NeurIPS 2025 Papers

In the single-positive multi-label (SPML) setting, each image in a dataset is labeled with the presence of a single class, while the true presence of other classes remains unknown. The challenge is to narrow the performance gap between this partially-labeled setting and fully-supervised learning, which often requires a significant annotation budget. Prior SPML methods were developed and benchmarked on synthetic datasets created by randomly sampling single positive labels from fully-annotated datasets like Pascal VOC, COCO, NUS-WIDE, and CUB200. However, this synthetic approach does not reflect real-world scenarios and fails to capture the fine-grained complexities that can lead to difficult misclassifications. In this work, we introduce the L48 dataset, a fine-grained, real-world multi-label dataset derived from recordings of bird sounds. L48 provides a natural SPML setting with single-positive annotations on a challenging, fine-grained domain, as well as two extended settings in which domain priors give access to additional negative labels. We benchmark existing SPML methods on L48 and observe significant performance differences compared to synthetic datasets and analyze method weaknesses, underscoring the need for more realistic and difficult benchmarks.

We investigate language generation in the limit – a model by Kleinberg and Mullainathan and extended by Li, Raman, and Tewari. While Kleinberg and Mullainathan proved generation is possible for all countable collections, Li, Raman, and Tewari defined a hierarchy of generation notions (uniform, non-uniform, and generatable) and explored their feasibility for uncountable collections. Our first set of results resolve two open questions of Li et al. by proving finite unions of generatable or non-uniformly generatable classes need not be generatable. These follow from a stronger result: there is non-uniformly generatable class and a uniformly generatable class whose union is non-generatable. This adds to the aspects along which language generation in the limit is different from traditional tasks in statistical learning theory like classification, which are closed under finite unions. In particular, it implies that given two generators for different collections, one cannot combine them to obtain a single "more powerful" generator, prohibiting this notion of boosting. Our construction also addresses a third of Li et al.'s open questions on whether there are uncountable classes that are non-uniformly generatable and do not satisfy the eventually unbounded closure (EUC) condition introduced by Li et al. Our approach utilizes carefully constructed classes along with a novel diagonalization argument that could be of independent interest in the growing area of language generation.

Training large language models (LLMs) is highly resource-intensive due to their massive number of parameters and the overhead of optimizer states. While recent work has aimed to reduce memory consumption, such efforts often entail trade-offs among memory efficiency, training time, and model performance. Yet, true democratization of LLMs requires simultaneous progress across all three dimensions. To this end, we propose SubTrack++ that leverages Grassmannian gradient subspace tracking combined with projection-aware optimizers, enabling Adam’s internal statistics to adapt to subspace changes. Additionally, employing recovery scaling, a technique that restores information lost through low-rank projections, further enhances model performance. Our method demonstrates SOTA convergence by exploiting Grassmannian geometry, **reducing pre-training wall-time by up to 65% and fine-tuning time by 36%** compared to existing SOTA methods, while maintaining the same memory footprint. Code is at https://github.com/criticalml-uw/SubTrack.

While foundation models have shown promise across a variety of fields, astronomy lacks a unified framework for joint modeling across its highly diverse data modalities. In this paper, we present AION-1, the first large-scale multimodal foundation family of models for astronomy. AION-1 enables arbitrary transformations between heterogeneous data types using a two-stage architecture: modality-specific tokenization followed by transformer-based masked modeling of cross-modal token sequences. Trained on over 200M astronomical objects, AION-1 demonstrates strong performance across regression, classification, generation, and object retrieval tasks. Beyond astronomy, AION-1 provides a scalable blueprint for multimodal scientific foundation models that can seamlessly integrate heterogeneous combinations of real-world observations. Our model release is entirely open source, including the dataset, training script, and weights.

