NeurIPS 2025 Papers

The hypothesis that Convolutional Neural Networks (CNNs) are inherently texture-biased has shaped much of the discourse on feature use in deep learning. We revisit this hypothesis by examining limitations in the cue-conflict experiment by Geirhos et al. To address these limitations, we propose a domain-agnostic framework that quantifies feature reliance through systematic suppression of shape, texture, and color cues, avoiding the confounds of forced-choice conflicts. By evaluating humans and neural networks under controlled suppression conditions, we find that CNNs are not inherently texture-biased but predominantly rely on local shape features. Nonetheless, this reliance can be substantially mitigated through modern training strategies or architectures (ConvNeXt, ViTs). We further extend the analysis across computer vision, medical imaging, and remote sensing, revealing that reliance patterns differ systematically: computer vision models prioritize shape, medical imaging models emphasize color, and remote sensing models exhibit a stronger reliance on texture. Code is available at https://github.com/tomburgert/feature-reliance.

Latent diffusion models (LDMs) dominate high-quality image generation, yet integrating representation learning with generative modeling remains a challenge. We introduce a novel generative image modeling framework that seamlessly bridges this gap by leveraging a diffusion model to jointly model low-level image latents (from a variational autoencoder) and high-level semantic features (from a pretrained self-supervised encoder like DINO). Our latent-semantic diffusion approach learns to generate coherent image-feature pairs from pure noise, significantly enhancing both generative quality and training efficiency, all while requiring only minimal modifications to standard Diffusion Transformer architectures. By eliminating the need for complex distillation objectives, our unified design simplifies training and unlocks a powerful new inference strategy: Representation Guidance, which leverages learned semantics to steer and refine image generation. Evaluated in both conditional and unconditional settings, our method delivers substantial improvements in image quality and training convergence speed, establishing a new direction for representation-aware generative modeling.

Graphon models provide a flexible nonparametric framework for estimating latent connectivity probabilities in networks, enabling a range of downstream applications such as link prediction and data augmentation. However, accurate graphon estimation typically requires a large graph, whereas in practice, one often only observes a small-sized network. One approach to addressing this issue is to adopt a transfer learning framework, which aims to improve estimation in a small target graph by leveraging structural information from a larger, related source graph. In this paper, we propose a novel method, namely GTRANS, a transfer learning framework that integrates neighborhood smoothing and Gromov-Wasserstein optimal transport to align and transfer structural patterns between graphs. To prevent negative transfer, GTRANS includes an adaptive debiasing mechanism that identifies and corrects for target-specific deviations via residual smoothing. We provide theoretical guarantees on the stability of the estimated alignment matrix and demonstrate the effectiveness of GTRANS in improving the accuracy of target graph estimation through extensive synthetic and real data experiments. These improvements translate directly to enhanced performance in downstream applications, such as the graph classification task and the link prediction task.

Process reward models (PRMs) play a central role in guiding inference-time scaling algorithms for large language models (LLMs). However, we observe that even state-of-the-art PRMs can be poorly calibrated. Specifically, they tend to overestimate the success probability that a partial reasoning step will lead to a correct final answer, particularly when smaller LLMs are used to complete the reasoning trajectory. To address this, we present a calibration approach—performed via quantile regression—that adjusts PRM outputs to better align with true success probabilities. Leveraging these calibrated success estimates and their associated confidence bounds, we introduce an instance-adaptive scaling (IAS) framework that dynamically adjusts the compute budget based on the estimated likelihood that a partial reasoning trajectory will yield a correct final answer. Unlike conventional methods that allocate a fixed number of reasoning trajectories per query, this approach adapts to each instance and reasoning step when using our calibrated PRMs. Experiments on mathematical reasoning benchmarks show that (i) our PRM calibration method achieves small calibration error, outperforming the baseline methods, (ii) calibration is crucial for enabling effective IAS, and (iii) the proposed IAS strategy reduces inference costs while maintaining final answer accuracy, utilizing less compute on more confident problems as desired.

