Chuan Shi

Shaohua Fan, Xiao Wang, Yanhu Mo et al.

Most Graph Neural Networks (GNNs) predict the labels of unseen graphs by learning the correlation between the input graphs and labels. However, by presenting a graph classification investigation on the training graphs with severe bias, surprisingly, we discover that GNNs always tend to explore the spurious correlations to make decision, even if the causal correlation always exists. This implies that existing GNNs trained on such biased datasets will suffer from poor generalization capability. By analyzing this problem in a causal view, we find that disentangling and decorrelating the causal and bias latent variables from the biased graphs are both crucial for debiasing. Inspiring by this, we propose a general disentangled GNN framework to learn the causal substructure and bias substructure, respectively. Particularly, we design a parameterized edge mask generator to explicitly split the input graph into causal and bias subgraphs. Then two GNN modules supervised by causal/bias-aware loss functions respectively are trained to encode causal and bias subgraphs into their corresponding representations. With the disentangled representations, we synthesize the counterfactual unbiased training samples to further decorrelate causal and bias variables. Moreover, to better benchmark the severe bias problem, we construct three new graph datasets, which have controllable bias degrees and are easier to visualize and explain. Experimental results well demonstrate that our approach achieves superior generalization performance over existing baselines. Furthermore, owing to the learned edge mask, the proposed model has appealing interpretability and transferability. Code and data are available at: https://github.com/googlebaba/DisC.

Deyu Bo, Chuan Shi, Lele Wang et al.

Spectral graph neural networks (GNNs) learn graph representations via spectral-domain graph convolutions. However, most existing spectral graph filters are scalar-to-scalar functions, i.e., mapping a single eigenvalue to a single filtered value, thus ignoring the global pattern of the spectrum. Furthermore, these filters are often constructed based on some fixed-order polynomials, which have limited expressiveness and flexibility. To tackle these issues, we introduce Specformer, which effectively encodes the set of all eigenvalues and performs self-attention in the spectral domain, leading to a learnable set-to-set spectral filter. We also design a decoder with learnable bases to enable non-local graph convolution. Importantly, Specformer is equivariant to permutation. By stacking multiple Specformer layers, one can build a powerful spectral GNN. On synthetic datasets, we show that our Specformer can better recover ground-truth spectral filters than other spectral GNNs. Extensive experiments of both node-level and graph-level tasks on real-world graph datasets show that our Specformer outperforms state-of-the-art GNNs and learns meaningful spectrum patterns. Code and data are available at https://github.com/bdy9527/Specformer.

Zhongjian Zhang, Xiao Wang, Huichi Zhou et al.

Graph neural networks (GNNs) are vulnerable to adversarial attacks, especially for topology perturbations, and many methods that improve the robustness of GNNs have received considerable attention. Recently, we have witnessed the significant success of large language models (LLMs), leading many to explore the great potential of LLMs on GNNs. However, they mainly focus on improving the performance of GNNs by utilizing LLMs to enhance the node features. Therefore, we ask: Will the robustness of GNNs also be enhanced with the powerful understanding and inference capabilities of LLMs? By presenting the empirical results, we find that despite that LLMs can improve the robustness of GNNs, there is still an average decrease of 23.1% in accuracy, implying that the GNNs remain extremely vulnerable against topology attacks. Therefore, another question is how to extend the capabilities of LLMs on graph adversarial robustness. In this paper, we propose an LLM-based robust graph structure inference framework, LLM4RGNN, which distills the inference capabilities of GPT-4 into a local LLM for identifying malicious edges and an LM-based edge predictor for finding missing important edges, so as to recover a robust graph structure. Extensive experiments demonstrate that LLM4RGNN consistently improves the robustness across various GNNs. Even in some cases where the perturbation ratio increases to 40%, the accuracy of GNNs is still better than that on the clean graph. The source code can be found in https://github.com/zhongjian-zhang/LLM4RGNN.

Xin Li, Weize Chen, Qizhi Chu et al.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Xumeng Gong, Cheng Yang, Chuan Shi

Contrastive learning (CL), which can extract the information shared between different contrastive views, has become a popular paradigm for vision representation learning. Inspired by the success in computer vision, recent work introduces CL into graph modeling, dubbed as graph contrastive learning (GCL). However, generating contrastive views in graphs is more challenging than that in images, since we have little prior knowledge on how to significantly augment a graph without changing its labels. We argue that typical data augmentation techniques (e.g., edge dropping) in GCL cannot generate diverse enough contrastive views to filter out noises. Moreover, previous GCL methods employ two view encoders with exactly the same neural architecture and tied parameters, which further harms the diversity of augmented views. To address this limitation, we propose a novel paradigm named model augmented GCL (MA-GCL), which will focus on manipulating the architectures of view encoders instead of perturbing graph inputs. Specifically, we present three easy-to-implement model augmentation tricks for GCL, namely asymmetric, random and shuffling, which can respectively help alleviate high- frequency noises, enrich training instances and bring safer augmentations. All three tricks are compatible with typical data augmentations. Experimental results show that MA-GCL can achieve state-of-the-art performance on node classification benchmarks by applying the three tricks on a simple base model. Extensive studies also validate our motivation and the effectiveness of each trick. (Code, data and appendix are available at https://github.com/GXM1141/MA-GCL. )

Zekai Yu, Qi Meng, Qizhi Chu et al.

