NeurIPS 2025 论文列表

Transformers have gained attention in atmospheric time series forecasting (ATSF) for their ability to capture global spatial-temporal correlations. However, their complex architectures lead to excessive parameter counts and extended training times, limiting their scalability to large-scale forecasting. In this paper, we revisit ATSF from a theoretical perspective of atmospheric dynamics and uncover a key insight: spatial-temporal position embedding (STPE) can inherently model spatial-temporal correlations even without attention mechanisms. Its effectiveness arises from integrating geographical coordinates and temporal features, which are intrinsically linked to atmospheric dynamics. Based on this, we propose **STELLA**, a **S**patial-**T**emporal knowledge **E**mbedded **L**ightweight mode**L** for ASTF, utilizing only STPE and an MLP architecture in place of Transformer layers. With 10k parameters and one hour of training, STELLA achieves superior performance on five datasets compared to other advanced methods. The paper emphasizes the effectiveness of spatial-temporal knowledge integration over complex architectures, providing novel insights for ATSF.

Large Language Models (LLMs) are typically trained on data mixtures: most data come from web scrapes, while a small portion is curated from high-quality sources with dense domain-specific knowledge. In this paper, we show that when training LLMs on such data mixtures, knowledge acquisition from knowledge-dense datasets—unlike training exclusively on knowledge-dense data—does not always follow a smooth scaling law but can exhibit phase transitions with respect to the mixing ratio and model size. Through controlled experiments on a synthetic biography dataset mixed with web-scraped data, we demonstrate that: (1) as we increase the model size to a critical value, the model suddenly transitions from memorizing very few to most of the biographies; (2) below a critical mixing ratio, the model memorizes almost nothing even with extensive training, but beyond this threshold, it rapidly memorizes more biographies. We attribute these phase transitions to a capacity allocation phenomenon: a model with bounded capacity must act like a knapsack problem solver to minimize the overall test loss, and the optimal allocation across datasets can change discontinuously as the model size or mixing ratio varies. We formalize this intuition in an information-theoretic framework and reveal that these phase transitions are predictable, with the critical mixing ratio following a power-law relationship with the model size. Our findings highlight a concrete case where a good mixing recipe for large models may not be optimal for small models, and vice versa.

Understanding how the human brain progresses from processing simple linguistic inputs to performing high-level reasoning is a fundamental challenge in neuroscience. While modern large language models (LLMs) are increasingly used to model neural responses to language, their internal representations are highly "entangled," mixing information about lexicon, syntax, meaning, and reasoning. This entanglement biases conventional brain encoding analyses toward linguistically shallow features (e.g., lexicon and syntax), making it difficult to isolate the neural substrates of cognitively deeper processes. Here, we introduce a residual disentanglement method that computationally isolates these components. By first probing an LM to identify feature-specific layers, our method iteratively regresses out lower-level representations to produce four nearly orthogonal embeddings for lexicon, syntax, meaning, and, critically, reasoning. We used these disentangled embeddings to model intracranial (ECoG) brain recordings from neurosurgical patients listening to natural speech. We show that: 1) This isolated reasoning embedding exhibits unique predictive power, accounting for variance in neural activity not explained by other linguistic features and even extending to the recruitment of visual regions beyond classical language areas. 2) The neural signature for reasoning is temporally distinct, peaking later (~350-400ms) than signals related to lexicon, syntax, and meaning, consistent with its position atop a processing hierarchy. 3) Standard, non-disentangled LLM embeddings can be misleading, as their predictive success is primarily attributable to linguistically shallow features, masking the more subtle contributions of deeper cognitive processing. Our work provides compelling neural evidence for an abstract reasoning computation during language comprehension and offers a robust framework for mapping distinct cognitive functions from artificial models to the human brain.

