distribution, potentially focusing on conditional means rather than broader distributional features. We introduce **VarFlow**, a method based on a **Score-Rule Variational Distillation (SRVD)** framework. VarFlow trains a one-step generator $g_{\phi}(\mathbf{z})$ by directly minimizing an energy distance (derived from the strictly proper energy score) between the student's induced noisy data distribution $p_{\phi,t}(\mathbf{x}_t)$ and the teacher's target noisy distribution $q_t(\mathbf{x}_t)$. This objective is estimated entirely using samples from these two distributions. Crucially, VarFlow bypasses the need to compute or approximate the intractable student score. By directly matching the full noisy marginal distributions, VarFlow aims for a more comprehensive and robust alignment between student and teacher, offering an efficient and theoretically grounded path to high-fidelity one-step generation.

Predictions and generations from large language models are increasingly being explored as an aid in limited data regimes, such as in computational social science and human subjects research. While prior technical work has mainly explored the potential to use model-predicted labels for unlabeled data in a principled manner, there is increasing interest in using large language models to generate entirely new synthetic samples (e.g., synthetic simulations), such as in responses to surveys. However, it remains unclear by what means practitioners can combine such data with real data and yet produce statistically valid conclusions upon them. In this paper, we introduce a new estimator based on generalized method of moments, providing a hyperparameter-free solution with strong theoretical guarantees to address this challenge. Intriguingly, we find that interactions between the moment residuals of synthetic data and those of real data (i.e., when they are predictive of each other) can greatly improve estimates of the target parameter. We validate the finite-sample performance of our estimator across different tasks in computational social science applications, demonstrating large empirical gains.

Color enhancement is a crucial yet challenging task in digital photography. It demands methods that are (i) expressive enough for fine-grained adjustments, (ii) adaptable to diverse inputs, and (iii) able to preserve texture. Existing approaches typically fall short in at least one of these aspects, yielding unsatisfactory results. We propose GenColor, a novel diffusion-based framework for sophisticated, texture-preserving color enhancement. GenColor reframes the task as conditional image generation. Leveraging ControlNet and a tailored training scheme, it learns advanced color transformations that adapt to diverse lighting and content. We train GenColor on ARTISAN, our newly collected large-scale dataset of 1.2M high-quality photographs specifically curated for enhancement tasks. To overcome texture preservation limitations inherent in diffusion models, we introduce a color-transfer network with a novel degradation scheme that simulates texture–color relationships. This network achieves pixel-perfect texture preservation while enabling fine-grained color matching with the diffusion-generated reference images. Extensive experiments show that GenColor produces visually compelling results comparable to those of expert colorists and surpasses state-of-the-art methods in both subjective and objective evaluations. We have released the code and dataset.

This work presents Orient Anything V2, an enhanced foundation model for unified understanding of object 3D orientation and rotation from single or paired images. Building upon Orient Anything V1, which defines orientation via a single unique front face, V2 extends this capability to handle objects with diverse rotational symmetries and directly estimate relative rotations. These improvements are enabled by four key innovations: 1) Scalable 3D assets synthesized by generative models, ensuring broad category coverage and balanced data distribution; 2) An efficient, model-in-the-loop annotation system that robustly identifies 0 to N valid front faces for each object; 3) A symmetry-aware, periodic distribution fitting objective that captures all plausible front-facing orientations, effectively modeling object rotational symmetry; 4) A multi-frame architecture that directly predicts relative object rotations. Extensive experiments show that Orient Anything V2 achieves state-of-the-art zero-shot performance on orientation estimation, 6DoF pose estimation, and object symmetry recognition across 11 widely used benchmarks. The model demonstrates strong generalization, significantly broadening the applicability of orientation estimation in diverse downstream tasks.

Inverse design aims to design the input variables of a physical system to optimize a specified objective function, typically formulated as a search or optimization problem. However, in 3D domains, the design space grows exponentially, rendering exhaustive grid-based searches infeasible. Recent advances in deep learning have accelerated inverse design by providing powerful generative priors and differentiable surrogate models. Nevertheless, current methods tend to approximate the 3D design space using 2D projections or fine-tune existing 3D shapes. These approaches sacrifice volumetric detail and constrain design exploration, preventing true 3D design from scratch. In this paper, we propose a 3D Inverse Design (3DID) framework that directly navigates the 3D design space by coupling a continuous latent representation with a physics-aware optimization strategy. We first learn a unified physics–geometry embedding that compactly captures shape and physical field data in a continuous latent space. Then, we introduce a two-stage strategy to perform physics-aware optimization. In the first stage, a gradient-guided diffusion sampler explores the global latent manifold. In the second stage, an objectivedriven, topology-preserving refinement further sculpts each candidate toward the target objective. This enables 3DID to generate high-fidelity 3D geometries, outperforming existing methods in both solution quality and design versatility.

Drug recommendation systems aim to identify optimal drug combinations for patient care, balancing therapeutic efficacy and safety. Advances in large-scale longitudinal EHRs have enabled learning-based approaches that leverage patient histories such as diagnoses, procedures, and previously prescribed drugs, to model complex patient-drug relationships. Yet, many existing solutions overlook standard clinical practices that favor certain drugs for specific conditions and fail to fully integrate the influence of molecular substructures on drug efficacy and safety. In response, we propose \textbf{SubRec}, a unified framework that integrates representation learning across both patient and drug spaces. Specifically, SubRec introduces a conditional information bottleneck to extract core drug substructures most relevant to patient conditions, thereby enhancing interpretability and clinical alignment. Meanwhile, an adaptive vector quantization mechanism is designed to generate patient–drug interaction patterns into a condition-aware codebook which reuses clinically meaningful patterns, reduces training overhead, and provides a controllable latent space for recommendation. Crucially, the synergy between condition-specific substructure learning and discrete patient prototypes allows SubRec to make accurate and personalized drug recommendations. Experimental results on the real-world MIMIC III and IV demonstrate our model's advantages. The source code is available at \href{https://anonymous.4open.science/r/DrugRecommendation-5173}{https://anonymous.4open.science/}.