Tool calling extends large language models (LLMs) by enabling grounded interaction with external executable interfaces, thereby supporting environment-coupled problem solving. However, mainstream in-context learning (ICL) approaches typically incorporate detailed tool documentation and usage examples directly into the context. This results in substantial inference overhead and heightened risks of hallucination as the context length grows. Conversely, while tuning-based methods improve general tool-calling capabilities, they often fail to effectively internalize the specific details of previously seen tools, thereby retaining a dependency on in-context documentation. To address these limitations, we propose ParaTool, a framework that projects each tool into a dedicated, loadable set of parameters. By equipping a dynamic integration of these parameterized tools, the LLM can perform tool calling without relying on in-context documents or examples. Specifically, our approach consists of three stages: (1) parametric tool pre-training encapsulates the knowledge of different tools into independent parameter modules; (2) soft tool selection employs a gating network to dynamically weigh and aggregate relevant tool parameters; and (3) parametric tool fine-tuning jointly updates tool parameters to align the training and inference processes. Experiments on Stable ToolBench and BFCL demonstrate that ParaTool significantly outperforms strong ICL-based baselines, achieving superior performance while reducing computational complexity.

Yang Liu, Deyu Bo, Chuan Shi

The increasing amount of graph data places requirements on the efficient training of graph neural networks (GNNs). The emerging graph distillation (GD) tackles this challenge by distilling a small synthetic graph to replace the real large graph, ensuring GNNs trained on real and synthetic graphs exhibit comparable performance. However, existing methods rely on GNN-related information as supervision, including gradients, representations, and trajectories, which have two limitations. First, GNNs can affect the spectrum (i.e., eigenvalues) of the real graph, causing spectrum bias in the synthetic graph. Second, the variety of GNN architectures leads to the creation of different synthetic graphs, requiring traversal to obtain optimal performance. To tackle these issues, we propose Graph Distillation with Eigenbasis Matching (GDEM), which aligns the eigenbasis and node features of real and synthetic graphs. Meanwhile, it directly replicates the spectrum of the real graph and thus prevents the influence of GNNs. Moreover, we design a discrimination constraint to balance the effectiveness and generalization of GDEM. Theoretically, the synthetic graphs distilled by GDEM are restricted spectral approximations of the real graphs. Extensive experiments demonstrate that GDEM outperforms state-of-the-art GD methods with powerful cross-architecture generalization ability and significant distillation efficiency. Our code is available at https://github.com/liuyang-tian/GDEM.

Nian Liu, Xiao Wang, Hui Han et al.

Heterogeneous graph neural networks (HGNNs) as an emerging technique have shown superior capacity of dealing with heterogeneous information network (HIN). However, most HGNNs follow a semi-supervised learning manner, which notably limits their wide use in reality since labels are usually scarce in real applications. Recently, contrastive learning, a self-supervised method, becomes one of the most exciting learning paradigms and shows great potential when there are no labels. In this paper, we study the problem of self-supervised HGNNs and propose a novel co-contrastive learning mechanism for HGNNs, named HeCo. Different from traditional contrastive learning which only focuses on contrasting positive and negative samples, HeCo employs cross-view contrastive mechanism. Specifically, two views of a HIN (network schema and meta-path views) are proposed to learn node embeddings, so as to capture both of local and high-order structures simultaneously. Then the cross-view contrastive learning, as well as a view mask mechanism, is proposed, which is able to extract the positive and negative embeddings from two views. This enables the two views to collaboratively supervise each other and finally learn high-level node embeddings. Moreover, to further boost the performance of HeCo, two additional methods are designed to generate harder negative samples with high quality. Besides the invariant factors, view-specific factors complementally provide the diverse structure information between different nodes, which also should be contained into the final embeddings. Therefore, we need to further explore each view independently and propose a modified model, called HeCo++. Specifically, HeCo++ conducts hierarchical contrastive learning, including cross-view and intra-view contrasts, which aims to enhance the mining of respective structures.

Nian Liu, Xiao Wang, Deyu Bo et al.

Graph Contrastive Learning (GCL), learning the node representations by augmenting graphs, has attracted considerable attentions. Despite the proliferation of various graph augmentation strategies, some fundamental questions still remain unclear: what information is essentially encoded into the learned representations by GCL? Are there some general graph augmentation rules behind different augmentations? If so, what are they and what insights can they bring? In this paper, we answer these questions by establishing the connection between GCL and graph spectrum. By an experimental investigation in spectral domain, we firstly find the General grAph augMEntation (GAME) rule for GCL, i.e., the difference of the high-frequency parts between two augmented graphs should be larger than that of low-frequency parts. This rule reveals the fundamental principle to revisit the current graph augmentations and design new effective graph augmentations. Then we theoretically prove that GCL is able to learn the invariance information by contrastive invariance theorem, together with our GAME rule, for the first time, we uncover that the learned representations by GCL essentially encode the low-frequency information, which explains why GCL works. Guided by this rule, we propose a spectral graph contrastive learning module (SpCo), which is a general and GCL-friendly plug-in. We combine it with different existing GCL models, and extensive experiments well demonstrate that it can further improve the performances of a wide variety of different GCL methods.

Jinyu Yang, Cheng Yang, Junze Chen et al.

