NeurIPS 2025 Papers

Local convergence has emerged as a fundamental tool for analyzing sparse random graph models. We introduce a new notion of local convergence, _color convergence_, based on the Weisfeiler–Leman algorithm. Color convergence fully characterizes the class of random graphs that are well-behaved in the limit for message-passing graph neural networks. Building on this, we propose the _Refined Configuration Model_ (RCM), a random graph model that generalizes the configuration model. The RCM is universal with respect to local convergence among locally tree-like random graph models, including Erdős–Rényi, stochastic block and configuration models. Finally, this framework enables a complete characterization of the random trees that arise as local limits of such graphs.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates PRotein-protein INteraction prediction from a Graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

Graphs in the real world are fragmented and dynamic, lacking collaboration akin to that observed in human societies. Existing paradigms present collaborative information collapse and forgetting, making collaborative relationships poorly autonomous and interactive information insufficient. Moreover, collaborative information is prone to loss when the graph grows. Effective collaboration in heterogeneous dynamic graph environments becomes challenging. Inspired by social learning, this paper presents a Graph Socialized Learning (GSL) paradigm. We provide insights into graph socialization in GSL and boost the performance of agents through effective collaboration. It is crucial to determine with whom, what, and when to share and accumulate information for effective GSL. Thus, we propose the ''Graphs Help Graphs'' (GHG) method to solve these issues. Specifically, it uses a graph-driven organizational structure to select interacting agents and manage interaction strength autonomously. We produce customized synthetic graphs as an interactive medium based on the demand of agents, then apply the synthetic graphs to build prototypes in the life cycle to help select optimal parameters. We demonstrate the effectiveness of GHG in heterogeneous dynamic graphs by an extensive empirical study. The code is available through https://github.com/Jillian555/GHG.

The VC-dimension is a well-studied and fundamental complexity measure of a set system (or hypergraph) that is central to many areas of machine learning. We establish several new results on the complexity of computing the VC-dimension. In particular, given a hypergraph $\mathcal{H}=(\mathcal{V},\mathcal{E})$, we prove that the naive $2^{\mathcal{O}(|\mathcal{V}|)}$-time algorithm is asymptotically tight under the Exponential Time Hypothesis (ETH). We then prove that the problem admits a $1$-additive fixed-parameter approximation algorithm when parameterized by the maximum degree of $\mathcal{H}$ and a fixed-parameter algorithm when parameterized by its dimension, and that these are essentially the only such exploitable structural parameters. Lastly, we consider a generalization of the problem, formulated using graphs, which captures the VC-dimension of both set systems and graphs. We design a $2^{\mathcal{O}(\texttt{tw}\cdot \log \texttt{tw})}\cdot |V|$-time algorithm for any graph $G=(V,E)$ of treewidth $\texttt{tw}$ (which, for a set system, applies to the treewidth of its incidence graph). This is in contrast with closely related problems that require a double-exponential dependency on the treewidth (assuming the ETH).

Maintaining comprehensive and up-to-date knowledge graphs (KGs) is critical for modern AI systems, but manual curation struggles to scale with the rapid growth of scientific literature. This paper presents KARMA, a novel framework employing multi-agent large language models (LLMs) to automate KG enrichment through structured analysis of unstructured text. Our approach employs nine collaborative agents, spanning entity discovery, relation extraction, schema alignment, and conflict resolution that iteratively parse documents, verify extracted knowledge, and integrate it into existing graph structures while adhering to domain-specific schema. Experiments on 1,200 PubMed articles from three different domains demonstrate the effectiveness of KARMA in knowledge graph enrichment, with the identification of up to 38,230 new entities while achieving 83.1\% LLM-verified correctness and reducing conflict edges by 18.6\% through multi-layer assessments.

Dynamic graph modeling aims to uncover evolutionary patterns in real-world systems, enabling accurate social recommendation and early detection of cancer cells. Inspired by the success of recent state space models in efficiently capturing long-term dependencies, we propose DyG-Mamba by translating dynamic graph modeling into a long-term sequence modeling problem. Specifically, inspired by Ebbinghaus' forgetting curve, we treat the irregular timespans between events as control signals, allowing DyG-Mamba to dynamically adjust the forgetting of historical information. This mechanism ensures effective usage of irregular timespans, thereby improving both model effectiveness and inductive capability. In addition, inspired by Ebbinghaus' review cycle, we redefine core parameters to ensure that DyG-Mamba selectively reviews historical information and filters out noisy inputs, further enhancing the model’s robustness. Through exhaustive experiments on 12 datasets covering dynamic link prediction and node classification tasks, we show that DyG-Mamba achieves state-of-the-art performance on most datasets, while demonstrating significantly improved computational and memory efficiency. Our code is available at https://github.com/Clearloveyuan/DyG-Mamba.

