NeurIPS 2025 论文列表

Global biodiversity is declining at an unprecedented rate, yet little information is known about most species and how their populations are changing. Indeed, some 90% Earth’s species are estimated to be completely unknown. Machine learning has recently emerged as a promising tool to facilitate long-term, large-scale biodiversity monitoring, including algorithms for fine-grained classification of species from images. However, such algorithms typically are not designed to detect examples from categories unseen during training – the problem of open-set recognition (OSR) – limiting their applicability for highly diverse, poorly studied taxa such as insects. To address this gap, we introduce Open-Insect, a large-scale, fine-grained dataset to evaluate unknown species detection across different geographic regions with varying difficulty. We benchmark 38 OSR algorithms across three categories: post-hoc, training-time regularization, and training with auxiliary data, finding that simple post-hoc approaches remain a strong baseline. We also demonstrate how to leverage auxiliary data to improve species discovery in regions with limited data. Our results provide timely insights to guide the development of computer vision methods for biodiversity monitoring and species discovery.

Although receiving notable improvements, current multi-view clustering (MVC) techniques generally rely on feature library mechanisms to propagate accumulated knowledge from historical views to newly-arrived data, which overlooks the information pertaining to basis embedding within each view. Moreover, the mapping paradigm inevitably alters the values of learned landmarks and built affinities due to the uninterruption nature, accordingly disarraying the hierarchical cluster structures. To mitigate these two issues, we in the paper provide a named BSTM algorithm. Concretely, we firstly synchronize with the distinct dimensions by introducing a group of specialized projectors, and then establish unified anchors for all views collected so far to capture intrinsic patterns. Afterwards, departing from per-view architectures, we devise a shared bipartite graph construction via indicators to quantify similarity, which not only avoids redundant data-recalculations but alleviates the representation distortion caused by fusion. Crucially, there two components are optimized within an integrated framework, and collectively facilitate knowledge transfer upon encountering incoming views. Subsequently, to flexibly do transformation on anchors and meanwhile maintain numerical consistency, we develop a bit-swapping scheme operating exclusively on 0 and 1. It harmonizes anchors on current view and that on previous views through one-hot encoded row and column attributes, and the graph structures are correspondingly reordered to reach a matched configuration. Furthermore, a computationally efficient four-step updating strategy with linear complexity is designed to minimize the associated loss. Extensive experiments organized on publicly-available benchmark datasets with varying missing percentages confirm the superior effectiveness of our BSTM.

Pretrained Transformers demonstrate remarkable in-context learning (ICL) capabilities, enabling them to adapt to new tasks from demonstrations without parameter updates. However, theoretical studies often rely on simplified architectures (e.g., omitting MLPs), data models (e.g., linear regression with isotropic inputs), and single-source training—limiting their relevance to realistic settings. In this work, we study ICL in pretrained Transformers with nonlinear MLP heads on nonlinear tasks drawn from multiple data sources with heterogeneous input, task, and noise distributions. We analyze a model where the MLP comprises two layers, with the first layer trained via a single gradient step and the second layer fully optimized. Under high-dimensional asymptotics, we prove that such models are equivalent in ICL error to structured polynomial predictors, leveraging results from the theory of Gaussian universality and orthogonal polynomials. This equivalence reveals that nonlinear MLPs meaningfully enhance ICL performance—particularly on nonlinear tasks—compared to linear baselines. It also enables a precise analysis of data mixing effects: we identify key properties of high-quality data sources (low noise, structured covariances) and show that feature learning emerges only when the task covariance exhibits sufficient structure. These results are validated empirically across various activation functions, model sizes, and data distributions. Finally, we experiment with a real-world scenario involving multilingual sentiment analysis where each language is treated as a different source. Our experimental results for this case exemplify how our findings extend to real-world cases. Overall, our work advances the theoretical foundations of ICL in Transformers and provides actionable insight into the role of architecture and data in ICL.

