NeurIPS 2025 Papers

Dense metric depth estimation has witnessed great developments in recent years. While single-image-based methods have demonstrated commendable performance in certain circumstances, they may encounter challenges regarding scale ambiguities and visual illusions in real world. Traditional depth-from-focus methods are constrained by low sampling rates during data acquisition. In this paper, we introduce a novel approach to enhance dense metric depth estimation by fusing events with image foundation models via a prompting approach. Specifically, we build Event-based Differential Focus Volumes (EDFV) using events triggered through focus sweeping, which are subsequently transformed into sparse metric depth maps. These maps are then utilized for prompting dense depth estimation via our proposed Event-based Depth Prompting Network. We further construct synthetic and real-captured datasets to facilitate the training and evaluation of both frame-based and event-based methods. Quantitative and qualitative results, including both in-domain and zero-shot experiments, demonstrate the superior performance of our method compared to existing approaches. Code and data will be available at https://github.com/liboyu02/EDFV/.

The advent of foundation models in AI has significantly advanced general-purpose learning, enabling remarkable capabilities in zero-shot inference and in-context learning. However, training such models on physics data, including solutions to partial differential equations (PDEs), poses a unique challenge due to varying dimensionalities across different systems. Traditional approaches either fix a maximum dimension or employ separate encoders for different dimensionalities, resulting in inefficiencies. To address this, we propose a dimension-agnostic neural network architecture, the Axial Neural Network (XNN), inspired by parameter-sharing structures such as Deep Sets and Graph Neural Networks. XNN generalizes across varying tensor dimensions while maintaining computational efficiency. We convert existing PDE foundation models into axial neural networks and evaluate their performance across three training scenarios: training from scratch, pretraining on multiple PDEs, and fine-tuning on a single PDE. Our experiments show that XNNs perform competitively with original models and exhibit superior generalization to unseen dimensions, highlighting the importance of multidimensional pretraining for foundation models.

Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction. We present a two-stage method for ligand conformation generation guided by such templates. In the first stage, we introduce a molecular alignment approach based on flow-matching to generate 3D coordinates for the ligand, using the template structure as a reference. In the second stage, a differentiable pose optimization procedure refines this conformation based on shape and pharmacophore similarities, internal energy, and, optionally, the protein binding pocket. We introduce a new benchmark of ligand pairs co-crystallized with the same target to evaluate our approach and show that it outperforms standard docking tools and open-access alignment methods, especially in cases involving low similarity to the template or high ligand flexibility.

Attention-based encoder decoder models remain a popular choice for state-of-the-art automatic speech recognition (ASR). These models combine a powerful audio encoder that extracts rich acoustic features with a decoder that autoregressively produces the ASR output. The decoder handles two critical tasks: (1) building rich text-only context and (2) merging acoustic information from the encoder to ensure the predictions remain faithful to the audio. We observe a systematic pattern across the attention distributions of decoder layers in prior architectures: the initial layers direct most attention towards building textual context, while the later layers largely focus on merging acoustic and textual information for the final predictions. Leveraging this key insight, we propose **BlockDecoder**, a novel decoder architecture comprising two distinct components: a text encoder that is purely text-based, and a **Merger** that combines information from the audio encoder and text encoder to generate output tokens. Unlike traditional decoders, the **Merger** autoregressively predicts a sequence of K tokens within a *block* of size K, while relying on the same precomputed contextual information from both text and audio encoders across the block. This design choice allows for the efficient reuse of encoder representations. The separation of the decoder into the text encoder and the **Merger** promotes modularity and more flexible control of parameters via the number of text encoder and **Merger** layers. As a result, **BlockDecoder** yields a significant speedup ($\sim2$x) compared to traditional decoders, across diverse datasets, languages, and speech tasks, without any degradation in performance. The code is available at https://github.com/csalt-research/blockdecoder.