Deep neural networks (DNNs) have been shown to memorize their training data, but similar analyses for graph neural networks (GNNs) remain under-explored. We introduce NCMemo (Node Classification Memorization), the first framework to quantify label memorization in semi-supervised node classification. We establish an inverse relationship between memorization and graph homophily, i.e the tendency of connected nodes to share labels or features. Lower homophily significantly increases memorization, indicating that GNNs rely on label memorization when learning less homophilic graphs. We then analyze GNN training dynamics and find that increased memorization in low-homophily graphs is tightly coupled to GNNs' implicit bias toward using graph structure. When structure is less informative, models instead memorize node labels to minimize training loss. Finally, we show that nodes with higher label inconsistency in their feature-space neighborhood are more prone to memorization. Based on these insights, we investigate graph rewiring as a mitigation strategy. Our results show that rewiring reduces memorization without harming model performance, while also lowering the privacy risk for previously memorized data points. Thus, our work advances understanding of GNN learning and supports more privacy-preserving GNN deployment.

Transformers have achieved remarkable success across natural language processing (NLP) and computer vision (CV). However, deep transformer models often suffer from an over-smoothing issue, in which token representations converge to similar values as they pass through successive transformer blocks. In this paper, we establish an equivalence between the hidden-state dynamics induced by stacked attention layers and graph neural diffusion on a complete graph. From this perspective, over-smoothing can be interpreted as a consequence of the dissipative nature of the underlying diffusion dynamics. Motivated by this physical interpretation, we propose Wavy Transformer, which consists of a novel attention layer based on second-order wavy dynamics. We also introduce a feed-forward network and a normalization layer designed to preserve the physical state-velocity relationship under the chain rule, thereby extending the transformer architecture. We further validate our proposed techniques on various transformer models for NLP and CV tasks. The results consistently demonstrate that Wavy Transformer improves performance with minimal additional parameters and no extra hyperparameter tuning.

Evaluating the open-form textual responses generated by Large Language Models (LLMs) typically requires measuring the semantic similarity of the response to a (human generated) reference. However, there is evidence that current semantic similarity methods may capture syntactic or lexical forms over semantic content. While benchmarks exist for semantic equivalence, they often suffer from high generation costs due to reliance on subjective human judgment, limited availability for domain-specific applications, and unclear definitions of equivalence. This paper introduces a novel method for generating benchmarks to evaluate semantic similarity methods for LLM outputs, specifically addressing these limitations. Our approach leverages knowledge graphs (KGs) to generate pairs of natural-language statements that are semantically similar or dissimilar, with dissimilar pairs categorized into one of four sub-types. We generate benchmark datasets in four different domains (general knowledge, biomedicine, finance, biology), and conduct a comparative study of semantic similarity methods including traditional natural language processing scores and LLM-as-a-judge predictions. We observe that the sub-type of semantic variation, as well as the domain of the benchmark impact the performance of semantic similarity methods, with no method being consistently superior. Our results present important implications for the use of LLM-as-a-judge in detecting the semantic content of text. Code is available at \url{https://github.com/QiyaoWei/semantic-kg} and the dataset is available at \url{https://huggingface.co/datasets/QiyaoWei/Semantic-KG}.

Large Language Models (LLMs) are expected to possess comprehensive medical knowledge to support real-world clinical applications. While domain-specific fine-tuning effectively injects medical knowledge into LLMs, it often causes catastrophic forgetting of previously acquired knowledge and instruction-following capabilities. In this paper, we investigate this issue and reveal a pattern of proximity-dependent forgetting: knowledge that is semantically or topically close to the injected content is more likely to be forgotten, while unrelated knowledge shows minimal degradation. Moreover, we observe that existing mitigation techniques fail to address this type of forgetting effectively. Motivated by this observation and inspired by human learning mechanisms, we proposeInternAL (\Internal Knowledge Augmentation Learning), a novel approach that leverages LLMs' own internal knowledge to mitigate forgetting. InternAL first probes internal knowledge closely related to the injection by prompting the model with questions derived from the injected knowledge. This knowledge is then used to augment the original injection dataset, guiding the model to retain related prior knowledge during training. Experimental results on multiple LLMs (LLaMA, Qwen) demonstrate that InternAL significantly mitigates proximity-related forgetting while maintaining strong knowledge injection performance. Our findings provide new insights into the nature of catastrophic forgetting in medical knowledge injection and highlight a promising direction for robust domain adaptation in LLMs. Code and datasets are available at https://github.com/THUMLP/InternAL.

