NeurIPS 2025 论文列表

As hypothesis generation becomes increasingly automated, a new bottleneck has emerged: hypothesis assessment. Modern systems can surface thousands of statistical relationships—correlations, trends, causal links—but offer little guidance on which ones are novel, non-trivial, or worthy of expert attention. In this work, we study the complementary problem to hypothesis generation: automatic hypothesis assessment. Specifically, we ask—given a large set of statistical relationships, can we automatically assess which ones are novel and worth further exploration? We focus on correlations as they are a common entry point in exploratory data analysis that often serve as the basis for forming deeper scientific or causal hypotheses. To support automatic assessment, we propose to leverage the vast knowledge encoded in LLMs' weights to derive a prior distribution over the correlation value of a variable pair. If an LLM's prior expects the correlation value observed, then such correlation is not surprising, and vice versa. We propose the Logit-based Calibrated Prior, an LLM-elicited correlation prior that transforms the model’s raw output logits into a calibrated, continuous predictive distribution over correlation values. We evaluate the prior on a benchmark of 2,096 real-world variable pairs and it achieves a sign accuracy of 78.8%, a mean absolute error of 0.26, and 95% credible interval coverage of 89.2% in predicting Pearson correlation coefficient. It also outperforms a fine-tuned RoBERTa classifier in binary correlation prediction and achieves higher precision@K in hypothesis ranking. We further show that the prior generalizes to correlations not seen during LLM pretraining, reflecting context-sensitive reasoning rather than memorization.

Federated Graph Learning (FGL) has been shown to be particularly effective in enabling collaborative training of Graph Neural Networks (GNNs) in decentralized settings. Model-heterogeneous FGL further enhances practical applicability by accommodating client preferences for diverse model architectures. However, existing model-heterogeneous approaches primarily target Euclidean data and fail to account for a crucial aspect of graph-structured data: topological relationships. To address this limitation, we propose **TRUST**, a novel knowledge distillation-based **model-heterogeneous FGL** framework. Specifically, we propose Progressive Curriculum Node Scheduler to progressively introduce challenging nodes based on learning difficulty. In Adaptive Curriculum Distillation Modulator, we propose an adaptive temperature modulator that dynamically adjusts knowledge distillation temperature to accommodate varying client capabilities and graph complexity. Moreover, we leverage Wasserstein‑Driven Affinity Distillation to enable models to capture cross-class structural relationships through optimal transport. Extensive experiments on multiple graph benchmarks and model-heterogeneous settings show that **TRUST** outperforms existing methods, achieving an average 3.6\% $\uparrow$ performance gain, particularly under moderate heterogeneity conditions. The code is available for anonymous access at https://anonymous.4open.science/r/TRUST-NeurIPS2025.

*Quantification learning* is the task of predicting the label distribution of a set of instances. We study this problem in the context of graph-structured data, where the instances are vertices. Previously, this problem has only been addressed via node clustering methods. In this paper, we extend the popular *Adjusted Classify & Count* (ACC) method to graphs. We show that the prior probability shift assumption upon which ACC relies is often not applicable to graph quantification problems. To address this issue, we propose structural importance sampling (SIS), the first graph quantification method that is applicable under (structural) covariate shift. Additionally, we propose Neighborhood-aware ACC, which improves quantification in the presence of non-homophilic edges. We show the effectiveness of our techniques on multiple graph quantification tasks.

Machine unlearning techniques aim to mitigate unintended memorization in large language models (LLMs). However, existing approaches predominantly focus on the explicit removal of isolated facts, often overlooking latent inferential dependencies and the non-deterministic nature of knowledge within LLMs. Consequently, facts presumed forgotten may persist implicitly through correlated information. To address these challenges, we propose a knowledge unlearning evaluation framework that more accurately captures the implicit structure of real-world knowledge by representing relevant factual contexts as knowledge graphs with associated confidence scores. We further develop an inference-based evaluation protocol leveraging powerful LLMs as judges; these judges reason over the extracted knowledge subgraph to determine unlearning success. Our LLM judges utilize carefully designed prompts and are calibrated against human evaluations to ensure their trustworthiness and stability. Extensive experiments on our newly constructed benchmark demonstrate that our framework provides a more realistic and rigorous assessment of unlearning performance. Moreover, our findings reveal that current evaluation strategies tend to overestimate unlearning effectiveness.