Relational databases (RDBs) remain the cornerstone of modern data systems and support diverse predictive tasks. Recent relational deep learning (RDL) methods enable end-to-end prediction by converting RDBs into graphs, where rows are represented as nodes and inter-table interactions are represented as edges, and then applying graph-based models for representation learning. Despite the strong capability of RDL, effective self-supervised pre-training for RDBs remains non-trivial. RDB tasks often require multi-faceted information across different perspectives and granularities. For example, user churn classification may rely more on interaction patterns, whereas consumption value prediction requires both user-item behaviors and intrinsic user attributes for fine-grained regression. Such heterogeneous needs challenge RDB representation learning, as pre-training objectives should cover comprehensive information for downstream adaptation. However, existing SSL methods typically derive supervision from a single facet, such as node-level intrinsic attributes or subgraph-level relational structures, providing limited adaptability. To this end, we propose RelPrism, a multi-faceted self-supervised learning framework for RDBs. RelPrism constructs intrinsic, relational, and hybrid attributes from distinct perspectives, and applies multi-granularity clustering to each perspective to form corresponding pseudo-task pools. Pre-training over these pools exposes representations to broader perspectives and granularity levels, yielding a stronger basis for downstream adaptation. Experiments on 14 tasks across 5 real-world datasets show that RelPrism improves ROC-AUC by 4.15% for classification and reduces MAE by 10.75% for regression over state-of-the-art baselines. Our code is available at https://anonymous.4open.science/r/RelPrism.

Yue Yu, Xiao Wang, Mengmei Zhang et al.

Graph Contrastive Learning (GCL) has emerged as a popular training approach for learning node embeddings from augmented graphs without labels. Despite the key principle that maximizing the similarity between positive node pairs while minimizing it between negative node pairs is well established, some fundamental problems are still unclear. Considering the complex graph structure, are some nodes consistently well-trained and following this principle even with different graph augmentations? Or are there some nodes more likely to be untrained across graph augmentations and violate the principle? How to distinguish these nodes and further guide the training of GCL? To answer these questions, we first present experimental evidence showing that the training of GCL is indeed imbalanced across all nodes. To address this problem, we propose the metric "node compactness", which is the lower bound of how a node follows the GCL principle related to the range of augmentations. We further derive the form of node compactness theoretically through bound propagation, which can be integrated into binary cross-entropy as a regularization. To this end, we propose the PrOvable Training (POT) for GCL, which regularizes the training of GCL to encode node embeddings that follows the GCL principle better. Through extensive experiments on various benchmarks, POT consistently improves the existing GCL approaches, serving as a friendly plugin.

Bo Yan, Cheng Yang, Chuan Shi et al.

The explosive growth of cyber attacks nowadays, such as malware, spam, and intrusions, caused severe consequences on society. Securing cyberspace has become an utmost concern for organizations and governments. Traditional Machine Learning (ML) based methods are extensively used in detecting cyber threats, but they hardly model the correlations between real-world cyber entities. In recent years, with the proliferation of graph mining techniques, many researchers investigated these techniques for capturing correlations between cyber entities and achieving high performance. It is imperative to summarize existing graph-based cybersecurity solutions to provide a guide for future studies. Therefore, as a key contribution of this paper, we provide a comprehensive review of graph mining for cybersecurity, including an overview of cybersecurity tasks, the typical graph mining techniques, and the general process of applying them to cybersecurity, as well as various solutions for different cybersecurity tasks. For each task, we probe into relevant methods and highlight the graph types, graph approaches, and task levels in their modeling. Furthermore, we collect open datasets and toolkits for graph-based cybersecurity. Finally, we outlook the potential directions of this field for future research.

Qian Zhao, Shuo Yang, Binbin Hu et al.

Temporal link prediction, as one of the most crucial work in temporal graphs, has attracted lots of attention from the research area. The WSDM Cup 2022 seeks for solutions that predict the existence probabilities of edges within time spans over temporal graph. This paper introduces the solution of AntGraph, which wins the 1st place in the competition. We first analysis the theoretical upper-bound of the performance by removing temporal information, which implies that only structure and attribute information on the graph could achieve great performance. Based on this hypothesis, then we introduce several well-designed features. Finally, experiments conducted on the competition datasets show the superiority of our proposal, which achieved AUC score of 0.666 on dataset A and 0.902 on dataset B, the ablation studies also prove the efficiency of each feature. Code is publicly available at https://github.com/im0qianqian/WSDM2022TGP-AntGraph.

Ruijia Wang, Xiao Wang, Chuan Shi et al.

Recent studies show that graph convolutional network (GCN) often performs worse for low-degree nodes, exhibiting the so-called structural unfairness for graphs with long-tailed degree distributions prevalent in the real world. Graph contrastive learning (GCL), which marries the power of GCN and contrastive learning, has emerged as a promising self-supervised approach for learning node representations. How does GCL behave in terms of structural fairness? Surprisingly, we find that representations obtained by GCL methods are already fairer to degree bias than those learned by GCN. We theoretically show that this fairness stems from intra-community concentration and inter-community scatter properties of GCL, resulting in a much clear community structure to drive low-degree nodes away from the community boundary. Based on our theoretical analysis, we further devise a novel graph augmentation method, called GRAph contrastive learning for DEgree bias (GRADE), which applies different strategies to low- and high-degree nodes. Extensive experiments on various benchmarks and evaluation protocols validate the effectiveness of the proposed method.

Deyu Bo, Xiao Wang, Yang Liu et al.