Multimodal recommendation aims to integrate collaborative signals with heterogeneous content such as visual and textual information, but remains challenged by modality-specific noise, semantic inconsistency, and unstable propagation over user–item graphs. These issues are often exacerbated by naive fusion or shallow modeling strategies, leading to degraded generalization and poor robustness. While recent work has explored the frequency domain as a lens to separate stable from noisy signals, most methods rely on static filtering or reweighting, lacking the ability to reason over spectral structure or adapt to modality-specific reliability. To address these challenges, we propose a Structured Spectral Reasoning (SSR) framework for frequency-aware multimodal recommendation. Our method follows a four-stage pipeline: (i) Decompose graph-based multimodal signals into spectral bands via graph-guided transformations to isolate semantic granularity; (ii) Modulate band-level reliability with spectral band masking, a training-time masking with prediction-consistency objective that suppresses brittle frequency components; (iii) Fuse complementary frequency cues using hyperspectral reasoning with low-rank cross-band interaction; and (iv) Align modality-specific spectral features via contrastive regularization to promote semantic and structural consistency. Experiments on three real-world benchmarks show consistent gains over strong baselines, particularly under sparse and cold-start settings. Additional analyses indicate that structured spectral modeling improves robustness and provides clearer diagnostics of how different bands contribute to performance.

Crossmodal matching in single-cell omics is essential for explaining biological regulatory mechanisms and enhancing downstream analyses. However, current single-cell crossmodal models often suffer from three limitations: sparse modality signals, underutilization of biological attributes, and insufficient modeling of regulatory interactions. These challenges hinder generalization in data-scarce settings and restrict the ability to uncover fine-grained biologically meaningful crossmodal relationships. Here, we present a novel framework which reformulates crossmodal matching as a graph classification task on Attributed Bipartite Graphs (ABGs). It models single-cell ATAC-RNA data as an ABG, where each expressed ATAC and RNA is treated as a distinct node with unique IDs and biological features. To model crossmodal interaction patterns on the constructed ABG, we propose $\text{Bi}^2\text{Former}$, a **bi**ologically-driven **bi**partite graph trans**former** that learns interpretable attention over ATAC–RNA pairs. This design enables the model to effectively learn and explain biological regulatory relationships between ATAC and RNA modalities. Extensive experiments demonstrate that $\text{Bi}^2\text{Former}$ achieves state-of-the-art performance in crossmodal matching across diverse datasets, remains robust under sparse training data, generalizes to unseen cell types and datasets, and reveals biologically meaningful regulatory patterns. This work pioneers an ABG-based approach for single-cell crossmodal matching, offering a powerful framework for uncovering regulatory interactions at the single-cell omics. Our code is available at: https://github.com/wangxiaotang0906/Bi2Former.

Continual Structured Knowledge Reasoning (CSKR) focuses on training models to handle sequential tasks, where each task involves translating natural language questions into structured queries grounded in structured knowledge. Existing general continual learning approaches face significant challenges when applied to this task, including poor generalization to heterogeneous structured knowledge and inefficient reasoning due to parameter growth as tasks increase. To address these limitations, we propose a novel CSKR framework, \textsc{K-DeCore}, which operates with a fixed number of tunable parameters. Unlike prior methods, \textsc{K-DeCore} introduces a knowledge decoupling mechanism that disentangles the reasoning process into task-specific and task-agnostic stages, effectively bridging the gaps across diverse tasks. Building on this foundation, \textsc{K-DeCore} integrates a dual-perspective memory consolidation mechanism for distinct stages and introduces a structure-guided pseudo-data synthesis strategy to further enhance the model's generalization capabilities. Extensive experiments on four benchmark datasets demonstrate the superiority of \textsc{K-DeCore} over existing continual learning methods across multiple metrics, leveraging various backbone large language models.

Graph Neural Networks (GNNs) have achieved impressive results across diverse network modeling tasks, but accurately estimating uncertainty on graphs remains difficult—especially under distributional shifts. Unlike traditional uncertainty estimation, graph-based uncertainty must account for randomness arising from both the graph’s structure and its label distribution, which adds complexity. In this paper, making an analogy between the evolution of a stochastic partial differential equation (SPDE) driven by Mat\'ern Gaussian Process and message passing using GNN layers, we present a principled way to design a novel message passing scheme that incorporates spatial-temporal noises motivated by the Gaussian Process approach to SPDE. Our method simultaneously captures uncertainty across space and time and allows explicit control over the covariance kernel’s smoothness, thereby enhancing uncertainty estimates on graphs with both low and high label informativeness. Our extensive experiments on Out-of-Distribution (OOD) detection on graph datasets with varying label informativeness demonstrate the soundness and superiority of our model to existing approaches.

