NeurIPS 2025 Papers

Graph machine learning architectures are typically tailored to specific tasks on specific datasets, which hinders their broader applicability. This has led to a new quest in graph machine learning: \emph{how to build graph foundation models (GFMs)} capable of generalizing across arbitrary graphs and features? In this work, we present a recipe for designing GFMs for node-level tasks from first principles. The key ingredient underpinning our study is a systematic investigation of the symmetries that a graph foundation model must respect. In a nutshell, we argue that label permutation-equivariance alongside feature permutation-invariance are necessary in addition to the common node permutation-equivariance on each local neighborhood of the graph. To this end, we first characterize the space of linear transformations that are equivariant to permutations of nodes and labels, and invariant to permutations of features. We then prove that the resulting network is a universal approximator on multisets that respect the aforementioned symmetries. Our recipe uses such layers on the multiset of features induced by the local neighborhood of the graph to obtain a class of graph foundation models for node property prediction. We validate our approach through extensive experiments on 29 real-world node classification datasets, demonstrating both strong zero-shot empirical performance and consistent improvement as the number of training graphs increases.

Direct Preference Optimization (DPO) is a key framework for aligning text-to-image models with human preferences, extended by Stepwise Preference Optimization (SPO) to leverage intermediate steps for preference learning, generating more aesthetically pleasing images with significantly less computational cost. While effective, SPO's underlying mechanisms remain underexplored. In light of this, we critically re-examine SPO by formalizing its mechanism as gradient guidance. This new lens shows that SPO uses biased temporal weighting, giving too little weight to later generative steps, and unlike likelihood centric views it reveals substantial noise in the gradient estimates. Leveraging these insights, our GradSPO algorithm introduces a simplified loss and a targeted, variance-informed noise reduction strategy, enhancing training stability. Evaluations on SD 1.5 and SDXL show GradSPO substantially outperforms leading baselines in human preference, yielding images with markedly improved aesthetics and semantic faithfulness, leading to more robust alignment. Code and models are available at https://github.com/JoshuaTTJ/GradSPO.

Biological circuits have evolved to incorporate multiple modules that perform similar functions. In the fly olfactory circuit, both lateral inhibition (LI) and neuronal spike frequency adaptation (SFA) are thought to enhance pattern separation for odor learning. However, it remains unclear whether these mechanisms play redundant or distinct roles in this process. In this study, we present a computational model of the fly olfactory circuit to investigate odor discrimination under varying noise conditions that simulate complex environments. Our results show that LI primarily enhances odor discrimination in low‑ and medium‑noise scenarios, but this benefit diminishes and may reverse under higher‑noise conditions. In contrast, SFA consistently improves discrimination across all noise levels. LI is preferentially engaged in low‑ and medium‑noise environments, whereas SFA dominates in high‑noise settings. When combined, these two sparsification mechanisms enable optimal discrimination performance. This work demonstrates that seemingly redundant modules in biological circuits can, in fact, be essential for achieving optimal learning in complex contexts.

In this paper, we establish global non-asymptotic convergence guarantees for the BFGS quasi-Newton method without requiring strong convexity or the Lipschitz continuity of the gradient or Hessian. Instead, we consider the setting where the objective function is strictly convex and strongly self-concordant. For an arbitrary initial point and any arbitrary positive-definite initial Hessian approximation, we prove global linear and superlinear convergence guarantees for BFGS when the step size is determined using a line search scheme satisfying the weak Wolfe conditions. Moreover, all our global guarantees are affine-invariant, with the convergence rates depending solely on the initial error and the strongly self-concordant constant. Our results extend the global non-asymptotic convergence theory of BFGS beyond traditional assumptions and, for the first time, establish affine-invariant convergence guarantees—aligning with the inherent affine invariance of the BFGS method.