Graph neural networks (GNNs) have attracted considerable attention from the research community. It is well established that GNNs are usually roughly divided into spatial and spectral methods. Despite that spectral GNNs play an important role in both graph signal processing and graph representation learning, existing studies are biased toward spatial approaches, and there is no comprehensive review on spectral GNNs so far. In this paper, we summarize the recent development of spectral GNNs, including model, theory, and application. Specifically, we first discuss the connection between spatial GNNs and spectral GNNs, which shows that spectral GNNs can capture global information and have better expressiveness and interpretability. Next, we categorize existing spectral GNNs according to the spectrum information they use, \ie, eigenvalues or eigenvectors. In addition, we review major theoretical results and applications of spectral GNNs, followed by a quantitative experiment to benchmark some popular spectral GNNs. Finally, we conclude the paper with some future directions.

Yuanxin Zhuang, Lingjuan Lyu, Chuan Shi et al.

Graph neural networks (GNNs) have been widely used in modeling graph structured data, owing to its impressive performance in a wide range of practical applications. Recently, knowledge distillation (KD) for GNNs has enabled remarkable progress in graph model compression and knowledge transfer. However, most of the existing KD methods require a large volume of real data, which are not readily available in practice, and may preclude their applicability in scenarios where the teacher model is trained on rare or hard to acquire datasets. To address this problem, we propose the first end-to-end framework for data-free adversarial knowledge distillation on graph structured data (DFAD-GNN). To be specific, our DFAD-GNN employs a generative adversarial network, which mainly consists of three components: a pre-trained teacher model and a student model are regarded as two discriminators, and a generator is utilized for deriving training graphs to distill knowledge from the teacher model into the student model. Extensive experiments on various benchmark models and six representative datasets demonstrate that our DFAD-GNN significantly surpasses state-of-the-art data-free baselines in the graph classification task.

Yue Yu, Ting Bai, HengZhi Lan et al.

The attribution technique enhances the credibility of LLMs by adding citations to the generated sentences, enabling users to trace back to the original sources and verify the reliability of the output. However, existing instruction-tuned attributed LLMs often fail to properly interpret the contextual semantics of citation symbols (e.g., [i]) during text generation. This shortcoming arises from their insufficient awareness of the context information surrounding citation markers, which in turn leads to disjointed references and poor integration of retrieved knowledge into the generated content. To address this issue, we propose a novel \textbf{C}ontextual-aware \textbf{C}itation generation framework (\textbf{C$^2$}-\textbf{Cite}) that explicitly integrates the semantic relationships between citation markers and their referenced content. Specifically, a contextual citation alignment mechanism is adopted: it first encodes the retrieved document contexts into the symbol representation of citations, then aligns the marker numbers by decoding information from a citation router function. This mechanism enables the transformation of citation markers from generic placeholders into active knowledge pointers that link to the referenced source information. Experimental results on the ALCE benchmark across three datasets validate our framework C$^2$-Cite++: it outperforms the SOTA baseline by an average of 5.8\% in citation quality and 17.4\% in response correctness. The implementation is publicly available at https://github.com/BAI-LAB/c2cite

Shaohua Fan, Shuyang Zhang, Xiao Wang et al.

Estimating the structure of directed acyclic graphs (DAGs) of features (variables) plays a vital role in revealing the latent data generation process and providing causal insights in various applications. Although there have been many studies on structure learning with various types of data, the structure learning on the dynamic graph has not been explored yet, and thus we study the learning problem of node feature generation mechanism on such ubiquitous dynamic graph data. In a dynamic graph, we propose to simultaneously estimate contemporaneous relationships and time-lagged interaction relationships between the node features. These two kinds of relationships form a DAG, which could effectively characterize the feature generation process in a concise way. To learn such a DAG, we cast the learning problem as a continuous score-based optimization problem, which consists of a differentiable score function to measure the validity of the learned DAGs and a smooth acyclicity constraint to ensure the acyclicity of the learned DAGs. These two components are translated into an unconstraint augmented Lagrangian objective which could be minimized by mature continuous optimization techniques. The resulting algorithm, named GraphNOTEARS, outperforms baselines on simulated data across a wide range of settings that may encounter in real-world applications. We also apply the proposed approach on two dynamic graphs constructed from the real-world Yelp dataset, demonstrating our method could learn the connections between node features, which conforms with the domain knowledge.

Bin Wu, Guanyun Zou, Bingbing Wang et al.

A long-lived LLM agent, such as OpenClaw, earns its value by acting on a user's preferences and constraints across sessions, not just the current request. Yet today's agents keep what a user volunteers but rarely ask for what stays unspoken, leaving a proactivity gap in long-lived LLM agents: an agent cannot act on a preference it never obtained. As users delegate more of their affairs to agents, the impact of this gap grows. We isolate one concrete, controllable slice of this gap as Ask-to-Remember (ATR): the agent decides whether to ask now for a reusable user preference that the current task does not need but a later session with the same user will. ATR is hard even to evaluate: the right question is underdetermined and its payoff deferred to tasks that may never arise. ATRBench, to the best of our knowledge the first ATR benchmark, makes it measurable by fixing each user's preferences as hidden ground truth, so success demands asking, not recall. Across eight frontier LLM agents, defaults fall at least 62 points below an oracle handed the relevant preference, and prompting closes little of it. Diagnostics identify acquisition as the bottleneck. ATRBench surfaces this proactivity gap in current agents and offers a diagnostic testbed for closing it.

Yanbo Wang, Jiaxuan You, Chuan Shi et al.