Dynamic graph learning is crucial for accurately modeling complex systems by integrating topological structure and temporal information within graphs. While memory-based methods are commonly used and excel at capturing short-range temporal correlations, they struggle with modeling long-range dependencies, harmonizing long-range and short-range correlations, and integrating structural information effectively. To address these challenges, we present SALoM: Structure Aware Temporal Graph Networks with Long-Short Memory Updater. SALoM features a memory module that addresses gradient vanishing and information forgetting, enabling the capture of long-term dependencies across various time scales. Additionally, SALoM utilizes a long-short memory updater (LSMU) to dynamically balance long-range and short-range temporal correlations, preventing over-generalization. By integrating co-occurrence encoding and LSMU through information bottleneck-based fusion, SALoM effectively captures both the structural and temporal information within graphs. Experimental results across various graph datasets demonstrate SALoM's superior performance, achieving state-of-the-art results in dynamic graph link prediction. Our code is openly accessible at https://github.com/wave5418/SALoM.

Knowledge distillation (KD) is a core component in the training and deployment of modern generative models, particularly large language models (LLMs). While its empirical benefits are well documented---enabling smaller student models to emulate the performance of much larger teachers---the underlying mechanisms by which KD improves generative quality remain poorly understood. In this work, we present a minimal working explanation of KD in generative modeling. Using a controlled simulation with mixtures of Gaussians, we demonstrate that distillation induces a trade-off between precision and recall in the student model. As the teacher distribution becomes more selective, the student concentrates more probability mass on high-likelihood regions at the expense of coverage---a behavior modulated by a single entropy-controlling parameter. We then validate this effect in a large-scale language modeling setup using the SmolLM2 family of models. Empirical results reveal the same precision–recall dynamics observed in simulation, where precision corresponds to sample quality and recall to distributional coverage. This precision-recall trade-off in LLMs is found to be especially beneficial in scenarios where sample quality is more important than diversity, such as instruction tuning or downstream generation. Our analysis provides a simple and general explanation for the effectiveness of KD in generative modeling.

Open-vocabulary scene graph generation (OVSGG) extends traditional SGG by recognizing novel objects and relationships beyond predefined categories, leveraging the knowledge from pre-trained large-scale models. Existing OVSGG methods always adopt a two-stage pipeline: 1) Infusing knowledge into large-scale models via pre-training on large datasets; 2) Transferring knowledge from pre-trained models with fully annotated scene graphs during supervised fine-tuning. However, due to a lack of explicit interaction modeling, these methods struggle to distinguish between interacting and non-interacting instances of the same object category. This limitation induces critical issues in both stages of OVSGG: it generates noisy pseudo-supervision from mismatched objects during knowledge infusion, and causes ambiguous query matching during knowledge transfer. To this end, in this paper, we propose an interACtion-Centric end-to-end OVSGG framework (ACC) in an interaction-driven paradigm to minimize these mismatches. For interaction-centric knowledge infusion, ACC employs a bidirectional interaction prompt for robust pseudo-supervision generation to enhance the model's interaction knowledge. For interaction-centric knowledge transfer, ACC first adopts interaction-guided query selection that prioritizes pairing interacting objects to reduce interference from non-interacting ones. Then, it integrates interaction-consistent knowledge distillation to bolster robustness by pushing relational foreground away from the background while retaining general knowledge. Extensive experimental results on three benchmarks show that ACC achieves state-of-the-art performance, demonstrating the potential of interaction-centric paradigms for real-world applications.

Graph Neural Networks learn on graph-structured data by iteratively aggregating local neighborhood information. While this local message passing paradigm imparts a powerful inductive bias and exploits graph sparsity, it also yields three key challenges: (i) oversquashing of long-range information, (ii) oversmoothing of node representations, and (iii) limited expressive power. In this work we inject randomized global embeddings of node features, which we term Sketched Random Features, into standard GNNs, enabling them to efficiently capture long-range dependencies. The embeddings are unique, distance-sensitive, and topology-agnostic---properties which we analytically and empirically show alleviate the aforementioned limitations when injected into GNNs. Experimental results on real-world graph learning tasks confirm that this strategy consistently improves performance over baseline GNNs, offering both a standalone solution and a complementary enhancement to existing techniques such as graph positional encodings.

We propose SCONE (**S**calable, **C**ontextualized, **O**ffloaded, **N**-gram **E**mbedding), a new method for extending input embedding layers to enhance language model performance. To avoid increased decoding costs, SCONE retains the original vocabulary while introducing embeddings for a set of frequent $n$-grams. These embeddings provide contextualized representation for each input token and are learned with a separate model during training. After training, embeddings are precomputed and stored in off-accelerator memory; during inference, querying them has minimal impact on latency due to the low complexity of embedding lookups. SCONE enables two new scaling strategies: increasing the number of $n$-gram embeddings and scaling the model used to learn them, both while maintaining fixed accelerator usage during inference (in terms of FLOPS and memory). We show that scaling both aspects enables a model with 1B accelerator-resident parameters to outperform a 1.9B-parameter baseline across diverse corpora, while using only about half the FLOPS and accelerator memory during inference.