Human behavior is characterized by continuous learning to reduce uncertainties about the world in pursuit of goals. When trying to understand such behavior from observations, it is essential to account for this adaptive nature and reason about the uncertainties that may have led to seemingly suboptimal decisions. Nevertheless, most inverse approaches to sequential decision-making focus on inferring cost functions underlying stationary behavior or are limited to low-dimensional tasks. In this paper, we address this gap by considering the problem of inferring an agent's knowledge or awareness about the environment based on a given trajectory. We assume that the agent aims to reach a goal in an environment they only partially know, and integrates new information into their plan as they act. We propose a Bayesian approach to infer their latent knowledge state, leveraging an approximate navigation model that optimistically incorporates partial information while accounting for uncertainty. By combining sample-based Bayesian inference with dynamic graph algorithms, we achieve an efficient method for computing posterior beliefs about the agent's knowledge. Empirical validation using simulated behavioral data and human data from an online experiment demonstrates that our model effectively captures human navigation under uncertainty and reveals interpretable insights into their environmental knowledge.

Deep model merging represents an emerging research direction that combines multiple fine-tuned models to harness their specialized capabilities across different tasks and domains. Current model merging techniques focus on merging all available models simultaneously, with weight interpolation-based methods being the predominant approach. However, these conventional approaches are not well-suited for scenarios where models become available sequentially, and they often suffer from high memory requirements and potential interference between tasks. In this study, we propose a training-free projection-based continual merging method that processes models sequentially through orthogonal projections of weight matrices and adaptive scaling mechanisms. Our method operates by projecting new parameter updates onto subspaces orthogonal to existing merged parameter updates while using an adaptive scaling mechanism to maintain stable parameter distances, enabling efficient sequential integration of task-specific knowledge. Our approach maintains constant memory complexity to the number of models, minimizes interference between tasks through orthogonal projections, and retains the performance of previously merged models through adaptive task vector scaling. Extensive experiments on CLIP-ViT models demonstrate that our method achieves a 5-8% average accuracy improvement while maintaining robust performance in different task orderings. Code is publicly available at https://github.com/tanganke/opcm .

Standard Retrieval-Augmented Generation (RAG) relies on chunk-based retrieval, whereas GraphRAG advances this approach by graph-based knowledge representation. However, existing graph-based RAG approaches are constrained by binary relations, as each edge in an ordinary graph connects only two entities, limiting their ability to represent the n-ary relations (n >= 2) in real-world knowledge. In this work, we propose HyperGraphRAG, the first hypergraph-based RAG method that represents n-ary relational facts via hyperedges. HyperGraphRAG consists of a comprehensive pipeline, including knowledge hypergraph construction, retrieval, and generation. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms both standard RAG and previous graph-based RAG methods in answer accuracy, retrieval efficiency, and generation quality.

The integration of logic programs with embedding models resulted in a class of neurosymbolic frameworks that jointly learn symbolic rules and representations for the symbols in the logic (constant or predicate). The key idea that enabled this integration was the differentiable relaxation of unification, the algorithm for variable instantiation during inference in logic programs. Unlike unification, its relaxed counterpart exploits the similarity between symbols in the embedding space to decide when two symbols are semantically equivalent. We show that this similarity between symbols violates the transitive law of equivalence, leading to undesirable side effects in learning and inference. To alleviate those side effects, we are the first to revamp the well-known possible world semantics of probabilistic logic programs into new semantics called equivalence semantics. In our semantics, a probabilistic logic program induces a probability distribution over all possible equivalence relations between symbols, instead of a probability distribution over all possible subsets of probabilistic facts. We propose a factorization of the equivalence distribution using latent random variables and characterize its expressivity. Additionally, we propose both exact and approximate techniques for reasoning in our semantics. Experiments on well-known benchmarks show that the equivalence semantics leads to neurosymbolic models with up to 42% higher results than state-of-the-art baselines.

Knowledge graphs (KGs) are vital for enabling knowledge reasoning across various domains. Recent KG reasoning methods that integrate both global and local information have achieved promising results. However, existing methods often suffer from score over-smoothing, which blurs the distinction between correct and incorrect answers and hinders reasoning effectiveness. To address this, we propose DuetGraph, a **coarse-to-fine** KG reasoning mechanism with **dual-pathway** global-local fusion. DuetGraph tackles over-smoothing by segregating—rather than stacking—the processing of local (via message passing) and global (via attention) information into two distinct pathways, preventing mutual interference and preserving representational discrimination. In addition, DuetGraph introduces a **coarse-to-fine** optimization, which partitions entities into high- and low-score subsets. This strategy narrows the candidate space and sharpens the score gap between the two subsets, which alleviates over-smoothing and enhances inference quality. Extensive experiments on various datasets demonstrate that DuetGraph achieves state-of-the-art (SOTA) performance, with up to an **8.7\%** improvement in reasoning quality and a **1.8$\times$** acceleration in training efficiency.