Relational Databases (RDBs) are the backbone of modern business, yet they lack foundation models comparable to those in text or vision. A key obstacle is that high-quality RDBs are private, scarce and structurally heterogeneous, making internet-scale pre-training infeasible. To overcome this data scarcity, We introduce $\textbf{RDB-PFN}$, the first relational foundation model trained purely via $\textbf{synthetic data}$. Inspired by Prior-Data Fitted Networks (PFNs) where synthetic data generated from Structural Causal Models (SCMs) enables reasoning on single tables, we design a $\textbf{Relational Prior Generator}$ to create an infinite stream of diverse RDBs from scratch. Pre-training on $\textbf{over 2 million}$ synthetic single-table and relational tasks, RDB-PFN learns to adapt to any new database instantly via genuine $\textbf{in-context learning}$. Experiments verify RDB-PFN achieves strong few-shot performance on 19 real-world relational prediction tasks, outperforming graph-based and single-table foundation-model baselines (given the same DFS-linearized inputs), while using a lightweight architecture and fast inference. The code is available at https://github.com/MuLabPKU/RDBPFN

Jiawei Liu, Cheng Yang, Zhiyuan Lu et al.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models in generalization and adaptation motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Zhongjian Zhang, Xiao Wang, Mengmei Zhang et al.

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph-related tasks, with the ultimate goal of developing a graph foundation model that generalizes diverse scenarios. The key challenge is to align graph data with language spaces so that LLMs can better comprehend graphs. As a popular paradigm, Graph-Tokenizing LLMs (GTokenLLMs) encode complex structures and lengthy texts into a graph token sequence, and then align them with text tokens via language instructions tuning. Despite their initial success, our information-theoretic analysis reveals that existing GTokenLLMs rely solely on text supervision from language instructions, which achieve only implicit graph-text alignment, resulting in a text-dominant bias that underutilizes graph context. To overcome this limitation, we first prove that the alignment objective is upper-bounded by the mutual information between the input graphs and their hidden representations in the LLM, which motivates us to improve this upper bound to achieve better alignment. To this end, we further propose a reconstructive graph instruction tuning pipeline, RGLM. Our key idea is to reconstruct the graph information from the LLM's graph token outputs, explicitly incorporating graph supervision to constrain the alignment process. Technically, we embody RGLM by exploring three distinct variants from two complementary perspectives: RGLM-Decoder from the input space; RGLM-Similarizer and RGLM-Denoiser from the latent space. Additionally, we theoretically analyze the alignment effectiveness of each variant. Extensive experiments on various benchmarks and task scenarios validate the effectiveness of the proposed RGLM, paving the way for new directions in GTokenLLMs' alignment research.

Zeyuan Guo, Enmao Diao, Cheng Yang et al.

The success of large pretrained Transformers is closely tied to tokenizers, which convert raw input into discrete symbols. Extending these models to graph-structured data remains a significant challenge. In this work, we introduce a graph tokenization framework that generates sequential representations of graphs by combining reversible graph serialization, which preserves graph information, with Byte Pair Encoding (BPE), a widely adopted tokenizer in large language models (LLMs). To better capture structural information, the graph serialization process is guided by global statistics of graph substructures, ensuring that frequently occurring substructures appear more often in the sequence and can be merged by BPE into meaningful tokens. Empirical results demonstrate that the proposed tokenizer enables Transformers such as BERT to be directly applied to graph benchmarks without architectural modifications. The proposed approach achieves state-of-the-art results on 14 benchmark datasets and frequently outperforms both graph neural networks and specialized graph transformers. This work bridges the gap between graph-structured data and the ecosystem of sequence models. Our code is available at \href{https://github.com/BUPT-GAMMA/Graph-Tokenization-for-Bridging-Graphs-and-Transformers}{\color{blue}here}.

Yuxin Guo, Deyu Bo, Cheng Yang et al.

The history of artificial intelligence (AI) has witnessed the significant impact of high-quality data on various deep learning models, such as ImageNet for AlexNet and ResNet. Recently, instead of designing more complex neural architectures as model-centric approaches, the attention of AI community has shifted to data-centric ones, which focuses on better processing data to strengthen the ability of neural models. Graph learning, which operates on ubiquitous topological data, also plays an important role in the era of deep learning. In this survey, we comprehensively review graph learning approaches from the data-centric perspective, and aim to answer three crucial questions: (1) when to modify graph data, (2) what part of the graph data needs modification to unlock the potential of various graph models, and (3) how to safeguard graph models from problematic data influence. Accordingly, we propose a novel taxonomy based on the stages in the graph learning pipeline, and highlight the processing methods for different data structures in the graph data, i.e., topology, feature and label. Furthermore, we analyze some potential problems embedded in graph data and discuss how to solve them in a data-centric manner. Finally, we provide some promising future directions for data-centric graph learning.

Yining Wang, Xumeng Gong, Shaochuan Li et al.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

Yu Hao, Qiuyu Wang, Cheng Yang et al.

