NeurIPS 2025 Papers

Expanding on neural operators, we propose a novel framework for stochastic process learning across arbitrary domains. In particular, we develop operator flow matching (OFM) for learning stochastic process priors on function spaces. OFM provides the probability density of the values of any collection of points and enables mathematically tractable functional regression at new points with mean and density estimation. Our method outperforms state-of-the-art models in stochastic process learning, functional regression, and prior learning.

Scaling language models unlocks impressive capabilities, but the accompanying computational and memory demands make both training and deployment expensive. Existing efficiency efforts typically target either parameter sharing or adaptive computation, leaving open the question of how to attain both simultaneously. We introduce Mixture-of-Recursions (MoR), a unified framework that combines the two axes of efficiency inside a single Recursive Transformer. MoR reuses a shared stack of layers across recursion steps to achieve parameter efficiency, while lightweight routers enable adaptive token-level thinking by dynamically assigning different recursion depths to individual tokens. This allows MoR to focus quadratic attention computation only among tokens still active at a given recursion depth, further improving memory access efficiency by selectively caching only their key-value pairs. Beyond these core mechanisms, we also propose a KV sharing variant that reuses KV pairs from the first recursion, specifically designed to further decrease memory footprint. Across model scales ranging from 135M to 1.7B parameters, MoR forms a new Pareto frontier: at equal training FLOPs and smaller model sizes, it significantly lowers validation perplexity and improves few-shot accuracy, while delivering higher throughput compared with vanilla and existing recursive baselines.

Directed acyclic graph (DAG) learning is a central task in structure discovery and causal inference. Although the field has witnessed remarkable advances over the past few years, it remains statistically and computationally challenging to learn a single (point estimate) DAG from data, let alone provide uncertainty quantification. We address the difficult task of quantifying graph uncertainty by developing a Bayesian variational inference framework based on novel, provably valid distributions that have support directly on the space of sparse DAGs. These distributions, which we use to define our prior and variational posterior, are induced by a projection operation that maps an arbitrary continuous distribution onto the space of sparse weighted acyclic adjacency matrices. While this projection is combinatorial, it can be solved efficiently using recent continuous reformulations of acyclicity constraints. We empirically demonstrate that our method, \texttt{ProDAG}, can outperform state-of-the-art alternatives in both accuracy and uncertainty quantification.

Accurate and safe medication recommendations are critical for effective clinical decision-making, especially in multimorbidity cases. However, existing systems rely on point-wise prediction paradigms that overlook synergistic drug effects and potential adverse drug-drug interactions (DDIs). We propose FLAME, a fine-grained list-wise alignment framework for large language models (LLMs), enabling drug-by-drug generation of drug lists. FLAME formulates recommendation as a sequential decision process, where each step adds or removes a single drug. To provide fine-grained learning signals, we devise step-wise Group Relative Policy Optimization (GRPO) with potential-based reward shaping, which explicitly models DDIs and optimizes the contribution of each drug to the overall prescription. Furthermore, FLAME enhances patient modeling by integrating structured clinical knowledge and collaborative information into the representation space of LLMs. Experiments on benchmark datasets demonstrate that FLAME achieves state-of-the-art performance, delivering superior accuracy, controllable safety–accuracy trade-offs, and strong generalization across diverse clinical scenarios. Our code is available at https://github.com/cxfann/Flame.

The sparse additive model (SpAM) offers a trade-off between interpretability and flexibility, and hence is a powerful model for high-dimensional research. This paper focuses on the variable selection, i.e., the univariate function selection problem in SpAM. We establish the minimax separation rates from both the perspectives of sparse multiple testing (FDR + FNR control) and support recovery (wrong recovery probability control). We further study how adaptation to unknown smoothness affects the minimax separation rate, and propose an adaptive selection procedure. Finally, we discuss the difference between estimation and selection in SpAM: Procedures achieving optimal function estimation may fail to achieve optimal univariate function selection.

Today, people can easily record memorable moments, ranging from concerts, sports events, lectures, family gatherings, and birthday parties with multiple consumer cameras. However, synchronizing these cross‑camera streams remains challenging. Existing methods assume controlled settings, specific targets, manual correction, or costly hardware. We present VisualSync, an optimization framework based on multi‑view dynamics that aligns unposed, unsynchronized videos at millisecond accuracy. Our key insight is that any moving 3D point, when co‑visible in two cameras, obeys epipolar constraints once properly synchronized. To exploit this, VisualSync leverages off‑the‑shelf 3D reconstruction, feature matching, and dense tracking to extract tracklets, relative poses, and cross‑view correspondences. It then jointly minimizes the epipolar error to estimate each camera’s time offset. Experiments on four diverse, challenging datasets show that VisualSync outperforms baseline methods, achieving an average synchronization error below 130 ms.