Efficient online decision-making in contextual bandits is challenging, as methods without informative priors often suffer from computational or statistical inefficiencies. In this work, we leverage pre-trained diffusion models as expressive priors to capture complex action dependencies and develop a practical algorithm that efficiently approximates posteriors under such priors, enabling both fast updates and sampling. Empirical results demonstrate the effectiveness and versatility of our approach across diverse contextual bandit settings.

Low-Rank Adaptation (LoRA) has become the de facto parameter-efficient fine-tuning (PEFT) method for large language models (LLMs) by constraining weight updates to low-rank matrices. Recent works such as Tied-LoRA, VeRA, and VB-LoRA push efficiency further by introducing additional constraints to reduce the trainable parameter space. In this paper, we show that the parameter space reduction strategies employed by these LoRA variants can be formulated within a unified framework, Uni-LoRA, where the LoRA parameter space, flattened as a high-dimensional vector space R^D, can be reconstructed through a projection from a subspace R^d, with d << D. We demonstrate that the fundamental difference among various LoRA methods lies in the choice of the projection matrix, P ∈ R^{D×d}. Most existing LoRA variants rely on layer-wise or structure-specific projections that limit cross-layer parameter sharing, thereby compromising parameter efficiency. In light of this, we introduce an efficient and theoretically grounded projection matrix that is isometric, enabling global parameter sharing and reducing computation overhead. Furthermore, under the unified view of Uni-LoRA, this design requires only a single trainable vector to reconstruct LoRA parameters for the entire LLM -- making Uni-LoRA both a unified framework and a “one-vector-only” solution. Extensive experiments on GLUE, mathematical reasoning, and instruction tuning benchmarks demonstrate that Uni-LoRA achieves state-of-the-art parameter efficiency while outperforming or matching prior approaches in predictive performance.

Variations in Magnetic resonance imaging (MRI) scanners and acquisition protocols cause distribution shifts that degrade reconstruction performance on unseen data. Test-time adaptation (TTA) offers a promising solution to address this discrepancies. However, previous single-shot TTA approaches are inefficient due to repeated training and suboptimal distributional models. Self-supervised learning methods may risk over-smoothing in scarce data scenarios. To address these challenges, we propose a novel Dual-Stage Distribution and Slice Adaptation (D2SA) via MRI implicit neural representation (MR-INR) to improve MRI reconstruction performance and efficiency, which features two stages. In the first stage, an MR-INR branch performs patient-wise distribution adaptation by learning shared representations across slices and modelling patient-specific shifts with mean and variance adjustments. In the second stage, single-slice adaptation refines the output from frozen convolutional layers with a learnable anisotropic diffusion module, preventing over-smoothing and reducing computation. Experiments across five MRI distribution shifts demonstrate that our method can integrate well with various self-supervised learning (SSL) framework, improving performance and accelerating convergence under diverse conditions.

Multimodal time series forecasting is foundational in various fields, such as utilizing satellite imagery and numerical data for predicting typhoons in climate science. However, existing multimodal approaches primarily focus on utilizing text data to help time series forecasting, leaving the visual data in existing time series datasets underexplored. Furthermore, it is challenging for models to effectively capture the physical information embedded in visual data, such as satellite imagery's temporal and geospatial context, which extends beyond images themselves. To address this gap, we propose physics-informed positional encoding (PIPE), a lightweight method that embeds physical information into vision language models (VLMs). PIPE introduces two key innovations: (1) a physics-informed positional indexing scheme for mapping physics to positional IDs, and (2) a variant-frequency positional encoding mechanism for encoding frequency information of physical variables and sequential order of tokens within the embedding space. By preserving both the physical information and sequential order information, PIPE significantly improves multimodal alignment and forecasting accuracy. Through the experiments on the most representative and the largest open-sourced satellite image dataset, PIPE achieves state-of-the-art performance in both deep learning forecasting and climate domain methods, demonstrating superiority across benchmarks, including a 12\% improvement in typhoon intensity forecasting over prior works.