Graph neural networks (GNNs) can efficiently process text-attributed graphs (TAGs) due to their message-passing mechanisms, but their training heavily relies on the human-annotated labels. Moreover, the complex and diverse local topologies of nodes of real-world TAGs make it challenging for a single mechanism to handle. Large language models (LLMs) perform well in zero-/few-shot learning on TAGs but suffer from a scalability challenge. Therefore, we propose a preference-driven knowledge distillation (PKD) framework to synergize the complementary strengths of LLMs and various GNNs for few-shot node classification. Specifically, we develop a GNN-preference-driven node selector that effectively promotes prediction distillation from LLMs to teacher GNNs. To further tackle nodes' intricate local topologies, we develop a node-preference-driven GNN selector that identifies the most suitable teacher GNN for each node, thereby facilitating tailored knowledge distillation from teacher GNNs to the student GNN. Extensive experiments validate the efficacy of our proposed framework in few-shot node classification on real-world TAGs. Our code can be available at <https://github.com/GEEX-Weixing/PKD>.

This paper presents PipeFusion, an innovative parallel methodology to tackle the high latency issues associated with generating high-resolution images using diffusion transformers (DiTs) models. PipeFusion partitions images into patches and the model layers across multiple GPUs. It employs a patch-level pipeline parallel strategy to orchestrate communication and computation efficiently. By capitalizing on the high similarity between inputs from successive diffusion steps, PipeFusion reuses one-step stale feature maps to provide context for the current pipeline step. This approach notably reduces communication costs compared to existing DiTs inference parallelism, including tensor parallel, sequence parallel and DistriFusion. PipeFusion enhances memory efficiency through parameter distribution across devices, ideal for large DiTs like Flux.1. Experimental results demonstrate that PipeFusion achieves state-of-the-art performance on 8$\times$L40 PCIe GPUs for Pixart, Stable-Diffusion 3, and Flux.1 models. Our Source code is available at \url{https://github.com/xdit-project/xDiT}.

Many emerging applications—such as adversarial training, AI alignment, and robust optimization—can be framed as zero-sum games between neural nets, with von Neumann–Nash equilibria (NE) capturing the desirable system behavior. While such games often involve non-convex non-concave objectives, empirical evidence shows that simple gradient methods frequently converge, suggesting a hidden geometric structure. In this paper, we provide a theoretical framework that explains this phenomenon through the lens of \emph{hidden convexity} and \emph{overparameterization}. We identify sufficient conditions spanning initialization, training dynamics, and network width—that guarantee global convergence to a NE in a broad class of non-convex min-max games. To our knowledge, this is the first such result for games that involve two-layer neural networks. Technically, our approach is twofold: (a) we derive a novel path-length bound for alternating gradient-descent-ascent scheme in min-max games; and (b) we show that games with hidden convex–concave geometry reduce to settings satisfying two-sided Polyak–Łojasiewicz (PL) and smoothness conditions, which hold with high probability under overparameterization, using tools from random matrix theory.

Understanding and reasoning over long videos pose significant challenges for large video language models (LVLMs) due to the difficulty in processing intensive video tokens beyond context window and retaining long-term sequential information. Retrieval-Augmented Generation (RAG) has demonstrated effectiveness in processing long context for Large Language Models (LLMs); however, applying RAG to long video faces challenges such as disrupted temporal dependencies and inclusion of irrelevant information that can hinder accurate reasoning. To address these limitations, we propose Vgent, a novel \textbf{graph-based retrieval-reasoning-augmented generation framework} to enhance LVLMs for long video understanding. Our approach introduces two key innovations: (i) It represents videos by structured graphs with semantic relationships across video clips preserved to improve retrieval effectiveness. (ii) It introduces an intermediate reasoning step to mitigate the reasoning limitation of LVLMs, which leverages structured verification to reduce retrieval noise and facilitate the explicit aggregation of relevant information across clips, resulting in more accurate and context-aware responses. We comprehensively evaluate our framework with various open-source LVLMs on three long-video understanding benchmarks. Our approach yielded an overall performance improvement of $3.0\%\sim 5.4\%$ over base models on MLVU, and outperformed state-of-the-art video RAG methods by $8.6\%$. Our code is publicly available at https://xiaoqian-shen.github.io/Vgent.

