NeurIPS 2025 论文列表

This paper establishes a continuous time approximation, a piece-wise continuous differential equation, for the discrete Heavy-Ball (HB) momentum method with explicit discretization error. Investigating continuous differential equations has been a promising approach for studying the discrete optimization methods. Despite the crucial role of momentum in gradient-based optimization methods, the gap between the original dynamics and the continuous time approximations due to the discretization error has not been comprehensively bridged yet. In this work, we study the HB momentum method in continuous time while putting more focus on the discretization error to provide additional theoretical tools to this area. In particular, we design a first-order piece-wise continuous differential equation, where we add a number of counter terms to account for the discretization error explicitly. As a result, we provide a continuous time model for the HB momentum method that allows the control of discretization error to arbitrary order of the learning rate. As an application, we leverage it to find a new implicit regularization of the directional smoothness and investigate the implicit bias of HB for diagonal linear networks, indicating how our results can be used in deep learning. Our theoretical findings are further supported by numerical experiments.

Heavy-tailed noise is pervasive in modern machine learning applications, arising from data heterogeneity, outliers, and non-stationary stochastic environments. While second-order methods can significantly accelerate convergence in light-tailed or bounded-noise settings, such algorithms are often brittle and lack guarantees under heavy-tailed noise—precisely the regimes where robustness is most critical. In this work, we take a first step toward a theoretical understanding of second-order optimization under heavy-tailed noise. We consider a setting where stochastic gradients and Hessians have only bounded $p$-th moments, for some $p\in (1,2]$, and establish tight lower bounds on the sample complexity of any second-order method. We then develop a variant of normalized stochastic gradient descent that leverages second-order information and provably matches these lower bounds. To address the instability caused by large deviations, we introduce a novel algorithm based on gradient and Hessian clipping, and prove high-probability upper bounds that nearly match the fundamental limits. Our results provide the first comprehensive sample complexity characterization for second-order optimization under heavy-tailed noise. This positions Hessian clipping as a robust and theoretically sound strategy for second-order algorithm design in heavy-tailed regimes.

Accurately simulating physics is crucial across scientific domains, with applications spanning from robotics to materials science. While traditional mesh-based simulations are precise, they are often computationally expensive and require knowledge of physical parameters, such as material properties. In contrast, data-driven approaches like Graph Network Simulators (GNSs) offer faster inference but suffer from two key limitations: Firstly, they must be retrained from scratch for even minor variations in physical parameters, and secondly they require labor-intensive data collection for each new parameter setting. This is inefficient, as simulations with varying parameters often share a common underlying latent structure. In this work, we address these challenges by learning this shared structure through meta-learning, enabling fast adaptation to new physical parameters without retraining. To this end, we propose a novel architecture that generates a latent representation by encoding graph trajectories using conditional neural processes (CNPs). To mitigate error accumulation over time, we combine CNPs with a novel neural operator architecture. We validate our approach, Meta Neural Graph Operator (MaNGO), on several dynamics prediction tasks with varying material properties, demonstrating superior performance over existing GNS methods. Notably, MaNGO achieves accuracy on unseen material properties close to that of an oracle model.

Analysis of noninvasive microvascular blood flow can improve the diagnosis, prognosis, and management of many medical conditions, including cardiovascular, peripheral vascular, and sickle cell disease. This paper introduces SAM2Flow, an interactive optical flow estimation model to analyze long Oblique Back-illumination Microscopy (OBM) videos of *in vivo* microvascular flow. Inspired by the Segment Anything Model (SAM2), SAM2Flow enables users to specify regions of interest through user prompts for focused flow estimation. SAM2Flow also incorporates a dual memory attention mechanism, comprising both motion and context memory, to achieve efficient and stable flow estimations over extended video sequences. According to our experiments, SAM2Flow achieves SOTA accuracy in foreground optical flow estimation on both microvascular flow and public datasets, with a fast inference speed of over $20$ fps on $512\times512$ inputs. Based on the temporally robust flow estimation, SAM2Flow demonstrated superior performance in downstream physiological applications compared to existing models. The code and dataset will be published with this paper.