The distribution of data changes over time; models operating in dynamic environments need retraining. But knowing when to retrain, without access to labels, is an open challenge since some, but not all shifts degrade model performance. This paper formalizes and addresses the problem of post-deployment deterioration (PDD) monitoring. We propose D3M, a practical and efficient monitoring algorithm based on the disagreement of predictive models, achieving low false positive rates under non-deteriorating shifts and provides sample complexity bounds for high true positive rates under deteriorating shifts. Empirical results on both standard benchmark and a real-world large-scale internal medicine dataset demonstrate the effectiveness of the framework and highlight its viability as an alert mechanism for high-stakes machine learning pipelines.

We study the task of panoptic symbol spotting, which involves identifying both individual instances of countable \textit{things} and the semantic regions of uncountable \textit{stuff} in computer-aided design (CAD) drawings composed of vector graphical primitives. Existing methods typically rely on image rasterization, graph construction, or point-based representation, but these approaches often suffer from high computational costs, limited generality, and loss of geometric structural information. In this paper, we propose \textit{VecFormer}, a novel method that addresses these challenges through \textit{line-based representation} of primitives. This design preserves the geometric continuity of the original primitive, enabling more accurate shape representation while maintaining a computation-friendly structure, making it well-suited for vector graphic understanding tasks. To further enhance prediction reliability, we introduce a \textit{Branch Fusion Refinement} module that effectively integrates instance and semantic predictions, resolving their inconsistencies for more coherent panoptic outputs. Extensive experiments demonstrate that our method establishes a new state-of-the-art, achieving 91.1 PQ, with Stuff-PQ improved by 9.6 and 21.2 points over the second-best results under settings with and without prior information, respectively—highlighting the strong potential of line-based representation as a foundation for vector graphic understanding.

Organisms constantly pivot between tasks such as evading predators, foraging, traversing rugged terrain, and socializing, often within milliseconds. Remarkably, they preserve knowledge of once-learned environments sans catastrophic forgetting, a phenomenon neuroscientists hypothesize, is due to a singular neural circuitry dynamically overlayed by neuromodulatory agents such as dopamine and acetylcholine. In parallel, deep learning research addresses analogous challenges via domain generalization ($\textbf{DG}$) and continual learning ($\textbf{CL}$), yet these methods remain siloed, despite the brain’s ability to perform them seamlessly. In particular, prior work has not explored architectures involving associative memories ($\textbf{AM}$s), which are an integral part of biological systems, to jointly address these tasks. We propose Memory-Integrated Reconfigurable Adapters ($\textbf{MIRA}$), a unified framework that integrates Hopfield-style associative memory modules atop a shared backbone. These memory modules store adapter-weight updates as values and retrieve them via learned keys. Associative memory keys are learned post-hoc to index and retrieve an affine combination of stored adapter updates for any given task or domain on a per-sample basis. By varying only the task-specific objectives, we demonstrate that $\textbf{MIRA}$ seamlessly accommodates domain shifts and sequential task exposures under one roof. Empirical evaluations on standard benchmarks confirm that our $\textbf{AM}$-augmented architecture significantly enhances adaptability and retention: in $\textbf{DG}$, $\textbf{MIRA}$ achieves SoTA out-of-distribution accuracy, and in incremental learning settings, it outperforms architectures explicitly designed to handle catastrophic forgetting using generic $\textbf{CL}$ algorithms. Extensive ablation studies validate the necessity of both associative memory storage and post-hoc key learning for robust interpolated retrieval of adapters. By unifying adapter-based modulation with biologically inspired associative memory, $\textbf{MIRA}$ delivers rapid task switching and enduring knowledge retention in a single extensible architecture, charting a path toward more versatile and memory-augmented AI systems.

Flexible docking, which predicts the binding conformations of both proteins and small molecules by modeling their structural flexibility, plays a vital role in structure-based drug design. Although recent generative approaches, particularly diffusion-based models, have shown promising results, they require iterative sampling to generate candidate structures and depend on separate scoring functions for pose selection. This leads to an inefficient pipeline that is difficult to scale in real-world drug discovery workflows. To overcome these challenges, we introduce FIGRDock, a fast and accurate flexible docking framework that understands complicated interactions between molecules and proteins with a regression-based approach. FIGRDock leverages initial docking poses from conventional tools to distill interaction-aware distance patterns, which serve as explicit structural conditions to directly guide the prediction of the final protein-ligand complex via a regression model. This one-shot inference paradigm enables rapid and precise pose prediction without reliance on multi-step sampling or external scoring stages. Experimental results show that FIGRDock achieves up to 100× faster inference than diffusion-based docking methods, while consistently surpassing them in accuracy across standard benchmarks. These results suggest that FIGRDock has the potential to offer a scalable and efficient solution for flexible docking, advancing the pace of structure-based drug discovery.