The selection of hyperparameters, such as prompt templates in large language models (LLMs), must often strike a balance between reliability and cost. In many cases, structural relationships between the expected reliability levels of the hyperparameters can be inferred from prior information and held-out data -- e.g., longer prompt templates may be more detailed and thus more reliable. However, existing hyperparameter selection methods either do not provide formal reliability guarantees or are unable to incorporate structured knowledge in the hyperparameter space. This paper introduces reliability graph-based Pareto testing (RG-PT), a novel multi-objective hyperparameter selection framework that maintains formal reliability guarantees in terms of false discovery rate (FDR), while accounting for known relationships among hyperparameters via a directed acyclic graph. Edges in the graph reflect expected reliability and cost trade-offs among hyperparameters, which are inferred via the Bradley-Terry (BT) ranking model from prior information and held-out data. Experimental evaluations demonstrate that RG-PT significantly outperforms existing methods such as learn-then-test (LTT) and Pareto testing (PT) through a more efficient exploration of the hyperparameter space.

In recent times, the standard practice for developing MLLMs is to feed features from vision encoder(s) into the LLM and train with natural language supervision. This approach often causes models to lean towards language comprehension and undermine the rich visual perception signals present in the data, which are critical for tasks involving spatial reasoning in the domain of embodied AI and robotics. Is it possible to optimize both at the same time? In this work, we propose VisPer-LM, the first approach that infuses visual perception knowledge from expert vision encoders into the LLM's (of an MLLM) hidden representations. We start by investigating MLLMs trained solely with natural language supervision and identify a positive correlation between the quality of visual representations within these models and their downstream performance. Given this insight, we formulate the objective during the pretraining stage in MLLMs as a coupled optimization of predictive visual embedding and next (text) token prediction. Moreover, through extensive probing, we observe improved visual representation quality due to embedding optimization, underscoring the effectiveness of our probing setup. We demonstrate that our VisPer-LM outperforms the single and multi-encoder baselines, proving our approach's superiority over explicitly feeding the corresponding features to the LLM. In particular, VisPer-LM boosts performance by an average margin of up to 2.5% on various benchmarks, with a notable improvement of 8.7% on the Depth task in CV-Bench.

Graph incremental learning (GIL), which continuously updates graph models by sequential knowledge acquisition, has garnered significant interest recently. However, existing GIL approaches focus on task-incremental and class-incremental scenarios within a single domain. Graph domain-incremental learning (Domain-IL), aiming at updating models across multiple graph domains, has become critical with the development of graph foundation models (GFMs), but remains unexplored in the literature. In this paper, we propose **Graph** Domain-Incremental Learning via **K**nowledge Dis**e**ntangl**e**ment and **P**res**er**vation (**GraphKeeper**), to address catastrophic forgetting in Domain-IL scenario from the perspectives of embedding shifts and decision boundary deviations. Specifically, to prevent embedding shifts and confusion across incremental graph domains, we first propose the domain-specific parameter-efficient fine-tuning together with intra- and inter-domain disentanglement objectives. Consequently, to maintain a stable decision boundary, we introduce deviation-free knowledge preservation to continuously fit incremental domains. Additionally, for graphs with unobservable domains, we perform domain-aware distribution discrimination to obtain precise embeddings. Extensive experiments demonstrate the proposed GraphKeeper achieves state-of-the-art results with 6.5%\~16.6% improvement over the runner-up with negligible forgetting. Moreover, we show GraphKeeper can be seamlessly integrated with various representative GFMs, highlighting its broad applicative potential.