Aerial-Ground person re-identification (AG-ReID) is an emerging yet challenging task that aims to match pedestrian images captured from drastically different viewpoints, typically from unmanned aerial vehicles (UAVs) and ground-based surveillance cameras. The task poses significant challenges due to extreme viewpoint discrepancies, occlusions, and domain gaps between aerial and ground imagery. While prior works have made progress by learning cross-view representations, they remain limited in handling severe pose variations and spatial misalignment. To address these issues, we propose a Geometric and Semantic Alignment Network (GSAlign) tailored for AG-ReID. GSAlign introduces two key components to jointly tackle geometric distortion and semantic misalignment in aerial-ground matching: a Learnable Thin Plate Spline (LTPS) Transformation Module and a Dynamic Alignment Module (DAM). The LTPS module adaptively warps pedestrian features based on a set of learned keypoints, effectively compensating for geometric variations caused by extreme viewpoint changes. In parallel, the DAM estimates visibility-aware representation masks that highlight visible body regions at the semantic level, thereby alleviating the negative impact of occlusions and partial observations in cross-view correspondence. Extensive experiments on the challenging CARGO benchmark demonstrate the effectiveness of GSAlign, achieving significant improvements of +18.8\% in mAP and +16.8\% in Rank-1 accuracy over previous state-of-the-art methods.

Current benchmarks for evaluating the reasoning capabilities of Large Language Models (LLMs) face significant limitations: task oversimplification, data contamination, and flawed evaluation items. These deficiencies necessitate more rigorous assessment methods. To address these limitations, we introduce PHYBench, a benchmark of 500 original physics problems ranging from high school to Physics Olympiad difficulty. PHYBench addresses data contamination through original content and employs a systematic curation pipeline to eliminate flawed items. Evaluations show that PHYBench activates more tokens and provides stronger differentiation between reasoning models compared to other baselines like AIME 2024, OlympiadBench and GPQA. Even the best-performing model, Gemini 2.5 Pro, achieves only 36.9\% accuracy compared to human experts' 61.9\%. To further enhance evaluation precision, we introduce the Expression Edit Distance (EED) Score for mathematical expression assessment, which improves sample efficiency by 204\% over binary scoring. Moreover, PHYBench effectively elicits multi-step and multi-condition reasoning, providing a platform for examining models' reasoning robustness, preferences, and deficiencies. The benchmark results and dataset are publicly available at https://www.phybench.cn/.

Computationally resolving turbulence remains a central challenge in fluid dynamics due to its multi-scale interactions. Fully resolving large-scale turbulence through direct numerical simulation (DNS) is computationally prohibitive, motivating data-driven machine learning alternatives. In this work, we propose EddyFormer, a Transformer-based spectral-element (SEM) architecture for large-scale turbulence simulation that combines the accuracy of spectral methods with the scalability of the attention mechanism. We introduce an SEM tokenization that decomposes the flow into grid-scale and subgrid-scale components, enabling capture of both local and global features. We create a new three-dimensional isotropic turbulence dataset and train EddyFormer to achieves DNS-level accuracy at 256^3 resolution, providing a 30x speedup over DNS. When applied to unseen domains up to 4x larger than in training, EddyFormer preserves accuracy on physics-invariant metrics-energy spectra, correlation functions, and structure functions-showing domain generalization. On The Well benchmark suite of diverse turbulent flows, EddyFormer resolves cases where prior ML models fail to converge, accurately reproducing complex dynamics across a wide range of physical conditions.

To address these challenges, we propose the Reconfigurable Continuum Gaussian Stream, dubbed ReCon-GS, a novel storage-aware framework that enables high-fidelity online dynamic scene reconstruction and real-time rendering. Specifically, we dynamically allocate multi-level Anchor Gaussians in a density-adaptive fashion to capture inter-frame geometric deformations, thereby decomposing scene motion into compact coarse-to-fine representations. Then, we design a dynamic hierarchy reconfiguration strategy that preserves localized motion expressiveness through on-demand anchor re-hierarchization, while ensuring temporal consistency through intra-hierarchical deformation inheritance that confines transformation priors to their respective hierarchy levels. Furthermore, we introduce a storage-aware optimization mechanism that flexibly adjusts the density of Anchor Gaussians at different hierarchy levels, enabling a controllable trade-off between reconstruction fidelity and memory usage. Extensive experiments on three widely used datasets demonstrate that, compared to state‐of‐the‐art methods, ReCon-GS improves training efficiency by approximately 15% and achieves superior FVV synthesis quality with enhanced robustness and stability. Moreover, at equivalent rendering quality, ReCon-GS slashes memory requirements by over 50% compared to leading state‑of‑the‑art methods. Code is avaliable at: https://github.com/jyfu-vcl/ReCon-GS/.