Large language models (LLMs) facilitate the development of autonomous agents. As a core component of such agents, task planning aims to decompose complex natural language requests into concrete, solvable sub-tasks. Since LLM-generated plans are frequently prone to hallucinations and sensitive to long-context prom-pts, recent research has introduced plan verifiers to identify and correct potential flaws. However, most existing approaches still rely on an LLM as the verifier via additional prompting for plan review or self-reflection. LLM-based verifiers can be misled by plausible narration and struggle to detect failures caused by structural relations across steps, such as type mismatches, missing intermediates, or broken dependencies. To address these limitations, we propose a graph-based verifier for LLM task planning. Specifically, the proposed method has four major components: Firstly, we represent a plan as a directed graph with enriched attributes, where nodes denote sub-tasks and edges encode execution order and dependency constraints. Secondly, a graph neural network (GNN) then performs structural evaluation and diagnosis, producing a graph-level plausibility score for plan acceptance as well as node/edge-level risk scores to localize erroneous regions. Thirdly, we construct controllable perturbations from ground truth plan graphs, and automatically generate training data with fine-grained annotations. Finally, guided by the feedback from our GNN verifier, we enable an LLM to conduct local edits (e.g., tool replacement or insertion) to correct the plan when the graph-level score is insufficient. Extensive experiments across diverse datasets, backbone LLMs, and planners demonstrate that our GNNVerifier achieves significant gains in improving plan quality. Our data and code is available at https://github.com/BUPT-GAMMA/GNNVerifier.

Bo Yan, Cheng Yang, Chuan Shi et al.

Abnormal event detection, which refers to mining unusual interactions among involved entities, plays an important role in many real applications. Previous works mostly over-simplify this task as detecting abnormal pair-wise interactions. However, real-world events may contain multi-typed attributed entities and complex interactions among them, which forms an Attributed Heterogeneous Information Network (AHIN). With the boom of social networks, abnormal event detection in AHIN has become an important, but seldom explored task. In this paper, we firstly study the unsupervised abnormal event detection problem in AHIN. The events are considered as star-schema instances of AHIN and are further modeled by hypergraphs. A novel hypergraph contrastive learning method, named AEHCL, is proposed to fully capture abnormal event patterns. AEHCL designs the intra-event and inter-event contrastive modules to exploit self-supervised AHIN information. The intra-event contrastive module captures the pair-wise and multivariate interaction anomalies within an event, and the inter-event module captures the contextual anomalies among events. These two modules collaboratively boost the performance of each other and improve the detection results. During the testing phase, a contrastive learning-based abnormal event score function is further proposed to measure the abnormality degree of events. Extensive experiments on three datasets in different scenarios demonstrate the effectiveness of AEHCL, and the results improve state-of-the-art baselines up to 12.0% in Average Precision (AP) and 4.6% in Area Under Curve (AUC) respectively.

Binbin Hu, Zhiyang Hu, Zhiqiang Zhang et al.

Knowledge representation learning has been commonly adopted to incorporate knowledge graph (KG) into various online services. Although existing knowledge representation learning methods have achieved considerable performance improvement, they ignore high-order structure and abundant attribute information, resulting unsatisfactory performance on semantics-rich KGs. Moreover, they fail to make prediction in an inductive manner and cannot scale to large industrial graphs. To address these issues, we develop a novel framework called KGNN to take full advantage of knowledge data for representation learning in the distributed learning system. KGNN is equipped with GNN based encoder and knowledge aware decoder, which aim to jointly explore high-order structure and attribute information together in a fine-grained fashion and preserve the relation patterns in KGs, respectively. Extensive experiments on three datasets for link prediction and triplet classification task demonstrate the effectiveness and scalability of KGNN framework.

Mengmei Zhang, Mingwei Sun, Peng Wang et al.

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

Chunjing Gan, Binbin Hu, Bo Huang et al.

In this paper, we highlight that both conformity and risk preference matter in making fund investment decisions beyond personal interest and seek to jointly characterize these aspects in a disentangled manner. Consequently, we develop a novel M ulti-granularity Graph Disentangled Learning framework named MGDL to effectively perform intelligent matching of fund investment products. Benefiting from the well-established fund graph and the attention module, multi-granularity user representations are derived from historical behaviors to separately express personal interest, conformity and risk preference in a fine-grained way. To attain stronger disentangled representations with specific semantics, MGDL explicitly involve two self-supervised signals, i.e., fund type based contrasts and fund popularity. Extensive experiments in offline and online environments verify the effectiveness of MGDL.

Bo Yan, Yang Cao, Haoyu Wang et al.

The heterogeneous information network (HIN), which contains rich semantics depicted by meta-paths, has emerged as a potent tool for mitigating data sparsity in recommender systems. Existing HIN-based recommender systems operate under the assumption of centralized storage and model training. However, real-world data is often distributed due to privacy concerns, leading to the semantic broken issue within HINs and consequent failures in centralized HIN-based recommendations. In this paper, we suggest the HIN is partitioned into private HINs stored on the client side and shared HINs on the server. Following this setting, we propose a federated heterogeneous graph neural network (FedHGNN) based framework, which facilitates collaborative training of a recommendation model using distributed HINs while protecting user privacy. Specifically, we first formalize the privacy definition for HIN-based federated recommendation (FedRec) in the light of differential privacy, with the goal of protecting user-item interactions within private HIN as well as users' high-order patterns from shared HINs. To recover the broken meta-path based semantics and ensure proposed privacy measures, we elaborately design a semantic-preserving user interactions publishing method, which locally perturbs user's high-order patterns and related user-item interactions for publishing. Subsequently, we introduce an HGNN model for recommendation, which conducts node- and semantic-level aggregations to capture recovered semantics. Extensive experiments on four datasets demonstrate that our model outperforms existing methods by a substantial margin (up to 34% in HR@10 and 42% in NDCG@10) under a reasonable privacy budget.

Boyu Chen, Zirui Guo, Zidan Yang et al.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Donglin Xia, Xiao Wang, Nian Liu et al.