In the classic expert problem, $\Phi$-regret measures the gap between the learner's total loss and that achieved by applying the best action transformation $\phi \in \Phi$. A recent work by Lu et al., [2025] introduced an adaptive algorithm whose regret against a comparator $\phi$ depends on a certain sparsity-based complexity measure of $\phi$, recovering and interpolating optimal bounds for standard regret notions such as external, internal, and swap regret. In this work, we propose a general idea to achieve an even better comparator-adaptive $\Phi$-regret bound via much simpler algorithms compared to Lu et al., [2025]. Specifically, we discover a prior distribution over all possible binary transformations and show that it suffices to achieve prior-dependent regret against these transformations. Then, we propose two concrete and efficient algorithms to achieve so, where the first one combines multiple copies of the kernelized Hedge algorithm of Farina et al., [2022], and the second one combines multiple copies of a variant of the BM-reduction [Blum and Mansour, 2007]. To further showcase the power of our methods and the advantages over Lu et al., [2025] besides the simplicity and better regret bounds, we also show that our second approach can be extended to the game setting to achieve accelerated and adaptive convergence rate to $\Phi$-equilibria for a class of general-sum games. When specified to the special case of correlated equilibria, our bound improves over the existing ones from Anagnostides et al., [2022a,b].

Physics-informed neural networks (PINNs) have emerged as a promising framework to develop complex scientific surrogate models, yet their scalability and accuracy often degrade in non-canonical geometries, such as non-rectangular domains or three-dimensional (3D) domains with high aspect ratios. These limitations hinder the broader adoption of vanilla PINNs in real-world, practical systems. In this work, we introduce a multi-domain PINN (MDPINN) framework designed to address the scalability and generalization challenges inherent in 3D non-rectangular domains governed by nonlinear fluid dynamics. The target domain consists of intersecting 3D fluid channels with a high aspect ratio, inducing complex flow features such as deflections, mixing, and recirculations. Our approach is grounded in two key innovations: 1) domain decomposition, which partitions the channel volumes into multiple cubic-like subdomains, each modeled by an individual PINN, 2) enforcement of global dynamics (MDPINN-GD), which ensures that the total mass flow rate entering the domain equals that exiting. These innovations reduce the complexity of the problem imposed on individual PINNs and guide effective network optimization toward physically consistent solutions throughout the domain. We demonstrate that our method achieves: 1) 74.8\% accuracy improvement over a single-network PINN, and 2) 52.9\% accuracy improvement over MDPINN that do not enforce global mass conservation. Furthermore, the MDPINN-GD framework exhibits accurate prediction even in highly complex regions-such as the channel intersecting zone and the outlet zone characterized by intense flow mixing and large velocity gradients-achieving maximum normalized mean absolute errors below 14.9\% for velocity predictions compared to simulation results. This work establishes a path towards scalable, physically grounded surrogate modeling approach that is extensible to multiphysics and high-dimensional scientific problems.

Multi-class tissue-type classification of colorectal cancer (CRC) histopathologic images is a significant step in the development of downstream machine learning models for diagnosis and treatment planning. However, publicly available CRC datasets used to build tissue classifiers often suffer from insufficient morphologic diversity, class imbalance, and low-quality image tiles, limiting downstream model performance and generalizability. To address this research gap, we introduce STARC-9 (STAnford coloRectal Cancer), a large-scale dataset for multi-class tissue classification. STARC-9 comprises 630,000 histopathologic image tiles uniformly sampled across nine clinically relevant tissue classes (each represented by 70,000 tiles), systematically extracted from hematoxylin & eosin-stained whole-slide images (WSI) from 200 CRC patients at the Stanford University School of Medicine. To construct STARC-9, we propose a novel framework, DeepCluster++, consisting of two primary steps to ensure diversity within each tissue class, followed by pathologist verification. First, an encoder from an autoencoder trained specifically on histopathologic images is used to extract feature vectors from all tiles within a given input WSI. Next, K-means clustering groups morphologically similar tiles, followed by an equal-frequency binning method to sample diverse patterns within each tissue class. Finally, the selected tiles are verified by expert gastrointestinal pathologists to ensure classification accuracy. This semi-automated approach significantly reduces the manual effort required for dataset curation while producing high-quality training examples. To validate the utility of STARC-9, we benchmarked baseline convolutional neural networks, transformers, and pathology-specific foundation models on downstream multi-class CRC tissue classification and segmentation tasks when trained on STARC-9 versus publicly available datasets, demonstrating superior generalizability of models trained on STARC-9. Although we demonstrate the utility of DeepCluster++ on CRC as a pilot use-case, it is a flexible framework that can be used for constructing high-quality datasets from large WSI repositories across a wide range of cancer and non-cancer applications.