Recent advancements in reasoning capability of Multimodal Large Language Models (MLLMs) demonstrate its effectiveness in tackling complex visual tasks. However, existing MLLM-based Video Anomaly Detection (VAD) methods remain limited to shallow anomaly descriptions without deep reasoning. In this paper, we propose a new task named Video Anomaly Reasoning (VAR), which aims to enable deep analysis and understanding of anomalies in the video by requiring MLLMs to think explicitly before answering. To this end, we propose Vad-R1, an end-to-end MLLM-based framework for VAR. Specifically, we design a Perception-to-Cognition Chain-of-Thought (P2C-CoT) that simulates the human process of recognizing anomalies, guiding the MLLMs to reason about anomalies step-by-step. Based on the structured P2C-CoT, we construct Vad-Reasoning, a dedicated dataset for VAR. Furthermore, we propose an improved reinforcement learning algorithm AVA-GRPO, which explicitly incentivizes the anomaly reasoning capability of MLLMs through a self-verification mechanism with limited annotations. Experimental results demonstrate that Vad-R1 achieves superior performance, outperforming both open-source and proprietary models on VAD and VAR tasks.

Pre-trained encoders for offline feature extraction followed by multiple instance learning (MIL) aggregators have become the dominant paradigm in computational pathology (CPath), benefiting cancer diagnosis and prognosis. However, performance limitations arise from the absence of encoder fine-tuning for downstream tasks and disjoint optimization with MIL. While slide-level supervised end-to-end (E2E) learning is an intuitive solution to this issue, it faces challenges such as high computational demands and suboptimal results. These limitations motivate us to revisit E2E learning. We argue that prior work neglects inherent E2E optimization challenges, leading to performance disparities compared to traditional two-stage methods. In this paper, we pioneer the elucidation of optimization challenge caused by sparse-attention MIL and propose a novel MIL called ABMILX. ABMILX mitigates this problem through global correlation-based attention refinement and multi-head mechanisms. With the efficient multi-scale random patch sampling strategy, an E2E trained ResNet with ABMILX surpasses SOTA foundation models under the two-stage paradigm across multiple challenging benchmarks, while remaining computationally efficient ($<$ 10 RTX3090 GPU hours). We demonstrate the potential of E2E learning in CPath and calls for greater research focus in this area. The code is https://github.com/DearCaat/E2E-WSI-ABMILX.

We introduce RFMPose, a novel generative framework for category-level 6D object pose estimation that learns deterministic pose trajectories through Riemannian Flow Matching (RFM). Existing discriminative approaches struggle with multi-hypothesis predictions (e.g., symmetry ambiguities) and often require specialized network architectures. RFMPose advances this paradigm through three key innovations: (1) Ensuring geometric consistency via geodesic interpolation on Riemannian manifolds combined with bi-invariant metric constraints; (2) Alleviating symmetry-induced ambiguities through Riemannian Optimal Transport for probability mass redistribution without ad-hoc design; (3) Enabling end-to-end likelihood estimation through Hutchinson trace approximation, thereby eliminating auxiliary model dependencies. Extensive experiments on the Omni6DPose demonstrate state-of-the-art performance of the proposed method, with significant improvements of $\textbf{+4.1}$ in $\mathrm{\textbf{IoU}_{25}}$ and $\textbf{+2.4}$ in $\textbf{5°2cm}$ metrics compared to prior generative approaches. Furthermore, the proposed RFM framework exhibits robust sim-to-real transfer capabilities and facilitates pose tracking extensions with minimal architectural adaptation.

Generative modeling of non-negative, discrete data, such as symbolic music, remains challenging due to two persistent limitations in existing methods. Firstly, many approaches rely on modeling continuous embeddings, which is suboptimal for inherently discrete data distributions. Secondly, most models optimize variational bounds rather than exact data likelihood, resulting in inaccurate likelihood estimates and degraded sampling quality. While recent diffusion-based models have addressed these issues separately, we tackle them jointly. In this work, we introduce the Information-Theoretic Discrete Poisson Diffusion Model (ItDPDM), inspired by photon arrival process, which combines exact likelihood estimation with fully discrete-state modeling. Central to our approach is an information-theoretic Poisson Reconstruction Loss (PRL) that has a provable exact relationship with the true data likelihood. ItDPDM achieves improved likelihood and sampling performance over prior discrete and continuous diffusion models on a variety of synthetic discrete datasets. Furthermore, on real-world datasets such as symbolic music and images, ItDPDM attains superior likelihood estimates and competitive generation quality—demonstrating a proof of concept for distribution-robust discrete generative modeling.