We consider the problem of maximizing a submodular function with access to a _noisy_ value oracle for the function instead of an exact value oracle. Similar to prior work, we assume that the noisy oracle is persistent in that multiple calls to the oracle for a specific set always return the same value. In this model, Hassidim and Singer (2017) design a $(1-1/e)$-approximation algorithm for monotone submodular maximization subject to a cardinality constraint, and Huang et al (2022) design a $(1-1/e)/2$-approximation algorithm for monotone submodular maximization subject to any arbitrary matroid constraint. In this paper, we design a meta-algorithm that allows us to take any "robust" algorithm for exact submodular maximization as a black box and transform it into an algorithm for the noisy setting while retaining the approximation guarantee. By using the meta-algorithm with the measured continuous greedy algorithm, we obtain a $(1-1/e)$-approximation (resp. $1/e$-approximation) for monotone (resp. non-monotone) submodular maximization subject to a matroid constraint under noise. Furthermore, by using the meta-algorithm with the double greedy algorithm, we obtain a $1/2$-approximation for unconstrained (non-monotone) submodular maximization under noise.

Increasing demand for Large Language Models (LLMs) services imposes substantial deployment and computation costs on providers. LLM routing offers a cost-efficient solution by directing queries to the optimal LLM based on model and query features. However, existing works primarily focus on offline scenarios and struggle to adapt to online settings with high query volume and constrained token budgets. In this work, we introduce the first training-free algorithm for online routing scenarios. Our algorithm leverages approximate nearest neighbor search to efficiently estimate the features of queries and performs a one-time optimization over a small set of initial queries to learn a set of routing weights that guide future routing. We provide a theoretical guarantee that the algorithm achieves a competitive ratio of $1 - o(1)$ under natural assumptions, which is further validated by extensive experiments across 3 benchmark datasets and 8 baselines, showing an average improvement of 3.55$\times$ in performance, 1.85$\times$ in cost efficiency, and nearly 4.25$\times$ in throughput. Our code is available at https://github.com/fzwark/PORT.

Conformal prediction methods are statistical tools designed to quantify uncertainty and generate predictive sets with guaranteed coverage probabilities. This work introduces an innovative refinement to these methods for classification tasks, specifically tailored for scenarios where multiple observations (multi-inputs) of a single instance are available at prediction time. Our approach is particularly motivated by applications in citizen science, where multiple images of the same plant or animal are captured by individuals. Our method integrates the information from each observation into conformal prediction, enabling a reduction in the size of the predicted label set while preserving the required class-conditional coverage guarantee. The approach is based on the aggregation of conformal p-values computed from each observation of a multi-input. By exploiting the exact distribution of these p-values, we propose a general aggregation framework using an abstract scoring function, encompassing many classical statistical tools. Knowledge of this distribution also enables refined versions of standard strategies, such as majority voting. We evaluate our method on simulated and real data, with a particular focus on Pl@ntNet, a prominent citizen science platform that facilitates the collection and identification of plant species through user-submitted images.

Achieving fine-grained spatio-temporal understanding in videos remains a major challenge for current Video Large Multimodal Models (Video LMMs). Addressing this challenge requires mastering two core capabilities: video referring understanding, which captures the semantics of video regions, and video grounding, which segments object regions based on natural language descriptions. However, most existing approaches tackle these tasks in isolation, limiting progress toward unified, referentially grounded video interaction. We identify a key bottleneck in the lack of high-quality, unified video instruction data and a comprehensive benchmark for evaluating referentially grounded video chat. To address these challenges, we contribute in three core aspects: dataset, model, and benchmark. First, we introduce SAMA-239K, a large-scale dataset comprising 15K videos specifically curated to enable joint learning of video referring understanding, grounding, and multi-turn video chat. Second, we propose the SAMA model, which incorporates a versatile spatio-temporal context aggregator and a Segment Anything Model to jointly enhance fine-grained video comprehension and precise grounding capabilities. Finally, we establish SAMA-Bench, a meticulously designed benchmark consisting of 5,067 questions from 522 videos, to comprehensively evaluate the integrated capabilities of Video LMMs in multi-turn, spatio-temporal referring understanding and grounded dialogue. Extensive experiments and benchmarking results show that SAMA not only achieves strong performance on SAMA-Bench but also sets a new state-of-the-art on general grounding benchmarks, while maintaining highly competitive performance on standard visual understanding benchmarks.