Retrieval-Augmented Generation (RAG) based on knowledge graphs (KGs) enhances large language models (LLMs) by providing structured and interpretable external knowledge. However, existing KG-based RAG methods struggle to retrieve accurate and diverse information from text-rich KGs for complex real-world queries. Process Reward Models (PRMs) offer a way to align the retrieval process of KG-based RAG with query-specific knowledge requirements, but they heavily rely on process-level supervision signals that are expensive and hard to obtain on KGs. To address this challenge, we propose GraphFlow, a framework that efficiently retrieves accurate and diverse knowledge required for real-world queries from text-rich KGs. GraphFlow employs a transition-based flow matching objective to jointly optimize a retrieval policy and a flow estimator. The flow estimator factorizes the reward of the retrieval outcome into the intermediate retrieval states. Such reward factorization guides the retrieval policy to retrieve candidates from KGs in proportion to their reward. This allows GraphFlow to explore high-quality regions of KGs that yield diverse and relevant results. We evaluate GraphFlow on the STaRK benchmark, which includes real-world queries from multiple domains over text-rich KGs. GraphFlow outperforms strong KG-RAG baselines, including GPT-4o, by 10\% on average in hit rate and recall. It also shows strong generalization to unseen KGs, demonstrating its effectiveness and robustness.

Learning editable high-resolution scene representations for dynamic scenes is an open problem with applications across the domains from autonomous driving to creative editing - the most successful approaches today make a trade-off between editability and supporting scene complexity: neural atlases represent dynamic scenes as two deforming image layers, foreground and background, which are editable in 2D, but break down when multiple objects occlude and interact. In contrast, scene graph models make use of annotated data such as masks and bounding boxes from autonomous-driving datasets to capture complex 3D spatial relationships, but their implicit volumetric node representations are challenging to edit view-consistently. We propose Neural Atlas Graphs (NAGs), a hybrid high-resolution scene representation, where every graph node is a view-dependent neural atlas, facilitating both 2D appearance editing and 3D ordering and positioning of scene elements. Fit at test-time, NAGs achieve state-of-the-art quantitative results on the Waymo Open Dataset - by 5 dB PSNR increase compared to existing methods - and make environmental editing possible in high resolution and visual quality - creating counterfactual driving scenarios with new backgrounds and edited vehicle appearance. We find that the method also generalizes beyond driving scenes and compares favorably - by more than 7 dB in PSNR - to recent matting and video editing baselines on the DAVIS video dataset with a diverse set of human and animal-centric scenes. Project Page: https://princeton-computational-imaging.github.io/nag/

We present Fin3R, a simple, effective, and general fine-tuning method for feed-forward 3D reconstruction models. The family of feed-forward reconstruction model regresses pointmap of all input images to a reference frame coordinate system, along with other auxiliary outputs, in a single forward pass. However, we find that current models struggle with fine geometry and robustness due to (\textit{i}) the scarcity of high-fidelity depth and pose supervision and (\textit{ii}) the inherent geometric misalignment from multi-view pointmap regression. Fin3R jointly tackles two issues with an extra lightweight fine-tuning step. We freeze the decoder, which handles view matching, and fine-tune only the image encoder—the component dedicated to feature extraction. The encoder is enriched with fine geometric details distilled from a strong monocular teacher model on large, unlabeled datasets, using a custom, lightweight LoRA adapter. We validate our method on a wide range of models, including DUSt3R, MASt3R, CUT3R, and VGGT. The fine-tuned models consistently deliver sharper boundaries, recover complex structures, and achieve higher geometric accuracy in both single- and multi-view settings, while adding only the tiny LoRA weights, which leave test-time memory and latency virtually unchanged. Project page: \href{http://visual-ai.github.io/fin3r}{https://visual-ai.github.io/fin3r}