Data attribution methods aim to answer useful counterfactual questions like "what would a ML model's prediction be if it were trained on a different dataset?" However, estimation of data attribution models through techniques like empirical influence or "datamodeling" remains very computationally expensive. This causes a critical trust issue: if only a few computationally rich parties can obtain data attributions, how can resource-constrained parties trust that the provided attributions are indeed ``good,'' especially when they are used for important downstream applications (e.g., data pricing)? In this paper, we address this trust issue by proposing an interactive verification paradigm for data attribution. An untrusted and computationally powerful Prover learns data attributions, and then engages in an interactive proof with a resource-constrained Verifier. Our main result is a protocol that provides formal completeness, soundness, and efficiency guarantees in the sense of Probably-Approximately-Correct (PAC) verification (Goldwasser et al., 2021). Specifically, if both Prover and Verifier follow the protocol, the Verifier accepts data attributions that are $\varepsilon$-close to the optimal data attributions (in terms of the Mean Squared Error) with probability $1-\delta$. Conversely, if the Prover arbitrarily deviates from the protocol, even with infinite compute, then this is detected (or it still yields data attributions to the Verifier) except with probability $\delta$. Importantly, our protocol ensures the Verifier's workload, measured by the number of independent model retrainings it must perform, scales only as $O(1/\varepsilon^2)$; i.e., independently of the dataset size. At a technical level, our results apply to efficiently verifying any linear function over the boolean hypercube computed by the Prover, making them broadly applicable to various attribution tasks.

Large language models (LLMs) have demonstrated remarkable proficiency in mainstream academic disciplines such as mathematics, physics, and computer science. However, human knowledge encompasses over 200 specialized disciplines, far exceeding the scope of existing benchmarks. The capabilities of LLMs in many of these specialized fields-particularly in light industry, agriculture, and service-oriented disciplines-remain inadequately evaluated. To address this gap, we present SuperGPQA, a comprehensive benchmark that evaluates graduate-level knowledge and reasoning capabilities across 285 disciplines. Our benchmark employs a novel Human-LLM collaborative filtering mechanism to eliminate trivial or ambiguous questions through iterative refinement based on both LLM responses and expert feedback. Our experimental results reveal significant room for improvement in the performance of current state-of-the-art LLMs across diverse knowledge domains (e.g., the reasoning-focused model Gemini-2.5-Pro achieved the highest accuracy of 63.56% on SuperGPQA), highlighting the considerable gap between current model capabilities and artificial general intelligence. Additionally, we present comprehensive insights from our management of a large-scale annotation process, involving over 80 expert annotators and an interactive Human-LLM collaborative system, offering valuable methodological guidance for future research initiatives of comparable scope.

Dynamic scene reconstruction poses a persistent challenge in 3D vision. Deformable 3D Gaussian Splatting has emerged as an effective method for this task, offering real-time rendering and high visual fidelity. This approach decomposes a dynamic scene into a static representation in a canonical space and time-varying scene motion. Scene motion is defined as the collective movement of all Gaussian points, and for compactness, existing approaches commonly adopt implicit neural fields or sparse control points. However, these methods predominantly rely on gradient-based optimization for all motion information. Due to the high degree of freedom, they struggle to converge on real-world datasets exhibiting complex motion. To preserve the compactness of motion representation and address convergence challenges, this paper proposes heterogeneous 3D control points, termed \textbf{H3D control points}, whose attributes are obtained using a hybrid strategy combining optical flow back-projection and gradient-based methods. This design decouples directly observable motion components from those that are geometrically occluded. Specifically, components of 3D motion that project onto the image plane are directly acquired via optical flow back projection, while unobservable portions are refined through gradient-based optimization. Experiments on the Neu3DV and CMU-Panoptic datasets demonstrate that our method achieves superior performance over state-of-the-art deformable 3D Gaussian splatting techniques. Remarkably, our method converges within just 100 iterations and achieves a per-frame processing speed of 2 seconds on a single NVIDIA RTX 4070 GPU.