Differentiable vector graphics (VGs) are widely used in image vectorization and vector synthesis, while existing representations are costly to optimize and struggle to achieve high-quality rendering results for high-resolution images. This work introduces a new differentiable VG representation, dubbed Bézier Splatting, that enables fast yet high-fidelity VG rasterization. Bézier Splatting samples 2D Gaussians along Bézier curves, which naturally provide positional gradients at object boundaries. Thanks to the efficient splatting-based differentiable rasterizer, Bézier Splatting achieves 30× and 150× faster per forward and backward rasterization step for open curves compared to DiffVG. Additionally, we introduce an adaptive pruning and densification strategy that dynamically adjusts the spatial distribution of curves to escape local minima, further improving VG quality. Furthermore, our new VG representation supports conversion to standard XML-based SVG format, enhancing interoperability with existing VG tools and pipelines. Experimental results show that Bézier Splatting significantly outperforms existing methods with better visual fidelity and significant optimization speedup.

PU (Positive Unlabeled) learning is a variant of supervised classification learning in which the only labels revealed to the learner are of positively labeled instances. PU learning arises in many real-world applications. Most existing work relies on the simplifying assumption that the positively labeled training data is drawn from the restriction of the data generating distribution to positively labeled instances and/or that the proportion of positively labeled points (a.k.a. the class prior) is known apriori to the learner. This paper provides a theoretical analysis of the statistical complexity of PU learning under a wider range of setups. Unlike most prior work, our study does not assume that the class prior is known to the learner. We prove upper and lower bounds on the required sample sizes (of both the positively labeled and the unlabeled samples).

Solving systems of polynomial equations, particularly those with finitely many solutions, is a crucial challenge across many scientific fields. Traditional methods like Gröbner and Border bases are fundamental but suffer from high computational costs, which have motivated recent Deep Learning approaches to improve efficiency, albeit at the expense of output correctness. In this work, we introduce the Oracle Border Basis Algorithm, the first Deep Learning approach that accelerates Border basis computation while maintaining output guarantees. To this end, we design and train a Transformer-based oracle that identifies and eliminates computationally expensive reduction steps, which we find to dominate the algorithm's runtime. By selectively invoking this oracle during critical phases of computation, we achieve substantial speedup factors of up to 3.5x compared to the base algorithm, without compromising the correctness of results. To generate the training data, we develop a sampling method and provide the first sampling theorem for border bases. We construct a tokenization and embedding scheme tailored to monomial-centered algebraic computations, resulting in a compact and expressive input representation, which reduces the number of tokens to encode an $n$-variate polynomial by a factor of $O(n)$. Our learning approach is data efficient, stable, and a practical enhancement to traditional computer algebra algorithms and symbolic computation.

It is a challenging problem to reproduce rich spatial details while maintaining temporal consistency in real-world video super-resolution (Real-VSR), especially when we leverage pre-trained generative models such as stable diffusion (SD) for realistic details synthesis. Existing SD-based Real-VSR methods often compromise spatial details for temporal coherence, resulting in suboptimal visual quality. We argue that the key lies in how to effectively extract the degradation-robust temporal consistency priors from the low-quality (LQ) input video and enhance the video details while maintaining the extracted consistency priors. To achieve this, we propose a Dual LoRA Learning (DLoRAL) paradigm to train an effective SD-based one-step diffusion model, achieving realistic frame details and temporal consistency simultaneously. Specifically, we introduce a Cross-Frame Retrieval (CFR) module to aggregate complementary information across frames, and train a Consistency-LoRA (C-LoRA) to learn robust temporal representations from degraded inputs. After consistency learning, we fix the CFR and C-LoRA modules and train a Detail-LoRA (D-LoRA) to enhance spatial details while aligning with the temporal space defined by C-LoRA to keep temporal coherence. The two phases alternate iteratively for optimization, collaboratively delivering consistent and detail-rich outputs. During inference, the two LoRA branches are merged into the SD model, allowing efficient and high-quality video restoration in a single diffusion step. Experiments show that DLoRAL achieves strong performance in both accuracy and speed. Code and models will be released.