Recognizing symbols in architectural CAD drawings is critical for various advanced engineering applications. In this paper, we propose a novel CAD data annotation engine that leverages intrinsic attributes from systematically archived CAD drawings to automatically generate high-quality annotations, thus significantly reducing manual labeling efforts. Utilizing this engine, we construct ArchCAD-400K, a large-scale CAD dataset consisting of 413,062 chunks from 5538 highly standardized drawings, making it over 26 times larger than the largest existing CAD dataset. ArchCAD-400K boasts an extended drawing diversity and broader categories, offering line-grained annotations. Furthermore, we present a new baseline model for panoptic symbol spotting, termed Dual-Pathway Symbol Spotter (DPSS). It incorporates an adaptive fusion module to enhance primitive features with complementary image features, achieving state-of-the-art performance and enhanced robustness. Extensive experiments validate the effectiveness of DPSS, demonstrating the value of ArchCAD-400K and its potential to drive innovation in architectural design and construction.

Traditional photography composition approaches are dominated by 2D cropping-based methods. However, these methods fall short when scenes contain poorly arranged subjects. Professional photographers often employ perspective adjustment as a form of 3D recomposition, modifying the projected 2D relationships between subjects while maintaining their actual spatial positions to achieve better compositional balance. Inspired by this artistic practice, we propose photography perspective composition (PPC), extending beyond traditional cropping-based methods. However, implementing the PPC faces significant challenges: the scarcity of perspective transformation datasets and undefined assessment criteria for perspective quality. To address these challenges, we present three key contributions: (1) An automated framework for building PPC datasets through expert photographs. (2) A video generation approach that demonstrates the transformation process from less favorable to aesthetically enhanced perspectives. (3) A perspective quality assessment (PQA) model constructed based on human performance. Our approach is concise and requires no additional prompt instructions or camera trajectories, helping and guiding ordinary users to enhance their composition skills.

Event-based structured light (SL) systems have attracted increasing attention for their potential in high-performance 3D measurement. Despite the inherent HDR capability of event cameras, reflective and absorptive surfaces still cause event cluttering and absence, which produce overexposed and underexposed regions that degrade the reconstruction quality. In this work, we present the first HDR 3D measurement framework specifically designed for event-based SL systems. First, we introduce a multi-contrast HDR coding strategy that facilitates imaging of areas with different reflectance. Second, to alleviate inter-frame interference caused by overexposed and underexposed areas, we propose a universal confidence-driven stereo matching strategy. Specifically, we estimate a confidence map as the fusion weight for features via an energy-guided confidence estimation. Further, we propose the confidence propagation volume, an innovative cost volume that offers both effective suppression of inter-frame interference and strong representation capability. Third, we contribute an event-based SL simulator and propose the first event-based HDR SL dataset. We also collect a real-world benchmarking dataset with ground truth. We validate the effectiveness of our method with the proposed confidence-driven strategy on both synthetic and real-world datasets. Experimental results demonstrate that our proposed HDR framework enables accurate 3D measurement even under extreme conditions.

Large Language Models (LLMs) are being explored for applications in scientific research, including their capabilities to synthesize literature, answer research questions, generate research ideas, and even conduct computational experiments. Ultimately, our goal is for these to help scientists derive novel scientific insights. In many areas of science, such insights often arise from processing and visualizing data to understand its patterns. However, evaluating whether an LLM-mediated scientific workflow produces outputs conveying the correct scientific insights is challenging to evaluate and has not been addressed in past work. We introduce AstroVisBench, the first benchmark for both scientific computing and visualization in the astronomy domain. AstroVisBench judges a language model’s ability to both (1) create astronomy-specific workflows to process and analyze data and (2) visualize the results of these workflows through complex plots. Our evaluation of visualizations uses a novel LLM-as-a-judge workflow, which is validated against annotation by five professional astronomers. Using AstroVisBench we present an evaluation of state-of-the-art language models, showing a significant gap in their ability to engage in astronomy research as useful assistants. This evaluation provides a strong end-to-end evaluation for AI scientists that offers a path forward for the development of visualization-based workflows, which are central to a broad range of domains from physics to biology.