Spatio-Temporal Foundation Models (STFMs) promise zero/few-shot generalization across various datasets, yet joint spatio-temporal pretraining is computationally prohibitive and struggles with domain-specific spatial correlations. To this end, we introduce FactoST, a factorized STFM that decouples universal temporal pretraining from spatio-temporal adaptation. The first stage pretrains a space-agnostic backbone with multi-frequency reconstruction and domain-aware prompting, capturing cross-domain temporal regularities at low computational cost. The second stage freezes or further fine-tunes the backbone and attaches an adapter that fuses spatial metadata, sparsifies interactions, and aligns domains with continual memory replay. Extensive forecasting experiments reveal that, in few-shot setting, FactoST reduces MAE by up to 46.4% versus UniST, uses 46.2% fewer parameters, and achieves 68% faster inference than OpenCity, while remaining competitive with expert models. We believe this factorized view offers a practical and scalable path toward truly universal STFMs. The code will be released upon notification.

When agents trade in a Duality-based Cost Function prediction market, they collectively implement the learning algorithm Follow-The-Regularized-Leader [Abernethy et al., 2013]. We ask whether other learning algorithms could be used to inspire the design of prediction markets. By decomposing and modifying the Duality-based Cost Function Market Maker's (DCFMM) pricing mechanism, we propose a new prediction market, called the Smooth Quadratic Prediction Market, the incentivizes agents to collectively implement general steepest gradient descent. Relative to the DCFMM, the Smooth Quadratic Prediction Market has a better worst-case monetary loss for AD securities while preserving axiom guarantees such as the existence of instantaneous price, information incorporation, expressiveness, no arbitrage, and a form of incentive compatibility. To motivate the application of the Smooth Quadratic Prediction Market, we independently examine agents' trading behavior under two realistic constraints: bounded budgets and buy-only securities. Finally, we provide an introductory analysis of an approach to facilitate adaptive liquidity using the Smooth Quadratic Prediction Market. Our results suggest future designs where the price update rule is separate from the fee structure, yet guarantees are preserved.

In this work, we introduce TreeGen, a novel generative framework modeling distributions over hierarchies. We extend Bayesian Flow Networks (BFNs) to enable transitions between probabilistic and discrete hierarchies parametrized via categorical distributions. Our proposed scheduler provides smooth and consistent entropy decay across varying numbers of categories. We empirically evaluate TreeGen on the jet-clustering task in high-energy physics, demonstrating that it consistently generates valid trees that adhere to physical constraints and closely align with ground-truth log-likelihoods. Finally, by comparing TreeGen’s samples to the exact posterior distribution and performing likelihood maximization via rejection sampling, we demonstrate that TreeGen outperforms various baselines.

Low-Rank Adaptation (LoRA) is a crucial method for efficiently fine-tuning large language models (LLMs), with its effectiveness influenced by two key factors: rank selection and weight initialization. While numerous LoRA variants have been proposed to improve performance by addressing one of these aspects, they often compromise usability or computational efficiency. In this paper, we analyze and identify the core limitations of existing approaches and propose a novel framework—**GoRA** (**G**radient-driven Adaptive L**o**w **R**ank **A**daptation)—that simultaneously adapts both the rank and initialization strategy within a unified framework. GoRA leverages gradient information during training to dynamically assign optimal ranks and initialize low-rank adapter weights in an adaptive manner. To our knowledge, GoRA is the first method that not only addresses the limitations of prior approaches—which often focus on either rank selection or initialization in isolation—but also unifies both aspects within a single framework, enabling more effective and efficient adaptation. Extensive experiments across various architectures and modalities show that GoRA consistently outperforms existing LoRA-based methods while preserving the efficiency of vanilla LoRA. For example, when fine-tuning Llama3.1-8B-Base for mathematical reasoning, GoRA achieves a 5.13-point improvement over standard LoRA and even outperforms full fine-tuning by 2.05 points under high-rank settings. Code is available at: https://github.com/hhnqqq/MyTransformers.