In this paper, we present RigAnyFace (RAF), a scalable neural auto-rigging framework for facial meshes of diverse topologies, including those with multiple disconnected components. RAF deforms a static neutral facial mesh into industry-standard FACS poses to form an expressive blendshape rig. Deformations are predicted by a triangulation-agnostic surface learning network augmented with our tailored architecture design to condition on FACS parameters and efficiently process disconnected components. For training, we curated a dataset of facial meshes, with a subset meticulously rigged by professional artists to serve as accurate 3D ground truth for deformation supervision. Due to the high cost of manual rigging, this subset is limited in size, constraining the generalization ability of models trained exclusively on it. To address this, we design a 2D supervision strategy for unlabeled neutral meshes without rigs. This strategy increases data diversity and allows for scaled training, thereby enhancing the generalization ability of models trained on this augmented data. Extensive experiments demonstrate that RAF is able to rig meshes of diverse topologies on not only our artist-crafted assets but also in-the-wild samples, outperforming previous works in accuracy and generalizability. Moreover, our method advances beyond prior work by supporting multiple disconnected components, such as eyeballs, for more detailed expression animation.

Learning the solution operators of PDEs on arbitrary domains is challenging due to the diversity of possible domain shapes, in addition to the often intricate underlying physics. We propose an end-to-end graph neural network (GNN) based neural operator to learn PDE solution operators from data on point clouds in arbitrary domains. Our multi-scale model maps data between input/output point clouds by passing it through a downsampled regional mesh. The approach includes novel elements aimed at ensuring spatio-temporal resolution invariance. Our model, termed RIGNO, is tested on a challenging suite of benchmarks composed of various time-dependent and steady PDEs defined on a diverse set of domains. We demonstrate that RIGNO is significantly more accurate than neural operator baselines and robustly generalizes to unseen resolutions both in space and in time. Our code is publicly available at github.com/camlab-ethz/rigno.

The ultimate goal of code agents is to solve complex tasks autonomously. Although large language models (LLMs) have made substantial progress in code generation, real-world tasks typically demand full-fledged code repositories rather than simple scripts. Building such repositories from scratch remains a major challenge. Fortunately, GitHub hosts a vast, evolving collection of open-source repositories, which developers frequently reuse as modular components for complex tasks. Yet, existing frameworks like OpenHands and SWE-Agent still struggle to effectively leverage these valuable resources. Relying solely on README files provides insufficient guidance, and deeper exploration reveals two core obstacles: overwhelming information and tangled dependencies of repositories, both constrained by the limited context windows of current LLMs. To tackle these issues, we propose RepoMaster, an autonomous agent framework designed to explore and reuse GitHub repositories for solving complex tasks. For efficient understanding, RepoMaster constructs function-call graphs, module-dependency graphs, and hierarchical code trees to identify essential components, providing only identified core elements to the LLMs rather than the entire repository. During autonomous execution, it progressively explores related components using our exploration tools and prunes information to optimize context usage. Evaluated on the adjusted MLE-bench, RepoMaster achieves a 110\% relative boost in valid submissions over the strongest baseline OpenHands. On our newly released GitTaskBench, RepoMaster lifts the task-pass rate from 40.7% to 62.9% while reducing token usage by 95%. Our code and demonstration materials are publicly available at https://github.com/QuantaAlpha/RepoMaster.

Finding dense subgraphs is a fundamental problem with applications to community detection, clustering, and data mining. Our work focuses on finding approximate densest subgraphs in directed graphs in computational models for processing massive data. We consider two such models: Massively Parallel Computation (MPC) and semi-streaming. We show how to find a $(2+\varepsilon)$-approximation in $\tilde{O}(\sqrt{\log n})$ MPC rounds with sublinear memory per machine. This improves the state-of-the-art results by Bahmani et al. (WAW 2014) and Mitrovic \& Pan (ICML 2024). Moreover, we show how to find an $O(\log n)$-approximation in a single pass in semi-streaming. This is in stark contrast to prior work, which implies $\tilde{\Omega}(n^{1/6})$-approximation for a single pass; a better approximation is known only for randomized streams (Mitrovi\'c \& Pan). This is the first deterministic single-pass semi-streaming algorithm for the densest subgraph problem, both for undirected and directed graphs. Our semi-streaming approach is also an insertion-only dynamic algorithm, attaining the first directed densest subgraph algorithm with $O(\log^2 n)$ worst-case update time while using sub-linear memory. We empirically evaluate our approaches in two ways. First, we illustrate that our single-pass semi-streaming algorithm performs much better than the theoretical guarantee. Specifically, its approximation on temporal datasets matches the $(2+\varepsilon)$-approximation of an $O(\log n)$-pass algorithm by Bahmani et al. (VLDB 2012). Second, we demonstrate that our MPC algorithm requires fewer rounds than prior work.