System identification involving the geometry, appearance, and physical properties from video observations is a challenging task with applications in robotics and graphics. Recent approaches have relied on fully differentiable Material Point Method (MPM) and rendering for simultaneous optimization of these properties. However, they are limited to simplified object-environment interactions with planar colliders and fail in more challenging scenarios where objects collide with non-planar surfaces. We propose AS-DiffMPM, a differentiable MPM framework that enables physical property estimation with arbitrarily shaped colliders. Our approach extends existing methods by incorporating a differentiable collision handling mechanism, allowing the target object to interact with complex rigid bodies while maintaining end-to-end optimization. We show AS-DiffMPM can be easily interfaced with various novel view synthesis methods as a framework for system identification from visual observations.

Dynamic graph learning is crucial for accurately modeling complex systems by integrating topological structure and temporal information within graphs. While memory-based methods are commonly used and excel at capturing short-range temporal correlations, they struggle with modeling long-range dependencies, harmonizing long-range and short-range correlations, and integrating structural information effectively. To address these challenges, we present SALoM: Structure Aware Temporal Graph Networks with Long-Short Memory Updater. SALoM features a memory module that addresses gradient vanishing and information forgetting, enabling the capture of long-term dependencies across various time scales. Additionally, SALoM utilizes a long-short memory updater (LSMU) to dynamically balance long-range and short-range temporal correlations, preventing over-generalization. By integrating co-occurrence encoding and LSMU through information bottleneck-based fusion, SALoM effectively captures both the structural and temporal information within graphs. Experimental results across various graph datasets demonstrate SALoM's superior performance, achieving state-of-the-art results in dynamic graph link prediction. Our code is openly accessible at https://github.com/wave5418/SALoM.

Hand-Object Interaction (HOI) generation has significant application potential. However, current 3D HOI motion generation approaches heavily rely on predefined 3D object models and lab-captured motion data, limiting generalization capabilities. Meanwhile, HOI video generation methods prioritize pixel-level visual fidelity, often sacrificing physical plausibility. Recognizing that visual appearance and motion patterns share fundamental physical laws in the real world, we propose a novel framework that combines visual priors and dynamic constraints within a synchronized diffusion process to generate the HOI video and motion simultaneously. To integrate the heterogeneous semantics, appearance, and motion features, our method implements tri-modal adaptive modulation for feature aligning, coupled with 3D full-attention for modeling inter- and intra-modal dependencies. Furthermore, we introduce a vision-aware 3D interaction diffusion model that generates explicit 3D interaction sequences directly from the synchronized diffusion outputs, then feeds them back to establish a closed-loop feedback cycle. This architecture eliminates dependencies on predefined object models or explicit pose guidance while significantly enhancing video-motion consistency. Experimental results demonstrate our method's superiority over state-of-the-art approaches in generating high-fidelity, dynamically plausible HOI sequences, with notable generalization capabilities in unseen real-world scenarios. Project page at [https://droliven.github.io/SViMo_project](https://droliven.github.io/SViMo_project).

In this work, we study offline convex optimization with smooth objectives, where the classical Nesterov's Accelerated Gradient (**NAG**) method achieves the optimal accelerated convergence. Extensive research has aimed to understand **NAG** from various perspectives, and a recent line of work approaches this from the viewpoint of online learning and online-to-batch conversion, emphasizing the role of *optimistic online algorithms* for acceleration. In this work, we contribute to this perspective by proposing novel *optimistic online-to-batch conversions* that incorporate optimism theoretically into the analysis, thereby significantly simplifying the online algorithm design while preserving the optimal convergence rates. Specifically, we demonstrate the effectiveness of our conversions through the following results: *(i)* when combined with simple online gradient descent, our optimistic conversion achieves the optimal accelerated convergence; *(ii)* our conversion also applies to strongly convex objectives, and by leveraging both optimistic online-to-batch conversion and optimistic online algorithms, we achieve the optimal accelerated convergence rate for strongly convex and smooth objectives, for the first time through the lens of online-to-batch conversion; *(iii)* our optimistic conversion can achieve universality to smoothness~---~applicable to both smooth and non-smooth objectives without requiring knowledge of the smoothness coefficient~---~and remains efficient as non-universal methods by using only one gradient query in each iteration. Finally, we highlight the effectiveness of our optimistic online-to-batch conversions by a precise correspondence with **NAG**.