Graph neural networks (GNNs) have become increasingly popular in modeling graph-structured data due to their ability to learn node representations by aggregating local structure information. However, it is widely acknowledged that the test graph structure may differ from the training graph structure, resulting in a structure shift. In this paper, we experimentally find that the performance of GNNs drops significantly when the structure shift happens, suggesting that the learned models may be biased towards specific structure patterns. To address this challenge, we propose the Cluster Information Transfer (CIT) mechanism (Code available at https://github.com/BUPT-GAMMA/CITGNN), which can learn invariant representations for GNNs, thereby improving their generalization ability to various and unknown test graphs with structure shift. The CIT mechanism achieves this by combining different cluster information with the nodes while preserving their cluster-independent information. By generating nodes across different clusters, the mechanism significantly enhances the diversity of the nodes and helps GNNs learn the invariant representations. We provide a theoretical analysis of the CIT mechanism, showing that the impact of changing clusters during structure shift can be mitigated after transfer. Additionally, the proposed mechanism is a plug-in that can be easily used to improve existing GNNs. We comprehensively evaluate our proposed method on three typical structure shift scenarios, demonstrating its effectiveness in enhancing GNNs' performance.

Rizhuo Huang, Yifan Feng, Rundong Xue et al.

Knowledge hypergraphs surpass traditional binary knowledge graphs by encapsulating complex $n$-ary atomic facts, providing a more comprehensive paradigm for semantic representation. However, constructing high-quality hypergraphs remains challenging due to the \textit{scenario gap}: generic extractors struggle to generalize across diverse domains with specific jargon, while existing methods often fail to balance structural skeletons with fine-grained details. To bridge this gap, we propose \textbf{Hyper-KGGen}, a skill-driven framework that reformulates extraction as a dynamic skill-evolving process. First, Hyper-KGGen employs a \textit{coarse-to-fine} mechanism to systematically decompose documents, ensuring full-dimensional coverage from binary links to complex hyperedges. Crucially, it incorporates an \textit{adaptive skill acquisition} module that actively distills domain expertise into a Global Skill Library. This is achieved via a stability-based feedback loop, where extraction stability serves as a relative reward signal to induce high-quality skills from unstable traces and missed predictions. Additionally, we present \textbf{HyperDocRED}, a rigorously annotated benchmark for document-level knowledge hypergraph extraction. Experiments demonstrate that Hyper-KGGen significantly outperforms strong baselines, validating that evolved skills provide substantially richer guidance than static few-shot examples in multi-scenario settings.

Yibo Li, Yuan Fang, Mengmei Zhang et al.

Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the whole molecular graph and neglect frequently occurring subgraphs, known as motifs, which are essential for determining molecular properties. Without such fine-grained knowledge, these models struggle to generalize to unseen molecules and tasks that require motif-level insights. To bridge this gap, we propose FineMolTex, a novel Fine-grained Molecular graph-Text pre-training framework to jointly learn coarse-grained molecule-level knowledge and fine-grained motif-level knowledge. Specifically, FineMolTex consists of two pre-training tasks: a contrastive alignment task for coarse-grained matching and a masked multi-modal modeling task for fine-grained matching. In particular, the latter predicts the labels of masked motifs and words, which are selected based on their importance. By leveraging insights from both modalities, FineMolTex is able to understand the fine-grained matching between motifs and words. Finally, we conduct extensive experiments across three downstream tasks, achieving up to 230% improvement in the text-based molecule editing task. Additionally, our case studies reveal that FineMolTex successfully captures fine-grained knowledge, potentially offering valuable insights for drug discovery and catalyst design.

Yang Liu, Jinxuan Cai, Yishen Li et al.

Large language model-based (LLM-based) multi-agent systems (MAS) are increasingly used to extend agentic problem solving via role specialization and collaboration. MAS workflows can be naturally modeled as directed computation graphs, where nodes execute agents/sub-workflows and edges encode dependencies and message passing. However, implementing complex graph workflows in current frameworks still requires substantial manual effort, offers limited reuse, and makes it difficult to integrate heterogeneous external context sources. To overcome these limitations, we present MASFactory, a graph-centric framework for orchestrating LLM-based MAS. It introduces Vibe Graphing, a human-in-the-loop approach that compiles natural-language intent into an editable workflow specification and then into an executable graph. In addition, the framework provides reusable components and pluggable context integration, as well as a visualizer for topology preview, runtime tracing, and human-in-the-loop interaction. We evaluate MASFactory on seven public benchmarks, validating both reproduction consistency for representative MAS methods and the effectiveness of Vibe Graphing. Our code (https://github.com/BUPT-GAMMA/MASFactory) and video (https://youtu.be/ANynzVfY32k) are publicly available.

Xin Li, Qizhi Chu, Yubin Chen et al.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

Yuxia Wu, Shujie Li, Yuan Fang et al.

Large language models (LLMs) have presented significant opportunities to enhance various machine learning applications, including graph neural networks (GNNs). By leveraging the vast open-world knowledge within LLMs, we can more effectively interpret and utilize textual data to better characterize heterophilic graphs, where neighboring nodes often have different labels. However, existing approaches for heterophilic graphs overlook the rich textual data associated with nodes, which could unlock deeper insights into their heterophilic contexts. In this work, we explore the potential of LLMs for modeling heterophilic graphs and propose a novel two-stage framework: LLM-enhanced edge discriminator and LLM-guided edge reweighting. In the first stage, we fine-tune the LLM to better identify homophilic and heterophilic edges based on the textual content of their nodes. In the second stage, we adaptively manage message propagation in GNNs for different edge types based on node features, structures, and heterophilic or homophilic characteristics. To cope with the computational demands when deploying LLMs in practical scenarios, we further explore model distillation techniques to fine-tune smaller, more efficient models that maintain competitive performance. Extensive experiments validate the effectiveness of our framework, demonstrating the feasibility of using LLMs to enhance node classification on heterophilic graphs.