Graph condensation (GC) aims to distill the original graph into a small-scale graph, mitigating redundancy and accelerating GNN training. However, conventional GC approaches heavily rely on rigid GNNs and task-specific supervision. Such a dependency severely restricts their reusability and generalization across various tasks and architectures. In this work, we revisit the goal of ideal GC from the perspective of GNN optimization consistency, and then a generalized GC optimization objective is derived, by which those traditional GC methods can be viewed nicely as special cases of this optimization paradigm. Based on this, \textbf{Pre}-trained \textbf{G}raph \textbf{C}ondensation (\textbf{PreGC}) via optimal transport is proposed to transcend the limitations of task- and architecture-dependent GC methods. Specifically, a hybrid-interval graph diffusion augmentation is presented to suppress the weak generalization ability of the condensed graph on particular architectures by enhancing the uncertainty of node states. Meanwhile, the matching between optimal graph transport plan and representation transport plan is tactfully established to maintain semantic consistencies across source graph and condensed graph spaces, thereby freeing graph condensation from task dependencies. To further facilitate the adaptation of condensed graphs to various downstream tasks, a traceable semantic harmonizer from source nodes to condensed nodes is proposed to bridge semantic associations through the optimized representation transport plan in pre-training. Extensive experiments verify the superiority and versatility of PreGC, demonstrating its task-independent nature and seamless compatibility with arbitrary GNNs.

Temporal graph neural networks (TGNNs) have shown remarkable performance in temporal graph modeling. However, real-world temporal graphs often possess rich textual information, giving rise to temporal text-attributed graphs (TTAGs). Such combination of dynamic text semantics and evolving graph structures introduces heightened complexity. Existing TGNNs embed texts statically and rely heavily on encoding mechanisms that biasedly prioritize structural information, overlooking the temporal evolution of text semantics and the essential interplay between semantics and structures for synergistic reinforcement. To tackle these issues, we present $\textbf{CROSS}$, a flexible framework that seamlessly extends existing TGNNs for TTAG modeling. CROSS is designed by decomposing the TTAG modeling process into two phases: (i) temporal semantics extraction; and (ii) semantic-structural information unification. The key idea is to advance the large language models (LLMs) to $\textit{dynamically}$ extract the temporal semantics in text space and then generate $\textit{cohesive}$ representations unifying both semantics and structures. Specifically, we propose a Temporal Semantics Extractor in the CROSS framework, which empowers LLMs to offer the temporal semantic understanding of node's evolving contexts of textual neighborhoods, facilitating semantic dynamics. Subsequently, we introduce the Semantic-structural Co-encoder, which collaborates with the above Extractor for synthesizing illuminating representations by jointly considering both semantic and structural information while encouraging their mutual reinforcement. Extensive experiments show that CROSS achieves state-of-the-art results on four public datasets and one industrial dataset, with 24.7\% absolute MRR gain on average in temporal link prediction and 3.7\% AUC gain in node classification of industrial application.

Learning the causality between variables, known as DAG structure learning, is critical yet challenging due to issues such as insufficient data and noise. While prior knowledge can improve the learning process and refine the DAG structure, incorporating prior knowledge is not without pitfalls. In particular, we find that the gap between the imprecise prior knowledge and the exact weights modeled by existing methods may result in deviation in edge weights. Such deviation can subsequently cause significant inaccuracies when learning the DAG structure. This paper addresses this challenge by providing a theoretical analysis of the impact of deviation in edge weights during the optimization process of structure learning. We identify two special graph patterns that arise due to the deviation and show that their occurrence increases as the degree of deviation grows. Building on this analysis, we propose the Pattern-Guided Adaptive Prior (PGAP) framework. PGAP detects these patterns as structural signals during optimization and adaptively adjusts the structure learning process to counteract the identified weight deviation, thereby improving the integration of prior knowledge. Experiments verify the effectiveness and robustness of the proposed method.