Sample-wise learning curves plot performance versus training set size. They are useful for studying scaling laws and speeding up hyperparameter tuning and model selection. Learning curves are often assumed to be well-behaved: monotone (i.e. improving with more data) and convex. By constructing the Learning Curves Database 1.1 (LCDB 1.1), a large-scale database with high-resolution learning curves including more modern learners (CatBoost, TabNet, RealMLP, and TabPFN), we show that learning curves are less often well-behaved than previously thought. Using statistically rigorous methods, we observe significant ill-behavior in approximately 15% of the learning curves, almost twice as much as in previous estimates. We also identify which learners are to blame and show that specific learners are more ill-behaved than others. Additionally, we demonstrate that different feature scalings rarely resolve ill-behavior. We evaluate the impact of ill-behavior on downstream tasks, such as learning curve fitting and model selection, and find it poses significant challenges, underscoring the relevance and potential of LCDB 1.1 as a challenging benchmark for future research.

In this paper, we explore the asymptotically optimal tuning parameter choice in ridge regression for estimating nuisance functions of a statistical functional that has recently gained prominence in conditional independence testing and causal inference. Given a sample of size $n$, we study estimators of the Expected Conditional Covariance (ECC) between variables $Y$ and $A$ given a high-dimensional covariate $X \in \mathbb{R}^p$. Under linear regression models for $Y$ and $A$ on $X$ and the proportional asymptotic regime $p/n \to c \in (0, \infty)$, we evaluate three existing ECC estimators and two sample splitting strategies for estimating the required nuisance functions. Since no consistent estimator of the nuisance functions exists in the proportional asymptotic regime without imposing further structure on the problem, we first derive debiased versions of the ECC estimators that utilize the ridge regression nuisance function estimators. We show that our bias correction strategy yields $\sqrt{n}$-consistent estimators of the ECC across different sample splitting strategies and estimator choices. We then derive the asymptotic variances of these debiased estimators to illustrate the nuanced interplay between the sample splitting strategy, estimator choice, and tuning parameters of the nuisance function estimators for optimally estimating the ECC. Our analysis reveals that prediction-optimal tuning parameters (i.e., those that optimally estimate the nuisance functions) may not lead to the lowest asymptotic variance of the ECC estimator -- thereby demonstrating the need to be careful in selecting tuning parameters based on the final goal of inference. Finally, we verify our theoretical results through extensive numerical experiments.

Manhattan representations, defined by axis-aligned, orthogonal structures, are widely used in vision, robotics, and semiconductor design for their geometric regularity and algorithmic simplicity. In integrated circuit (IC) design, Manhattan geometry is key for routing, design rule checking, and lithographic manufacturability. However, as feature sizes shrink, optical system distortions lead to inconsistency between intended layout and printed wafer. Although Inverse Lithography Technology(ILT) is proposed to compensates these effects, learning-based ILT methods, while achieving high simulation fidelity, often generate curvilinear masks on continuous pixel grids, violating Manhattan constraints. Therefore, we propose TokMan, the first framework to formulate mask optimization as a discrete, structure-aware sequence modeling task. Our method leverages a Diffusion Transformer to tokenize layouts into discrete geometric primitives with polygon-wise dependencies and denoise Manhattan-aligned point sequences corrupted by optical proximity effects, while ensuring binary, manufacturable masks. Trained with self-supervised lithographic feedback through differentiable simulation and refined with ILT post-processing, TokMan achieves state-of-the-art fidelity, runtime efficiency, and strict manufacturing compliance on a large-scale dataset of IC layouts.