Few-shot learning (FSL) aims to classify unseen examples (query set) into labeled data (support set) through low-dimensional embeddings. However, the diversity and unpredictability of environments and capture devices make FSL more challenging in real-world applications. In this paper, we propose Dual Support Query Shift (DSQS), a novel challenge in FSL that integrates two key issues: inter-set shifts (between support and query sets) and intra-set shifts (within each set), which significantly hinder model performance. To tackle these challenges, we introduce a Dual Alignment framework (DUAL), whose core insight is that clean features can improve optimal transportation (OT) alignment. Firstly, DUAL leverages a robust embedding function enhanced by a repairer network trained with perturbed and adversarially generated “hard” examples to obtain clean features. Additionally, it incorporates a two-stage OT approach with a negative entropy regularizer, which aligns support set instances, minimizes intra-class distances, and uses query data as anchor nodes to achieve effective distribution alignment. We provide a theoretical bound of DUAL and experimental results on three image datasets, compared against 10 state-of-the-art baselines, showing that DUAL achieves a remarkable average performance improvement of 25.66%. Our code is available at https://github.com/siyang-jiang/DUAL.

Multimodal deep learning systems are deployed in dynamic scenarios due to the robustness afforded by multiple sensing modalities. Nevertheless, they struggle with varying compute resource availability (due to multi-tenancy, device heterogeneity, etc.) and fluctuating quality of inputs (from sensor feed corruption, environmental noise, etc.). Statically provisioned multimodal systems cannot adapt when compute resources change over time, while existing dynamic networks struggle with strict compute budgets. Additionally, both systems often neglect the impact of variations in modality quality. Consequently, modalities suffering substantial corruption may needlessly consume resources better allocated towards other modalities. We propose ADMN, a layer-wise Adaptive Depth Multimodal Network capable of tackling both challenges - it adjusts the total number of active layers across all modalities to meet compute resource constraints, and continually reallocates layers across input modalities according to their modality quality. Our evaluations showcase ADMN can match the accuracy of state-of-the-art networks while reducing up to 75% of their floating-point operations.

Accurately modeling the target-drug complex at atom level presents a significant challenge in the computer-aided drug design. Traditional methods that rely solely on rigid transformations often fail to capture the adaptive interactions between targets and drugs, particularly during substantial conformational changes in targets upon ligand binding, which becomes especially critical when learning target-drug interactions in drug design. Accurately modeling these changes is crucial for understanding target-drug interactions and improving drug efficacy. To address these challenges, we introduce DynaPhArM, an SE(3)-Equivariant Transformer model specifically designed to capture adaptive alterations occurring within target-drug interactions. DynaPhArM utilizes the cooperative scalar-vector representation, drug-specific embeddings, and a diffusion process to effectively model the evolving dynamics of interactions between targets and drugs. Furthermore, we integrate physical information and energetic principles that maintain essential geometric constraints, such as bond lengths, bond angles, van der Waals forces (vdW), within a multi-task learning (MTL) framework to enhance accuracy. Experimental results demonstrate that DynaPhArM achieves state-of-the-art performance with an overall root mean square deviation (RMSD) of 2.01 Å and a sc-RMSD of 0.29 Å while exhibiting higher success rates compared to existing methodologies. Additionally, DynaPhArM shows promise in enhancing drug specificity, thereby simulating how targets adapt to various drugs through precise modeling of atomic-level interactions and conformational flexibility.

Tokenization is the process of encoding strings into tokens of a fixed vocabulary size, and is widely utilized in Natural Language Processing applications. The leading tokenization algorithm today is Byte Pair Encoding (BPE), which formulates the tokenization problem as a compression problem and tackles it by performing sequences of merges. In this work, we formulate tokenization as an optimization objective, show that it is NP-hard via a simple reduction from vertex cover, and propose a polynomial-time greedy algorithm GreedTok. Our formulation naturally relaxes to the well-studied weighted maximum coverage problem which has a simple $(1 - 1/e)$-approximation algorithm GreedWMC. Through empirical evaluations on real-world corpora, we show that GreedTok outperforms BPE and Unigram on compression and achieves a covering score comparable to GreedWMC. Finally, our extensive pre-training for two transformer-based language models with 1 billion parameters, comparing the choices of BPE and GreedTok as the tokenizer, shows that GreedTok achieves a lower bit per byte even when we control for either the total dataset proportion or total training tokens.