Reinforcement learning (RL) often relies on manually designed reward functions, which are difficult to specify and can lead to issues such as reward hacking and suboptimal behavior. Alternatives like inverse RL and preference-based RL attempt to infer surrogate rewards from demonstrations or preferences but suffer from ambiguity and distribution mismatch. A more direct approach, inspired by imitation learning, avoids reward modeling by leveraging expert demonstrations. However, most existing methods align actions only at individual states, failing to capture the coherence of long-horizon trajectories. In this work, we study the problem of directly aligning policies with expert-labeled trajectories to preserve long-horizon behavior without relying on reward signals. Specifically, we aim to learn a policy that maximizes the probability of generating the expert trajectories. Nevertheless, we prove that, in its general form, this trajectory alignment problem is NP-complete. To address this, we propose Trajectory Graph Learning (TGL), a framework that leverages structural assumptions commonly satisfied in practice—such as bounded realizability of expert trajectories or a tree-structured MDP. These enable a graph-based policy planning algorithm that computes optimal policies in polynomial time under known dynamics. For settings with unknown dynamics, we develop a sample-efficient algorithm based on UCB-style exploration and establish sub-linear regret. Experiments on grid-world tasks demonstrate that TGL substantially outperforms standard imitation learning methods for long-trajectory planning.

Integrating logical constraints into object detection models for autonomous driving (AD) is a promising way to enhance their compliance with rules and thereby increase the safety of the system. T-norms have been utilized to calculate the constrained loss, i.e., the violations of logical constraints as losses. While prior works have statically selected a few t-norms, we conduct an extensive experimental study to identify the most effective choices, as suboptimal t-norms can lead to undesired model behavior. To this end, we present MOD-ECL, a neurosymbolic framework that implements a wide range of t-norms and applies them in an adaptive manner. It includes an algorithm that selects well-performing t-norms during training and a scheduler that regulates the impact of the constrained loss. We evaluate its effectiveness on the ROAD-R and ROAD-Waymo-R datasets for object detection in AD, using attached common-sense constraints. Our results show that careful selection of parameters is crucial for effective constrained loss behavior. Moreover, our framework not only reduces constraint violations but also, in some cases, improves detection performance. Additionally, our methods offer fine-grained control over the trade-off between accuracy and constraint violation.

Recent efforts to employ large language models (LLMs) as agents have demonstrated promising results in a wide range of multi-step agent tasks. However, existing agents lack an effective experience reuse approach to leverage historical completed tasks. In this paper, we propose a novel experience reuse framework MetaFlowLLM, which constructs a hierarchical experience tree from historically completed tasks. Each node in this experience tree is presented as a MetaFlow which contains static execution workflow and subtask required by agents to complete dynamically. Then, we propose a Hierarchical MetaFlow Merging algorithm to construct the hierarchical experience tree. When accomplishing a new task, MetaFlowLLM can first retrieve the most relevant MetaFlow node from the experience tree and then execute it accordingly. To effectively generate valid MetaFlows from historical data, we further propose a reinforcement learning pipeline to train the MetaFlowGen. Extensive experimental results on AppWorld and WorkBench demonstrate that integrating with MetaFlowLLM, existing agents (e.g., ReAct, Reflexion) can gain substantial performance improvement with reducing execution costs. Notably, MetaFlowLLM achieves an average success rate improvement of 32.3% on AppWorld and 6.2% on WorkBench, respectively.

Recent advancements in text-guided image editing have achieved notable success by leveraging natural language prompts for fine-grained semantic control. However, certain editing semantics are challenging to specify precisely using textual descriptions alone. A practical alternative involves learning editing semantics from paired source-target examples. Existing exemplar-based editing methods still rely on text prompts describing the change within paired examples or learning implicit text-based editing instructions. In this paper, we introduce PairEdit, a novel visual editing method designed to effectively learn complex editing semantics from a limited number of image pairs or even a single image pair, without using any textual guidance. We propose a target noise prediction that explicitly models semantic variations within paired images through a guidance direction term. Moreover, we introduce a content-preserving noise schedule to facilitate more effective semantic learning. We also propose optimizing distinct LoRAs to disentangle the learning of semantic variations from content. Extensive qualitative and quantitative evaluations demonstrate that PairEdit successfully learns intricate semantics while significantly improving content consistency compared to baseline methods. Code is available at https://github.com/xudonmao/PairEdit.