Estimating heterogeneous treatment effects (HTEs) of continuous-valued interventions on survival, that is, time-to-event (TTE) outcomes, is crucial in various fields, notably in clinical decision-making and in driving the advancement of next-generation clinical trials. However, while HTE estimation for continuous-valued (i.e., dosage-dependent) interventions and for TTE outcomes have been separately explored, their combined application remains largely overlooked in the machine learning literature. We propose DoseSurv, a varying-coefficient network designed to estimate HTEs for different dosage-dependent and non-dosage treatment options from TTE data. DoseSurv uses radial basis functions to model continuity in dose-response relationships and learns balanced representations to address covariate shifts arising in HTE estimation from observational TTE data. We present experiments across various treatment scenarios on both simulated and real-world data, demonstrating DoseSurv's superior performance over existing baseline models.

We introduce a new graph diffusion model for small drug molecule generation which simultaneously offers a 10-fold reduction in the number of diffusion steps when compared to existing methods, preservation of small molecule graph motifs via motif compression, and an average 3\% improvement in SMILES validity over the DiGress model across all real-world molecule benchmarking datasets. Furthermore, our approach outperforms the state-of-the-art DeFoG method with respect to motif-conservation by roughly 4\%, as evidenced by high ChEMBL-likeness, QED and newly introduced shingles distance scores. The key ideas behind the approach are to use a combination of deterministic and random subgraph perturbations, so that the node and edge noise schedules are codependent; to modify the loss function of the training process in order to exploit the deterministic component of the schedule; and, to ''compress'' a collection of highly relevant carbon ring and other motif structures into supernodes in a way that allows for simple subsequent integration into the molecular scaffold.

Large Language Models (LLMs) exhibit impressive performance across diverse domains but often suffer from overconfidence, limiting their reliability in critical applications. We propose SteerConf, a novel framework that systematically steers LLMs' confidence scores to improve their calibration and reliability. SteerConf introduces three key components: (1) a steering prompt strategy that guides LLMs to produce confidence scores in specified directions (e.g., conservative or optimistic) by leveraging prompts with varying steering levels; (2) a steered confidence consistency measure that quantifies alignment across multiple steered confidences to enhance calibration; and (3) a steered confidence calibration method that aggregates confidence scores using consistency measures and applies linear quantization for answer selection. SteerConf operates without additional training or fine-tuning, making it broadly applicable to existing LLMs. Experiments on seven benchmarks spanning professional knowledge, common sense, ethics, and reasoning tasks, using advanced LLM models (GPT-3.5, LLaMA 3, GPT-4), demonstrate that SteerConf significantly outperforms existing methods, often by a significant margin. Our findings highlight the potential of steering the confidence of LLMs to enhance their reliability for safer deployment in real-world applications. The implementation is at \url{https://github.com/scottjiao/SteerConf}.