360-degree monocular depth estimation plays a crucial role in scene understanding owing to its 180-degree by 360-degree field-of-view (FoV). To mitigate the distortions brought by equirectangular projection, existing methods typically divide 360-degree images into distortion-less perspective patches. However, since these patches are processed independently, depth inconsistencies are often introduced due to scale drift among patches. Recently, video depth estimation (VDE) models have leveraged temporal consistency for stable depth predictions across frames. Inspired by this, we propose to represent a 360-degree image as a sequence of perspective frames, mimicking the viewpoint adjustments users make when exploring a 360-degree scenario in virtual reality. Thus, the spatial consistency among perspective depth patches can be enhanced by exploiting the temporal consistency inherent in VDE models. To this end, we introduce a training-free pipeline for 360-degree monocular depth estimation, called ST²360D. Specifically, ST²360D transforms a 360-degree image into perspective video frames, predicts video depth maps using VDE models, and seamlessly merges these predictions into a complete 360-degree depth map. To generate sequenced perspective frames that align with VDE models, we propose two tailored strategies. First, a spherical-uniform sampling (SUS) strategy is proposed to facilitate uniform sampling of perspective views across the sphere, avoiding oversampling in polar regions typically with limited structural details. Second, a latitude-guided scanning (LGS) strategy is introduced to organize the frames into a coherent sequence, starting from the equator, prioritizing low-latitude slices, and progressively moving toward higher latitudes. Extensive experiments demonstrate that ST²360D achieves strong zero-shot capability on several datasets, supporting resolutions up to 4K.

Multimodal language models possess a remarkable ability to handle an open-vocabulary worth of objects. Yet the best models still suffer from hallucinations when reasoning about scenes in the real world, revealing a gap between their seemingly strong performance on existing perception benchmarks that are saturating and their reasoning in the real world. To address this gap, we build a novel benchmark of in-the-wild scenes that we call Common-O Bench with more than 10.5k examples using exclusively new images not found in web training data to avoid contamination, Common-O goes beyond just perception, inspired by cognitive tests for humans, to probe reasoning across scenes by asking ``what’s in common?''. We evaluate leading multimodal language models, including models specifically trained to reason. We find that perceiving objects in single images is easy for most models, yet reasoning across scenes is very challenging even for the best models, including reasoning models. Despite saturating many leaderboards focusing on perception, the best performing model only achieves 35\% on Common-O Bench---and on Common-O Complex, consisting of more complex scenes, the best model achieves only 1\%. Curiously, we find models are more prone to hallucinate when similar objects are present in the scene, suggesting models may be relying on object co-occurrence seen during training. Among the models we evaluated, we found scale can provide modest improvements while models explicitly trained with multi-image inputs show bigger improvements, suggesting scaled multi-image training may offer promise. We make our benchmark publicly available to spur research into the challenge of hallucination when reasoning across scenes.

Data duplication within large-scale corpora often impedes large language models' (LLMs) performance and privacy. In privacy-concerned federated learning scenarios, conventional deduplication methods typically rely on trusted third parties to perform uniform deletion, risking loss of informative samples while introducing privacy vulnerabilities. To address these gaps, we propose Federated ReWeighting (FedRW), the first privacy-preserving framework, to the best of our knowledge, that performs soft deduplication via sample reweighting instead of deletion in federated LLM training, without assuming a trusted third party. At its core, FedRW proposes a secure, frequency-aware reweighting protocol through secure multi-party computation, coupled with a parallel orchestration strategy to ensure efficiency and scalability. During training, FedRW utilizes an adaptive reweighting mechanism with global sample frequencies to adjust individual loss contributions, effectively improving generalization and robustness. Empirical results demonstrate that FedRW outperforms the state-of-the-art method by achieving up to $28.78\times$ speedup in preprocessing and approximately $11.42$\% improvement in perplexity, while offering enhanced security guarantees. FedRW thus establishes a new paradigm for managing duplication in federated LLM training.