While there has been significant progress in the field of 3D avatar creation from visual observations, modeling physically plausible dynamics of humans with loose garments remains a challenging problem. Although a few existing works address this problem by leveraging physical simulation, they suffer from limited accuracy or robustness to novel animation inputs. In this work, we present MPMAvatar, a framework for creating 3D human avatars from multi-view videos that supports highly realistic, robust animation, as well as photorealistic rendering from free viewpoints. For accurate and robust dynamics modeling, our key idea is to use a Material Point Method-based simulator, which we carefully tailor to model garments with complex deformations and contact with the underlying body by incorporating an anisotropic constitutive model and a novel collision handling algorithm. We combine this dynamics modeling scheme with our canonical avatar that can be rendered using 3D Gaussian Splatting with quasi-shadowing, enabling high-fidelity rendering for physically realistic animations. In our experiments, we demonstrate that MPMAvatar significantly outperforms the existing state-of-the-art physics-based avatar in terms of (1) dynamics modeling accuracy, (2) rendering accuracy, and (3) robustness and efficiency. Additionally, we present a novel application in which our avatar generalizes to unseen interactions in a zero-shot manner—which was not achievable with previous learning-based methods due to their limited simulation generalizability. Our code will be publicly available.

Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

Continuous time systems are often modeled using discrete time dynamics but this requires a small simulation step to maintain accuracy. In turn, this requires a large planning horizon which leads to computationally demanding planning problems and reduced performance. Previous work in model-free reinforcement learning has partially addressed this issue using action repeats where a policy is learned to determine a discrete action duration. Instead we propose to control the continuous decision timescale directly by using temporally-extended actions and letting the planner treat the duration of the action as an additional optimization variable along with the standard action variables. This additional structure has multiple advantages. It speeds up simulation time of trajectories and, importantly, it allows for deep horizon search in terms of primitive actions while using a shallow search depth in the planner. In addition, in the model-based reinforcement learning (MBRL) setting, it reduces compounding errors from model learning and improves training time for models. We show that this idea is effective and that the range for action durations can be automatically selected using a multi-armed bandit formulation and integrated into the MBRL framework. An extensive experimental evaluation both in planning and in MBRL, shows that our approach yields faster planning, better solutions, and that it enables solutions to problems that are not solved in the standard formulation.

Low-Rank Adaptation (LoRA), which introduces a product of two trainable low-rank matrices into frozen pre-trained weights, is widely used for efficient fine-tuning of language models in federated learning (FL). However, when combined with differentially private stochastic gradient descent (DP-SGD), LoRA faces substantial noise amplification: DP-SGD perturbs per-sample gradients, and the matrix multiplication of the LoRA update ($BA$) intensifies this effect. Freezing one matrix (*e.g.*, $A$) reduces the noise but restricts model expressiveness, often resulting in suboptimal adaptation. To address this, we propose $\texttt{FedSVD}$, a simple yet effective method that introduces a global reparameterization based on singular value decomposition (SVD). In our approach, each client optimizes only the $B$ matrix and transmits it to the server. The server aggregates the $B$ matrices, computes the product $BA$ using the previous $A$, and refactorizes the result via SVD. This yields a new adaptive $A$ composed of the orthonormal right singular vectors of $BA$, and an updated $B$ containing the remaining SVD components. This reparameterization avoids quadratic noise amplification, while allowing $A$ to better capture the principal directions of the aggregate updates. Moreover, the orthonormal structure of $A$ bounds the gradient norms of $B$ and preserves more signal under DP-SGD, as confirmed by our theoretical analysis. As a result, $\texttt{FedSVD}$ consistently improves stability and performance across a variety of privacy settings and benchmarks, outperforming relevant baselines under both private and non-private regimes.

In this work, we introduce CAD-Coder, a novel framework that reformulates text-to-CAD as the generation of CadQuery scripts—a Python-based, parametric CAD language. This representation enables direct geometric validation, a richer modeling vocabulary, and seamless integration with existing LLMs. To further enhance code validity and geometric fidelity, we propose a two-stage learning pipeline: (1) supervised fine-tuning on paired text–CadQuery data, and (2) reinforcement learning with Group Reward Policy Optimization (GRPO), guided by a CAD-specific reward comprising both a geometric reward (Chamfer Distance) and a format reward. We also introduce a chain-of-thought (CoT) planning process to improve model reasoning, and construct a large-scale, high-quality dataset of 110K text–CadQuery–3D model triplets and 1.5K CoT samples via an automated pipeline. Extensive experiments demonstrate that CAD-Coder enables LLMs to generate diverse, valid, and complex CAD models directly from natural language, advancing the state of the art of text-to-CAD generation and geometric reasoning.