A full understanding of the behavior of a large language model (LLM) requires our grasp of its input token space. If this space differs from our assumptions, our comprehension of and conclusions about the LLM will likely be flawed. We elucidate the structure of the token embeddings both empirically and theoretically. We present a novel statistical test assuming that the neighborhood around each token has a relatively flat and smooth structure as the null hypothesis. Failing to reject the null is uninformative, but rejecting it at a specific token $\psi$ implies an irregularity in the token subspace in a $\psi$-neighborhood, $B(\psi)$. The structure assumed in the null is a generalization of a manifold with boundary called a \emph{smooth fiber bundle} (which can be split into two spatial regimes -- small and large radius), so we denote our new hypothesis test as the ``fiber bundle hypothesis.'' By running our test over several open-source LLMs, each with unique token embeddings, we find that the null is frequently rejected, and so the evidence suggests that the token subspace is not a fiber bundle and hence also not a manifold. As a consequence of our findings, when an LLM is presented with two semantically equivalent prompts, if one prompt contains a token implicated by our test, the response to that prompt will likely exhibit less stability than the other.

Lifelong knowledge editing enables continuous, precise updates to outdated knowledge in large language models (LLMs) without computationally expensive full retraining. However, existing methods often accumulate errors throughout the editing process, causing a gradual decline in both editing accuracy and generalization. To tackle this problem, we propose Neuron-Specific Masked Knowledge Editing (NMKE), a novel fine-grained editing framework that combines neuron-level attribution with dynamic sparse masking. Leveraging neuron functional attribution, we identify two key types of knowledge neurons, with knowledge-general neurons activating consistently across prompts and knowledge-specific neurons activating to specific prompts. NMKE further introduces an entropy-guided dynamic sparse mask, locating relevant neurons to the target knowledge. This strategy enables precise neuron-level knowledge editing with fewer parameter modifications. Experimental results from thousands of sequential edits demonstrate that NMKE outperforms existing methods in maintaining high editing success rates and preserving model general capabilities in lifelong editing.

We investigate implications of the (extended) low-degree conjecture (recently formalized in [moitra et al2023]) in the context of the symmetric stochastic block model. Assuming the conjecture holds, we establish that no polynomial-time algorithm can weakly recover community labels below the Kesten-Stigum (KS) threshold. In particular, we rule out polynomial-time estimators that, with constant probability, achieve $n^{-0.49}$ correlation with the true communities. Whereas, above the KS threshold, polynomial-time algorithms are known to achieve constant correlation with the true communities with high probability [massoulie et al 2014,abbe et al 2015]. To our knowledge, we provide the first rigorous evidence for such sharp transition in recovery rate for polynomial-time algorithms at the KS threshold. Notably, under a stronger version of the low-degree conjecture, our lower bound remains valid even when the number of blocks diverges. Furthermore, our results provide evidence of a computational-to-statistical gap in learning the parameters of stochastic block models. In contrast, prior work either (i) rules out polynomial-time algorithms with $1 - o(1)$ success probability [Hopkins 18, bandeira et al 2021] under the low-degree conjecture, or (ii) degree-$\text{poly}(k)$ polynomials for learning the stochastic block model [Luo et al 2023]. For this, we design a hypothesis test which succeeeds with constant probability under symmetric stochastic block model, and $1-o(1)$ probability under the distribution of \Erdos \Renyi random graphs. Our proof combines low-degree lower bounds from [Hopkins 18, bandeira et al 2021] with graph splitting and cross-validation techniques. In order to rule out general recovery algorithms, we employ the correlation preserving projection method developed in [Hopkins et al 17].

We introduce AutoGraph, a scalable autoregressive model for attributed graph generation using decoder-only transformers. By flattening graphs into random sequences of tokens through a reversible process, AutoGraph enables modeling graphs as sequences without relying on additional node features that are expensive to compute, in contrast to diffusion-based approaches. This results in sampling complexity and sequence lengths that scale optimally linearly with the number of edges, making it scalable and efficient for large, sparse graphs. A key success factor of AutoGraph is that its sequence prefixes represent induced subgraphs, creating a direct link to sub-sentences in language modeling. Empirically, AutoGraph achieves state-of-the-art performance on synthetic and molecular benchmarks, with up to 100x faster generation and 3x faster training than leading diffusion models. It also supports substructure-conditioned generation without fine-tuning and shows promising transferability, bridging language modeling and graph generation to lay the groundwork for graph foundation models. Our code is available at https://github.com/BorgwardtLab/AutoGraph.