Federated continual learning (FCL) tackles scenarios of learning from continuously emerging task data across distributed clients, where the key challenge lies in addressing both temporal forgetting over time and spatial forgetting simultaneously. Recently, prompt-based FCL methods have shown advanced performance through task-wise prompt communication. In this study, we underscore that the existing prompt-based FCL methods are prone to class-wise knowledge coherence between prompts across clients. The class-wise knowledge coherence includes two aspects: (1) intra-class distribution gap across clients, which degrades the learned semantics across prompts, (2) inter-prompt class-wise relevance, which highlights cross-class knowledge confusion. During prompt communication, insufficient class-wise coherence exacerbates knowledge conflicts among new prompts and induces interference with old prompts, intensifying both spatial and temporal forgetting. To address these issues, we propose a novel Class-aware Client Knowledge Interaction (C$^2$Prompt) method that explicitly enhances class-wise knowledge coherence during prompt communication. Specifically, a local class distribution compensation mechanism (LCDC) is introduced to reduce intra-class distribution disparities across clients, thereby reinforcing intra-class knowledge consistency. Additionally, a class-aware prompt aggregation scheme (CPA) is designed to alleviate inter-class knowledge confusion by selectively strengthening class-relevant knowledge aggregation. Extensive experiments on multiple FCL benchmarks demonstrate that C$^2$Prompt achieves state-of-the-art performance. Our code will be released.

Large-scale pre-trained models have revolutionized Natural Language Processing (NLP) and Computer Vision (CV), showcasing remarkable cross-domain generalization abilities. However, in graph learning, models are typically trained on individual graph datasets, limiting their capacity to transfer knowledge across different graphs and tasks. This approach also heavily relies on large volumes of annotated data, which presents a significant challenge in resource-constrained settings. Unlike NLP and CV, graph-structured data presents unique challenges due to its inherent heterogeneity, including domain-specific feature spaces and structural diversity across various applications. To address these challenges, we propose a novel structure-aware self-supervised learning method for Text-Attributed Graphs (SSTAG). By leveraging text as a unified representation medium for graph learning, SSTAG bridges the gap between the semantic reasoning of Large Language Models (LLMs) and the structural modeling capabilities of Graph Neural Networks (GNNs). Our approach introduces a dual knowledge distillation framework that co-distills both LLMs and GNNs into structure-aware multilayer perceptrons (MLPs), enhancing the scalability of large-scale TAGs. Additionally, we introduce an in-memory mechanism that stores typical graph representations, aligning them with memory anchors in an in-memory repository to integrate invariant knowledge, thereby improving the model’s generalization ability. Extensive experiments demonstrate that SSTAG outperforms state-of-the-art models on cross-domain transfer learning tasks, achieves exceptional scalability, and reduces inference costs while maintaining competitive performance.

Growing data privacy demands, driven by regulations like GDPR and CCPA, require machine unlearning methods capable of swiftly removing the influence of specific training points. Although verified approaches like SISA, using data slicing and checkpointing, achieve efficient unlearning for single models by reverting to intermediate states, these methods struggle in teacher-student knowledge distillation settings. Unlearning in the teacher typically forces costly, complete student retraining due to pervasive information propagation during distillation. Our primary contribution is PURGE (Partitioned Unlearning with Retraining Guarantee for Ensembles), a novel framework integrating verified unlearning with distillation. We introduce constituent mapping and an incremental multi-teacher strategy that partitions the distillation process, confines each teacher constituent’s impact to distinct student data subsets, and crucially maintains data isolation. The PURGE framework substantially reduces retraining overhead—requiring only partial student updates—when teacher-side unlearning occurs. We provide both theoretical analysis, quantifying significant speed-ups in the unlearning process, and empirical validation on multiple datasets, demonstrating that PURGE achieves these efficiency gains while maintaining student accuracy comparable to standard baselines.

Higher-order information is crucial for relational learning in many domains where relationships extend beyond pairwise interactions. Hypergraphs provide a natural framework for modeling such relationships, which has motivated recent extensions of graph neural network (GNN) architectures to hypergraphs. Most of these architectures rely on message-passing to encode higher-order information. In this paper, we propose to instead use hypergraph-level encodings based on characteristics such as hypergraph Laplacians and discrete curvature notions. These encodings can be used on datasets that are naturally parametrized as hypergraphs and on graph-level datasets, which we reparametrize as hypergraphs to compute encodings. In both settings, performance increases significantly, on social networks by more than 10 percent. Our theoretical analysis shows that hypergraph-level encodings provably increase the representational power of message-passing graph neural networks beyond that of their graph-level counterparts. For complete reproducibility, we release our codebase: https://github.com/Weber-GeoML/Hypergraph_Encodings.