In the past decades, brain imaging research underwent a shift from mapping tasked evoked brain regions of activations towards identifying and characterizing the dynamic brain networks of multiple coordinating brain regions. Electrophysiological signals are the direct manifestation of brain activities, thus, characterizing the whole brain electrophysiological networks (WBEN) can serve as a fundamental tool for neuroscience studies and clinical applications. In this work, we introduce the first framework for the integration of scalp EEG and intracranial EEG (iEEG) for the WBEN estimation with a principled estimation framework based on state-space models, where an Expectation-Maximization (EM) algorithm is designed to infer the state variables and brain connectivity simultaneously. We validated the proposed method on synthetic data, and the results revealed improved performance compared to traditional two-step methods using scalp EEG only, demonstrating the importance of including iEEG signal for WBEN estimation. For real data with simultaneous EEG and iEEG, we applied the developed framework to understand the information flows of the encoding and maintenance phases during the working memory task. The information flows between the subcortical and cortical regions are delineated, highlighting more significant information flows from cortical to subcortical regions than maintenance phases. The results are consistent with previous research findings but with the view of the whole brain scope, which underscores the unique utility of the proposed framework.

Vision-Language Models (VLMs) have made significant progress in multimodal tasks. However, their performance often deteriorates in long-context scenarios, particularly long videos. While Rotary Position Embedding (RoPE) has been widely adopted for length generalization in Large Language Models (LLMs), extending vanilla RoPE to capture the intricate spatial-temporal dependencies in videos remains an unsolved challenge. Existing methods typically allocate different frequencies within RoPE to encode 3D positional information. However, these allocation strategies mainly rely on heuristics, lacking in-depth theoretical analysis. In this paper, we first study how different allocation strategies impact the long-context capabilities of VLMs. Our analysis reveals that current multimodal RoPEs fail to reliably capture semantic similarities over extended contexts. To address this issue, we propose HoPE, a Hybrid of Position Embedding designed to improve the long-context capabilities of VLMs. HoPE introduces a hybrid frequency allocation strategy for reliable semantic modeling over arbitrarily long contexts, and a dynamic temporal scaling mechanism to facilitate robust learning and flexible inference across diverse context lengths. Extensive experiments across four video benchmarks on long video understanding and retrieval tasks demonstrate that HoPE consistently outperforms existing methods, confirming its effectiveness.

The *law of supply and demand* asserts that in a perfectly competitive market, the price of a good adjusts to a *market clearing price*. In a market clearing price $p^\star$ the number of sellers willing to sell the good at $p^\star$ equals the number of sellers willing to buy the good at price $p^\star$. In this work, we provide a mathematical foundation on the law of supply and demand through the lens of online learning. Specifically, we demonstrate that if each seller employs a no-swap regret algorithm to set their individual selling price—aiming to maximize its individual revenue—the collective pricing dynamics converge to the market-clearing price $p^\star$ . Our findings offer a novel perspective on the law of supply and demand, framing it as the emergent outcome of an adaptive learning processes among sellers.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require differentiable proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation.

Parameter-efficient fine-tuning (PEFT) powerful pre-trained models for complex downstream tasks has proven effective in vision and language processing, yet this paradigm remains unexplored in scientific machine learning, where the objective is to model complex physical systems. We conduct the first systematic study of PEFT for pre-trained Large Operator Models (LOMs) obtained by scaling variants of Fourier Neural Operator. We observe that the widely used Low-Rank Adaptation (LoRA) yields markedly poorer performance on LOMs than Adapter tuning. We further theoretically establish that stacked LoRA incurs a depth-amplified lower bound on approximation error within Fourier layers, whereas adapters retain universal approximation capacity and, by concentrating parameters on energy-dominant low-frequency modes, attain exponentially decaying error with bottleneck width in the Fourier domain. Motivated by the robust empirical gains of adapters and by our theoretical characterization of PDE solutions as spectrally sparse, we introduce Frequency-Adaptive Adapter (F-Adapter). F-Adapter allocates adapter capacity based on spectral complexity, assigning higher-dimension modules to low-frequency components and lower-dimension modules to high-frequency components. Our F-Adapters establish state-of-the-art results on multiple challenging 3D Navier–Stokes benchmarks, markedly enhancing both generalization and spectral fidelity over LoRA and other PEFT techniques commonly used in LLMs. To the best of our knowledge, this work is the first to explore PEFT for scientific machine-learning and establishes F-Adapter as an effective paradigm for this domain. The code will be made publicly available upon acceptance.