The limited availability of high-quality training data poses a major obstacle in data-driven PDE solving, where expensive data collection and resolution constraints severely impact the ability of neural operator networks to learn and generalize the underlying physical system. To address this challenge, we propose DeltaPhi, a novel learning framework that transforms the PDE solving task from learning direct input-output mappings to learning the residuals between similar physical states, a fundamentally different approach to neural operator learning. This reformulation provides implicit data augmentation by exploiting the inherent stability of physical systems where closer initial states lead to closer evolution trajectories. DeltaPhi is architecture-agnostic and can be seamlessly integrated with existing neural operators to enhance their performance. Extensive experiments demonstrate consistent and significant improvements across diverse physical systems including regular and irregular domains, different neural architectures, multiple training data amount, and cross-resolution scenarios, confirming its effectiveness as a general enhancement for neural operators in data-limited PDE solving.

Machine learning (ML) is transforming modeling and control in the physical, engineering, and biological sciences. However, rapid development has outpaced the creation of standardized, objective benchmarks—leading to weak baselines, reporting bias, and inconsistent evaluations across methods. This undermines reproducibility, misguides resource allocation, and obscures scientific progress. To address this, we propose a Common Task Framework (CTF) for scientific machine learning. The CTF features a curated set of datasets and task-specific metrics spanning forecasting, state reconstruction, and generalization under realistic constraints, including noise and limited data. Inspired by the success of CTFs in fields like natural language processing and computer vision, our framework provides a structured, rigorous foundation for head-to-head evaluation of diverse algorithms. As a first step, we benchmark methods on two canonical nonlinear systems: Kuramoto-Sivashinsky and Lorenz. These results illustrate the utility of the CTF in revealing method strengths, limitations, and suitability for specific classes of problems and diverse objectives. Next, we are launching a competition around a global real world sea surface temperature dataset with a true holdout dataset to foster community engagement. Our long-term vision is to replace ad hoc comparisons with standardized evaluations on hidden test sets that raise the bar for rigor and reproducibility in scientific ML.

Vehicle GPS trajectories record how vehicles move over time, storing valuable travel semantics, including movement patterns and travel purposes. Learning travel semantics effectively and efficiently is crucial for real-world applications of trajectory data, which is hindered by two major challenges. First, travel purposes are tied to the functions of the roads and points-of-interest (POIs) involved in a trip. Such information is encoded in textual addresses and descriptions and introduces heavy computational burden to modeling. Second, real-world trajectories often contain redundant points, which harm both computational efficiency and trajectory embedding quality. To address these challenges, we propose TrajMamba, a novel approach for efficient and semantically rich vehicle trajectory learning. TrajMamba introduces a Traj-Mamba Encoder that captures movement patterns by jointly modeling both GPS and road perspectives of trajectories, enabling robust representations of continuous travel behaviors. It also incorporates a Travel Purpose-aware Pre-training procedure to integrate travel purposes into the learned embeddings without introducing extra overhead to embedding calculation. To reduce redundancy in trajectories, TrajMamba features a Knowledge Distillation Pre-training scheme to identify key trajectory points through a learnable mask generator and obtain effective compressed trajectory embeddings. Extensive experiments on two real-world datasets and three downstream tasks show that TrajMamba outperforms state-of-the-art baselines in both efficiency and accuracy.

Metal-Organic Frameworks (MOFs) have attracted considerable attention due to their unique properties including high surface area and tunable porosity, and promising applications in catalysis, gas storage, and drug delivery. Structure prediction for MOFs is a challenging task, as these frameworks are intrinsically periodic and hierarchically organized, where the entire structure is assembled from building blocks like metal nodes and organic linkers. To address this, we introduce MOF-BFN, a novel generative model for MOF structure prediction based on Bayesian Flow Networks (BFNs). Given the local geometry of building blocks, MOF-BFN jointly predicts the lattice parameters, as well as the positions and orientations of all building blocks within the unit cell. In particular, the positions are modelled in the fractional coordinate system to naturally incorporate the periodicity. Meanwhile, the orientations are modeled as unit quaternions sampled from learned Bingham distributions via the proposed Bingham BFN, enabling effective orientation generation on the 4D unit hypersphere. Experimental results demonstrate that MOF-BFN achieves state-of-the-art performance across multiple tasks, including structure prediction, geometric property evaluation, and de novo generation, offering a promising tool for designing complex MOF materials.