A central question in the theory of machine learning concerns the identification of classes of data distributions for which one can provide computationally efficient learning algorithms with provable statistical learning guarantees. Indeed, in the context of probably approximately correct (PAC) learning, there has been much interest in exploring intermediate PAC learning models that, unlike the realizable PAC learning setting, allow for some stochasticity in the labels, and unlike the fully agnostic PAC learning setting, also admit computationally efficient learning algorithms with finite sample complexity bounds. Some examples of such models include random classification noise (RCN), probabilistic concepts, Massart noise, and generalized linear models (GLMs); in general, most of this work has focused on binary classification problems. In this paper, we study what we call realizable-statistic models (RSMs), wherein we allow stochastic labels but assume that some vector-valued statistic of the conditional label distribution comes from some known function class. RSMs are a flexible class of models that interpolate between the realizable and fully agnostic settings, and that also recover several previously studied models as special cases. We show that for a broad range of RSM learning problems, where the statistic of interest can be accurately estimated via a convex ‘strongly proper composite’ surrogate loss, minimizing this convex surrogate loss yields a computationally efficient learning algorithm with finite sample complexity bounds. We then apply this result to show that various commonly used (and in some cases, not so commonly used) convex surrogate risk minimization algorithms yield computationally efficient learning algorithms with finite sample complexity bounds for a variety of RSM learning problems including binary classification, multiclass classification, multi-label prediction, and subset ranking. For the special case of binary classification with sigmoid-of-linear class probabilities (also a special case of GLMs), our results show that minimizing the standard binary logistic loss has a similar sample complexity as the GLM-tron algorithm of Kakade et al. (2011), but is computationally more efficient. In terms of the distribution over the domain/instance space, our results are all distribution-independent. To our knowledge, these are the first such results for PAC learning with stochastic labels for such a broad range of learning problems.

We propose IPSI, a general iterative framework for structural inference in interacting dynamical systems. It integrates a pretrained structural estimator and a joint inference module based on the Variational Autoencoder (VAE); these components are alternately updated to progressively refine the inferred structures. Initially, the structural estimator is trained on labels from either a meta-dataset or a baseline model to extract features and generate structural priors, which provide multi-level guidance for training the joint inference module. In subsequent iterations, pseudolabels from the joint module replace the initial labels. IPSI is compatible with various VAE-based models. Experiments on synthetic datasets of physical systems demonstrate that IPSI significantly enhances the performance of structural inference models such as Neural Relational Inference (NRI). Ablation studies reveal that feature and structural prior inputs to the joint module offer complementary improvements from representational and generative perspectives.

The growing interest in employing large language models (LLMs) for decision-making in social and economic contexts has raised questions about their potential to function as agents in these domains. A significant number of societal problems involve the distribution of resources, where fairness, along with economic efficiency, play a critical role in the desirability of outcomes. In this paper, we examine whether LLM responses adhere to fundamental fairness concepts such as equitability, envy-freeness, and Rawlsian maximin, and investigate their alignment with human preferences. We evaluate the performance of several LLMs, providing a comparative benchmark of their ability to reflect these measures. Our results demonstrate a lack of alignment between current LLM responses and human distributional preferences. Moreover, LLMs are unable to utilize money as a transferable resource to mitigate inequality. Nonetheless, we demonstrate a stark contrast when (some) LLMs are tasked with selecting from a predefined menu of options rather than generating one. In addition, we analyze the robustness of LLM responses to variations in semantic factors (e.g. intentions or personas) or non-semantic prompting changes (e.g. templates or orderings). Finally, we highlight potential strategies aimed at enhancing the alignment of LLM behavior with well-established fairness concepts.

Recent theoretical results show transformers cannot express sequential reasoning problems over long inputs, intuitively because their computational *depth* is bounded. However, prior work treats the depth as a constant, leaving it unclear to what degree bounded depth may suffice for solving problems over short inputs, or how increasing the transformer's depth affects its expressive power. We address these questions by analyzing transformers whose depth can grow minimally with context length $n$. We show even highly uniform transformers with depth $\Theta(\log n)$ can express two important problems: *recognizing regular languages*, which captures state tracking abilities and was known to be expressible only by an unconventional, non-uniform model of transformers, and *graph connectivity*, which underlies multi-step reasoning. Notably, both of these problems cannot be expressed by fixed-depth transformers under standard complexity conjectures, demonstrating the expressivity benefit of growing depth. Moreover, our theory quantitatively predicts how depth must grow with input length to express these problems, showing that depth scaling is more efficient than scaling width or chain-of-thought steps. Empirically, our detailed experiments designed to bridge the expressivity vs. learnability gap reveal that our theoretical depth requirements for regular language recognition closely match the practical depth requirements for successfully training transformers. Thus, our results clarify how depth affects a transformer's reasoning capabilities, and provide practical guidance for effective depth selection for sequential reasoning.