Large-scale pre-trained models hold significant potential for learning universal EEG representations. However, most existing methods, particularly autoregressive (AR) frameworks, primarily rely on straightforward temporal sequencing of multi-channel EEG data, which fails to capture the rich physiological characteristics inherent to EEG signals. Moreover, their time-centered modeling approach also limits the effective representation of the dynamic spatial topology of brain activity. To address these challenges and fully exploit the potential of large-scale EEG models, we propose a novel Topology Hierarchical Derived Brain Autoregressive Modeling (THD-BAR) for EEG generic representations. The core innovation of THD-BAR lies in the introduction of the Brain Topology Hierarchy (BTH), which establishes a multi-scale spatial order for EEG channels. This hierarchical structure enables a redefinition of autoregressive learning as a "next-scale-time prediction" problem, effectively capturing both spatial and temporal dynamics. Based on BTH, we design a Topology-Hierarchical Vector Quantized-Variational Autoencoder (THVQ-VAE) for multi-scale tokenization and develop an enhanced Brain Autoregressive (BAR) module with specialized masking strategies for prediction. Through extensive large-scale pre-training on 17 datasets, followed by rigorous validation on 10 downstream datasets spanning 5 distinct tasks, THD-BAR consistently outperforms existing methods. These results highlight the superior generalization and modeling capabilities of our proposed approach.

Visual anomaly detection is significant in safety-critical and reliability-sensitive scenarios. Prior studies mainly emphasize the design and training of scoring functions, while little effort has been devoted to constructing decision rules based on these score functions. A recent work Ma et al. (2025b) highlights this issue and proposes the SAC-BL algorithm to address it. This method consists of a strong anomaly constraint (SAC) network and a betting-like (BL) algorithm serving as the decision rule. The SAC-BL algorithm can control the false discovery rate (FDR). However the performance of SAC-BL algorithm on anomalous examples, or its false positive rate (FPR), has not been thoroughly investigated. This paper provides a deeper analysis of this problem and explores how to theoretically reduce its FPR. First, we show that as the number of testing examples tends to infinity, the SAC-BL algorithm performs well on abnormal data if the scores follow the generalized Gaussian-like distribution family. But such conditions about the number of testing examples and the distribution of scores are overly restrictive for the real-world applications. So, we attempt to decrease the FPR of the SAC-BL algorithm under the condition of finite samples for practical anomaly detection. To this end, we redesign the BL algorithm by incorporating a randomization strategy and propose a novel stochastic BL (SBL) algorithm. The combination of the SAC network and the SBL algorithm yields our method, SAC-SBL. Theoretical results show that the SAC-SBL algorithm can achieve smaller FPR than SAC-BL algorithm while controlling its FDR. Finally, extensive experimental results demonstrate the superiority of our method over SAC-BL algorithm on multiple visual anomaly detection benchmarks.

While methods exist for aligning flow matching models -- a popular and effective class of generative models -- with human preferences, existing approaches fail to achieve both adaptation efficiency and probabilistically sound prior preservation. In this work, we leverage the theory of optimal control and propose VGG-Flow, a gradient matching–based method for finetuning pretrained flow matching models. The key idea in this algorithm is that the optimal difference between the finetuned velocity field and the pretrained one should be matched with the gradient field of a value function. This method not only incorporates first-order information from the reward model but also benefits from heuristic initialization of the value function to enable fast adaptation. Empirically, we show on a popular text-to-image flow matching model, Stable Diffusion 3, that our method can finetune flow matching models under limited computational budgets while achieving effective and prior-preserving alignment.