Test-time scaling (TTS) has proven effective in enhancing the reasoning capabilities of large language models (LLMs). Verification plays a key role in TTS, simultaneously influencing (1) reasoning performance and (2) compute efficiency, due to the quality and computational cost of verification. In this work, we challenge the conventional paradigms of verification, and make the first attempt toward systematically investigating the impact of verification granularity—that is, how frequently the verifier is invoked during generation, beyond verifying only the final output or individual generation steps. To this end, we introduce Variable Granularity Search (VG-Search), a unified algorithm that generalizes beam search and Best-of-N sampling via a tunable granularity parameter $g$. Extensive experiments with VG-Search under varying compute budgets, generator-verifier configurations, and task attributes reveal that dynamically selecting $g$ can improve the compute efficiency and scaling behavior. Building on these findings, we propose adaptive VG-Search strategies that achieve accuracy gains of up to 3.1\% over Beam Search and 3.6\% over Best-of-N, while reducing FLOPs by over 52\%. We will open-source the code to support future research.

We consider the empirical distribution of the embeddings of a $k$-layer polynomial GNN on a semi-supervised node classification task and prove a central limit theorem for them. Assuming a community based model for the underlying graph, with growing average degree $\nu_n\to\infty$, we show that the empirical distribution of the centered features, when scaled by $\nu_{n}^{k-1/2}$ converge in 1-Wasserstein distance to a centered stable mixture of multivariate normal distributions. In addition, the joint empirical distribution of uncentered features and labels when normalized by $\nu_n^k$ approach that of mixture of multivariate normal distributions, with stable means and covariance matrices vanishing as $\nu_n^{-1}$. We explicitly identify the asymptotic means and covariances, showing that the mixture collapses towards a 1-D version as $k$ is increased. Our results provides a precise and nuanced lens on how oversmoothing presents itself in the large graph limit, in the sparse regime. In particular, we show that training with cross-entropy on these embeddings is asymptotically equivalent to training on these nearly collapsed Gaussian mixtures.

Causal reasoning and discovery, two fundamental tasks of causal analysis, often face challenges in applications due to the complexity, noisiness, and high-dimensionality of real-world data. Despite recent progress in identifying latent causal structures using causal representation learning (CRL), what makes learned representations useful for causal downstream tasks and how to evaluate them are still not well understood. In this paper, we reinterpret CRL using a measurement model framework, where the learned representations are viewed as proxy measurements of the latent causal variables. Our approach clarifies the conditions under which learned representations support downstream causal reasoning and provides a principled basis for quantitatively assessing the quality of representations using a new Test-based Measurement EXclusivity (T-MEX) score. We validate T-MEX across diverse causal inference scenarios, including numerical simulations and real-world ecological video analysis, demonstrating that the proposed framework and corresponding score effectively assess the identification of learned representations and their usefulness for causal downstream tasks.

Humans can efficiently extract knowledge and learn skills from the videos within only a few trials and errors. However, it poses a big challenge to replicate this learning process for autonomous agents, due to the complexity of visual input, the absence of action or reward signals, and the limitations of interaction steps. In this paper, we propose a novel, unsupervised, and sample-efficient framework to achieve imitation learning from videos (ILV), named Behavior Cloning from Videos via Latent Representations (BCV-LR). BCV-LR extracts action-related latent features from high-dimensional video inputs through self-supervised tasks, and then leverages a dynamics-based unsupervised objective to predict latent actions between consecutive frames. The pre-trained latent actions are fine-tuned and efficiently aligned to the real action space online (with collected interactions) for policy behavior cloning. The cloned policy in turn enriches the agent experience for further latent action finetuning, resulting in an iterative policy improvement that is highly sample-efficient. We conduct extensive experiments on a set of challenging visual tasks, including both discrete control and continuous control. BCV-LR enables effective (even expert-level on some tasks) policy performance with only a few interactions, surpassing state-of-the-art ILV baselines and reinforcement learning methods (provided with environmental rewards) in terms of sample efficiency across 24/28 tasks. To the best of our knowledge, this work for the first time demonstrates that videos can support extremely sample-efficient visual policy learning, without the need to access any other expert supervision.