Understanding the evolution of cellular microenvironments in spatiotemporal data is essential for deciphering tissue development and disease progression. While experimental techniques like spatial transcriptomics now enable high-resolution mapping of tissue organization across space and time, current methods that model cellular evolution operate at the single-cell level, overlooking the coordinated development of cellular states in a tissue. We introduce NicheFlow, a flow-based generative model that infers the temporal trajectory of cellular microenvironments across sequential spatial slides. By representing local cell neighborhoods as point clouds, NicheFlow jointly models the evolution of cell states and spatial coordinates using optimal transport and Variational Flow Matching. Our approach successfully recovers both global spatial architecture and local microenvironment composition across diverse spatiotemporal datasets, from embryonic to brain development.

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying thermodynamic stability remains incompletely understood. A better understanding would be of interest not only from a theoretical perspective, but also potentially provide the basis for stronger zero-shot stability prediction. In this paper, we take steps to clarify the free-energy foundations of inverse folding models. Our derivation reveals the standard practice of likelihood ratios as a simplistic approximation and suggests several paths towards better estimates of the relative stability. We empirically assess these approaches and demonstrate that considerable gains in zero-shot performance can be achieved with fairly simple means.

We introduce FAEclust, a novel functional autoencoder framework for cluster analysis of multi-dimensional functional data, data that are random realizations of vector-valued random functions. Our framework features a universal-approximator encoder that captures complex nonlinear interdependencies among component functions, and a universal-approximator decoder capable of accurately reconstructing both Euclidean and manifold-valued functional data. Stability and robustness are enhanced through innovative regularization strategies applied to functional weights and biases. Additionally, we incorporate a clustering loss into the network's training objective, promoting the learning of latent representations that are conducive to effective clustering. A key innovation is our shape-informed clustering objective, ensuring that the clustering results are resistant to phase variations in the functions. We establish the universal approximation property of our non-linear decoder and validate the effectiveness of our model through extensive experiments.

We present an open-vocabulary and zero-shot method for arbitrary referring expression segmentation (RES), targeting input expressions that are more general than what prior works were designed to handle. Specifically, our inputs encompass both object- and part-level labels as well as implicit references pointing to properties or qualities of object/part function, design, style, material, etc. Our model, coined RESAnything, leverages Chain-of-Thoughts (CoT) reasoning, where the key idea is attribute prompting. We generate detailed descriptions of object/part attributes including shape, color, and location for potential segment proposals through systematic prompting of a large language model (LLM), where the proposals are produced by a foundational image segmentation model. Our approach encourages deep reasoning about object or part attributes related to function, style, design, etc., enabling the system to handle implicit queries without any part annotations for training or fine-tuning. As the first zero-shot and LLM-based RES method, RESAnything achieves clearly superior performance among zero-shot methods on traditional RES benchmarks and significantly outperforms existing methods on challenging scenarios involving implicit queries and complex part-level relations. Finally, we contribute a new benchmark dataset to offer ~3K carefully curated RES instances to assess part-level, arbitrary RES solutions.

Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in an end-to-end fashion, directly mapping input instances to solutions. While this allows models to learn useful heuristics from data, it often results in limited generalization beyond the training distribution. In this work, we propose a novel approach to reasoning generalization by learning energy landscapes over the solution spaces of smaller, more tractable subproblems. At test time, we construct a global energy landscape for a given problem by combining the energy functions of multiple subproblems. This compositional approach enables the incorporation of additional constraints during inference, allowing the construction of energy landscapes for problems of increasing difficulty. To improve the sample quality from this newly constructed energy landscape, we introduce Parallel Energy Minimization (PEM). We evaluate our approach on a wide set of reasoning problems. Our method outperforms existing state-of-the-art methods, demonstrating its ability to generalize to larger and more complex problems. Project website can be found at: https://alexoarga.github.io/compositional_reasoning/