Data-driven molecular discovery leverages artificial intelligence/machine learning (AI/ML) and generative modeling to filter and design novel molecules. Discovering novel molecules requires accurate out-of-distribution (OOD) predictions, but ML models struggle to generalize OOD. Currently, no systematic benchmarks exist for molecular OOD prediction tasks. We present BOOM, $\textbf{b}$enchmarks for $\textbf{o}$ut-$\textbf{o}f$-$\textbf{d}$istribution $\textbf{m}$olecular property predictions: a chemically-informed benchmark for OOD performance on common molecular property prediction tasks. We evaluate over 150 model-task combinations to benchmark deep learning models on OOD performance. Overall, we find that no existing model achieves strong generalization across all tasks: even the top-performing model exhibited an average OOD error 3$\times$ higher than in-distribution. Current chemical foundation models do not show strong OOD extrapolation, while models with high inductive bias can perform well on OOD tasks with simple, specific properties. We perform extensive ablation experiments, highlighting how data generation, pre-training, hyperparameter optimization, model architecture, and molecular representation impact OOD performance. Developing models with strong OOD generalization is a new frontier challenge in chemical ML. This open-source benchmark is available at https://github.com/FLASK-LLNL/BOOM

Transferability estimation identifies the best pre-trained models for downstream tasks without incurring the high computational cost of full fine-tuning. This capability facilitates deployment and advances the pre-training and fine-tuning paradigm. However, existing methods often struggle to accurately assess transferability for emerging pre-trained models with diverse architectures, training strategies, and task alignments. In this work, we propose Implicit Transferability Modeling (ITM), a novel framework that implicitly models each model’s intrinsic transferability, coupled with a Divide-and-Conquer Variational Approximation (DVA) strategy to efficiently approximate embedding space evolution. This design enables generalization across a broader range of models and downstream tasks. Extensive experiments on a comprehensive benchmark—spanning extensive training regimes and a wider variety of model types—demonstrate that ITM consistently outperforms existing methods in terms of stability, effectiveness, and efficiency.

The brain is made up of a vast set of heterogeneous regions that dynamically organize into pathways as a function of task demands. Examples of such pathways can be found in the interactions between cortical and subcortical networks during learning, or in sub-networks specializing for task characteristics such as difficulty or modality. Despite the large role these pathways play in cognition, the mechanisms through which brain regions organize into pathways remain unclear. In this work, we use an extension of the Heterogeneous Mixture-of-Experts architecture to show that heterogeneous regions do not form processing pathways by themselves, implying that the brain likely implements specific constraints which result in the reliable formation of pathways. We identify three biologically relevant inductive biases that encourage pathway formation: a routing cost imposed on the use of more complex regions, a scaling factor that reduces this cost when task performance is low, and randomized expert dropout. When comparing our resulting Mixture-of-Pathways model with the brain, we observe that the artificial pathways in our model match how the brain uses cortical and subcortical systems to learn and solve tasks of varying difficulty. In summary, we introduce a novel framework for investigating how the brain forms task-specific pathways through inductive biases, and the effects these biases have on the behavior of Mixture-of-Experts models.

Most video-anomaly research stops at frame-wise detection, offering little insight into why an event is abnormal, typically outputting only frame-wise anomaly scores without spatial or semantic context. Recent video anomaly localization and video anomaly understanding methods improve explainability but remain data-dependent and task-specific. We propose a unified reasoning framework that bridges the gap between temporal detection, spatial localization, and textual explanation. Our approach is built upon a chained test-time reasoning process that sequentially connects these tasks, enabling holistic zero-shot anomaly analysis without any additional training. Specifically, our approach leverages intra-task reasoning to refine temporal detections and inter-task chaining for spatial and semantic understanding, yielding improved interpretability and generalization in a fully zero-shot manner. Without any additional data or gradients, our method achieves state-of-the-art zero-shot performance across multiple video anomaly detection, localization, and explanation benchmarks. The results demonstrate that careful prompt design with task-wise chaining can unlock the reasoning power of foundation models, enabling practical, interpretable video anomaly analysis in a fully zero-shot manner. Project Page: https://rathgrith.github.io/Unified_Frame_VAA/.