Vision-language models (VLMs) have recently been integrated into multiple instance learning (MIL) frameworks to address the challenge of few-shot, weakly supervised classification of whole slide images (WSIs). A key trend involves leveraging multi-scale information to better represent hierarchical tissue structures. However, existing methods often face two key limitations: (1) insufficient modeling of interactions within the same modalities across scales (e.g., 5x and 20x) and (2) inadequate alignment between visual and textual modalities on the same scale. To address these gaps, we propose HiVE-MIL, a hierarchical vision-language framework that constructs a unified graph consisting of (1) parent–child links between coarse (5x) and fine (20x) visual/textual nodes to capture hierarchical relationships, and (2) heterogeneous intra-scale edges linking visual and textual nodes on the same scale. To further enhance semantic consistency, HiVE-MIL incorporates a two-stage, text-guided dynamic filtering mechanism that removes weakly correlated patch–text pairs, and introduces a hierarchical contrastive loss to align textual semantics across scales. Extensive experiments on TCGA breast, lung, and kidney cancer datasets demonstrate that HiVE-MIL consistently outperforms both traditional MIL and recent VLM-based MIL approaches, achieving gains of up to 4.1% in macro F1 under 16-shot settings. Our results demonstrate the value of jointly modeling hierarchical structure and multimodal alignment for efficient and scalable learning from limited pathology data. The code is available at https://github.com/bryanwong17/HiVE-MIL.

Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior. Existing methods leverage optimal transport, Schrödinger bridge theory, or their variants to simultaneously infer stochastic, unbalanced dynamics from snapshot data. However, these approaches remain limited in their ability to account for cell-cell interactions. This integration is essential in real-world scenarios since intercellular communications are fundamental life processes and can influence cell state-transition dynamics. To address this challenge, we formulate the Unbalanced Mean-Field Schrödinger Bridge (UMFSB) framework to model unbalanced stochastic interaction dynamics from snapshot data. Inspired by this framework, we further propose CytoBridge, a deep learning algorithm designed to approximate the UMFSB problem. By explicitly modeling cellular transitions, proliferation, and interactions through neural networks, CytoBridge offers the flexibility to learn these processes directly from data. The effectiveness of our method has been extensively validated using both synthetic gene regulatory data and real scRNA-seq datasets. Compared to existing methods, CytoBridge identifies growth, transition, and interaction patterns, eliminates false transitions, and reconstructs the developmental landscape with greater accuracy. Code is available at: https://github.com/zhenyiizhang/CytoBridge-NeurIPS.

We present GOATex, a diffusion-based method for 3D mesh texturing that generates high-quality textures for both exterior and interior surfaces. While existing methods perform well on visible regions, they inherently lack mechanisms to handle occluded interiors, resulting in incomplete textures and visible seams. To address this, we introduce an occlusion-aware texturing framework based on the concept of hit levels, which quantify the relative depth of mesh faces via multi-view ray casting. This allows us to partition mesh faces into ordered visibility layers, from outermost to innermost. We then apply a two-stage visibility control strategy that progressively reveals interior regions with structural coherence, followed by texturing each layer using a pretrained diffusion model. To seamlessly merge textures obtained across layers, we propose a soft UV-space blending technique that weighs each texture’s contribution based on view-dependent visibility confidence. Empirical results demonstrate that GOATex consistently outperforms existing methods, producing seamless, high-fidelity textures across both visible and occluded surfaces. Unlike prior works, GOATex operates entirely without costly fine-tuning of a pretrained diffusion model and allows separate prompting for exterior and interior mesh regions, enabling fine-grained control over layered appearances.