This work presents a novel framework for few-shot 3D part segmentation. Recent advances have demonstrated the significant potential of 2D foundation models for low-shot 3D part segmentation. However, it is still an open problem that how to effectively aggregate 2D knowledge from foundation models to 3D. Existing methods either ignore geometric structures for 3D feature learning or neglects the high-quality grouping clues from SAM, leading to under-segmentation and inconsistent part labels. We devise a novel SAM segment graph-based propagation method, named SegGraph, to explicitly learn geometric features encoded within SAM's segmentation masks. Our method encodes geometric features by modeling mutual overlap and adjacency between segments while preserving intra-segment semantic consistency. We construct a segment graph, conceptually similar to an atlas, where nodes represent segments and edges capture their spatial relationships (overlap/adjacency). Each node adaptively modulates 2D foundation model features, which are then propagated via a graph neural network to learn global geometric structures. To enforce intra-segment semantic consistency, we map segment features to 3D points with a novel view-direction-weighted fusion attenuating contributions from low-quality segments. Extensive experiments on PartNet-E demonstrate that our method outperforms all competing baselines by at least 6.9% mIoU. Further analysis reveals that SegGraph achieves particularly strong performance on small components and part boundaries, demonstrating its superior geometric understanding.

Hybrid Optical Neural Networks (ONNs, typically consisting of an optical frontend and a digital backend) offer an energy-efficient alternative to fully digital deep networks for real-time, power-constrained systems. However, their adoption is limited by two main challenges: the accuracy gap compared to large-scale networks during training, and discrepancies between simulated and fabricated systems that further degrade accuracy. While previous work has proposed end-to-end optimizations for specific datasets (e.g., MNIST) and optical systems, these approaches typically lack generalization across tasks and hardware designs. To address these limitations, we propose a task-agnostic and hardware-agnostic pipeline that supports image classification and segmentation across diverse optical systems. To assist optical system design before training, we design the metasurface layout based on fabrication constraints. For training, we introduce Neural Tangent Knowledge Distillation (NTKD), which aligns optical models with electronic teacher networks, thereby narrowing the accuracy gap. After fabrication, NTKD also guides fine-tuning of the digital backend to compensate for implementation errors. Experiments on multiple datasets (e.g., MNIST, CIFAR, Carvana Masking) and hardware configurations show that our pipeline consistently improves ONN performance and enables practical deployment in both pre-fabrication simulations and physical implementations.

Large Language Models (LLMs) have shown the promising planning capabilities for robotic manipulation, which advances the development of embodied intelligence significantly. However, existing LLM-driven robotic manipulation approaches excel at simple pick-and-place tasks but are insufficient for complex manipulation tasks due to inaccurate procedural knowledge. Besides, for embodied intelligence, equipping a large scale LLM is energy-consuming and inefficient, which affects its real-world application. To address the above problems, we propose Hierarchical Procedural Knowledge Graphs (\textbf{HP-KG}) to enhance LLMs for complex robotic planning while significantly reducing the demand for LLM scale in robotic manipulation. Considering that the complex real-world tasks require multiple steps, and each step is composed of robotic-understandable atomic actions, we design a hierarchical knowledge graph structure to model the relationships between tasks, steps, and actions. This design bridges the gap between human instructions and robotic manipulation actions. To construct HP-KG, we develop an automatic knowledge graph construction framework powered by LLM-based multi-agents, which eliminates costly manual efforts while maintaining high-quality graph structures. The resulting HP-KG encompasses over 40k activity steps across more than 6k household tasks, spanning diverse everyday scenarios. Extensive experiments demonstrate that small scale LLMs (7B) enhanced by our HP-KG significantly improve the planning capabilities, which are stronger than 72B LLMs only. Encouragingly, our approach remains effective on the most powerful GPT-4o model.

Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies. KINDLE trains a teacher model that integrates prior knowledge with temporal gene expression dynamics and subsequently distills this encoded knowledge to a student model, enabling accurate GRN inference solely from expression data without access to any prior. KINDLE achieves state-of-the-art performance across four benchmark datasets. Notably, it successfully identifies key transcription factors governing mouse embryonic development and precisely characterizes their functional roles. In mouse hematopoietic stem cell data, KINDLE accurately predicts fate transition outcomes following knockout of two critical regulators (Gata1 and Spi1). These biological validations demonstrate our framework's dual capability in maintaining topological inference precision while preserving discovery potential for novel biological mechanisms.

Federated Learning (FL) has emerged as a privacy-preserving framework for training models on data generated at the edge. However, the heterogeneity of data silos (e.g., label skew and domain shift) often leads to inconsistent learning objectives and suboptimal model performance. Inspired by the data-driven approach, we propose Flick, a novel data generation framework for heterogeneous **F**ederated **L**earning w**i**th **C**ommonsense **K**nowledge from Large Language Models (LLMs). In Flick, the client performs the local data summary to capture client-specific knowledge in textual form. The central server then distills task-relevant, high-quality knowledge from the out-of-the-box LLM -- guided by cross-client-specific insights -- to generate informative text prompts. These prompts direct a generative model in producing synthetic data, enabling global model fine-tuning and local data compensation. This process gradually aligns the label and feature distributions across clients. Extensive results on three datasets demonstrate that Flick improves the global model accuracy by up to 11.43\%, and accelerates convergence by up to 12.9$\times$, validating its effectiveness in addressing data heterogeneity.

Clinical risk prediction plays a crucial role in early disease detection and personalized intervention. While recent models increasingly incorporate multimodal data, their development typically assumes access to large-scale, multimodal datasets and substantial computational resources. In practice, however, most clinical sites operate under resource constraints, with access limited to EHR data alone and insufficient capacity to train complicated models. This gap highlights the urgent need to democratize clinical risk prediction by enabling effective deployment in data- and resource-limited local clinical settings. In this work, we propose a cross-cohort cross-modal knowledge transfer framework that leverages the multimodal model trained on a nationwide cohort and adapts it to local cohorts with only EHR data. We focus on EHR and genetic data as representative multimodal inputs and address two key challenges. First, to mitigate the influence of noisy or less informative biological signals, we propose a novel mixture-of-aggregations design to enhance the modeling of informative and relevant genetic features. Second, to support rapid model adaptation in low-resource sites, we develop a lightweight graph-guided fine-tuning method that adapts pretrained phenotypical EHR representations to target cohorts using limited patient data. Extensive experiments on real-world clinical data validate the effectiveness of our proposed model.

Over time, a growing wave of large language models from various series has been introduced to the community. Researchers are striving to maximize the performance of language models with constrained parameter sizes. However, from a microscopic perspective, there has been limited research on how to better store knowledge in model parameters, particularly within MLPs, to enable more effective utilization of this knowledge by the model. In this work, we analyze twenty publicly available open-source large language models to investigate the relationship between their strong performance and the way knowledge is stored in their corresponding MLP parameters. Our findings reveal that as language models become more advanced and demonstrate stronger knowledge capabilities, their parameters exhibit increased specialization. Specifically, parameters in the MLPs tend to be more focused on encoding similar types of knowledge. We experimentally validate that this specialized distribution of knowledge contributes to improving the efficiency of knowledge utilization in these models. Furthermore, by conducting causal training experiments, we confirm that this specialized knowledge distribution plays a critical role in improving the model's efficiency in leveraging stored knowledge.

The goal of Root Cause Analysis (RCA) is to explain why an anomaly occurred by identifying where the fault originated. Several recent works model the anomalous event as resulting from a change in the causal mechanism at the root cause, i.e., as a soft intervention. RCA is then the task of identifying which causal mechanism changed. In real-world applications, one often has either few or only a single sample from the post-intervention distribution: a severe limitation for most methods, which assume one knows or can estimate the distribution. However, even those that do not are statistically ill-posed due to the need to probe regression models in regions of low probability density. In this paper, we propose simple, efficient methods to overcome both difficulties in the case where there is a single root cause and the causal graph is a polytree. When one knows the causal graph, we give guarantees for a traversal algorithm that requires only marginal anomaly scores and does not depend on specifying an arbitrary anomaly score cut-off. When one does not know the causal graph, we show that the heuristic of identifying root causes as the variables with the highest marginal anomaly scores is causally justified. To this end, we prove that anomalies with small scores are unlikely to cause those with larger scores in polytrees and give upper bounds for the likelihood of causal pathways with non-monotonic anomaly scores.

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>.