Boyu Chen, Tai Guo, Weiyu Cui et al.

Multimodal retrieval models are becoming increasingly important in scenarios such as food delivery, where rich multimodal features can meet diverse user needs and enable precise retrieval. Mainstream approaches typically employ a dual-tower architecture between queries and items, and perform joint optimization of intra-tower and inter-tower tasks. However, we observe that joint optimization often leads to certain modalities dominating the training process, while other modalities are neglected. In addition, inconsistent training speeds across modalities can easily result in the one-epoch problem. To address these challenges, we propose a staged pretraining strategy, which guides the model to focus on specialized tasks at each stage, enabling it to effectively attend to and utilize multimodal features, and allowing flexible control over the training process at each stage to avoid the one-epoch problem. Furthermore, to better utilize the semantic IDs that compress high-dimensional multimodal embeddings, we design both generative and discriminative tasks to help the model understand the associations between SIDs, queries, and item features, thereby improving overall performance. Extensive experiments on large-scale real-world Meituan data demonstrate that our method achieves improvements of 3.80%, 2.64%, and 2.17% on R@5, R@10, and R@20, and 5.10%, 4.22%, and 2.09% on N@5, N@10, and N@20 compared to mainstream baselines. Online A/B testing on the Meituan platform shows that our approach achieves a 1.12% increase in revenue and a 1.02% increase in click-through rate, validating the effectiveness and superiority of our method in practical applications.

Nian Liu, Shen Fan, Ting Bai et al.

Social relations have been widely incorporated into recommender systems to alleviate data sparsity problem. However, raw social relations don't always benefit recommendation due to their inferior quality and insufficient quantity, especially for inactive users, whose interacted items are limited. In this paper, we propose a novel social recommendation method called LSIR (\textbf{L}earning \textbf{S}ocial Graph for \textbf{I}nactive User \textbf{R}ecommendation) that learns an optimal social graph structure for social recommendation, especially for inactive users. LSIR recursively aggregates user and item embeddings to collaboratively encode item and user features. Then, graph structure learning (GSL) is employed to refine the raw user-user social graph, by removing noisy edges and adding new edges based on the enhanced embeddings. Meanwhile, mimic learning is implemented to guide active users in mimicking inactive users during model training, which improves the construction of new edges for inactive users. Extensive experiments on real-world datasets demonstrate that LSIR achieves significant improvements of up to 129.58\% on NDCG in inactive user recommendation. Our code is available at~\url{https://github.com/liun-online/LSIR}.

Cheng Yang, Yu Hao, Qi Zhang et al.

When testing data and training data come from different distributions, deep neural networks (DNNs) will face significant safety risks in practical applications. Therefore, out-of-distribution (OOD) detection techniques, which can identify OOD samples at test time and alert the system, are urgently needed. Existing graph OOD detection methods usually characterize fine-grained in-distribution (ID) patterns from multiple perspectives, and train end-to-end graph neural networks (GNNs) for prediction. However, due to the unavailability of OOD data during training, the absence of explicit supervision signals could lead to sub-optimal performance of end-to-end encoders. To address this issue, we follow the pre-training+prompting paradigm to utilize pre-trained GNN encoders, and propose Disentangled Graph Prompting (DGP), to capture fine-grained ID patterns with the help of ID graph labels. Specifically, we design two prompt generators that respectively generate class-specific and class-agnostic prompt graphs by modifying the edge weights of an input graph. We also design several effective losses to train the prompt generators and prevent trivial solutions. We conduct extensive experiments on ten datasets to demonstrate the superiority of our proposed DGP, which achieves a relative AUC improvement of 3.63% over the best graph OOD detection baseline. Ablation studies and hyper-parameter experiments further show the effectiveness of DGP. Code is available at https://github.com/BUPT-GAMMA/DGP.

Zeqi Chen, Zhaoyang Chu, Yi Gui et al.

Large Language Models (LLMs) have demonstrated remarkable performance in code intelligence tasks such as code generation, summarization, and translation. However, their reliance on linearized token sequences limits their ability to understand the structural semantics of programs. While prior studies have explored graphaugmented prompting and structure-aware pretraining, they either suffer from prompt length constraints or require task-specific architectural changes that are incompatible with large-scale instructionfollowing LLMs. To address these limitations, this paper proposes CGBridge, a novel plug-and-play method that enhances LLMs with Code Graph information through an external, trainable Bridge module. CGBridge first pre-trains a code graph encoder via selfsupervised learning on a large-scale dataset of 270K code graphs to learn structural code semantics. It then trains an external module to bridge the modality gap among code, graph, and text by aligning their semantics through cross-modal attention mechanisms. Finally, the bridge module generates structure-informed prompts, which are injected into a frozen LLM, and is fine-tuned for downstream code intelligence tasks. Experiments show that CGBridge achieves notable improvements over both the original model and the graphaugmented prompting method. Specifically, it yields a 16.19% and 9.12% relative gain in LLM-as-a-Judge on code summarization, and a 9.84% and 38.87% relative gain in Execution Accuracy on code translation. Moreover, CGBridge achieves over 4x faster inference than LoRA-tuned models, demonstrating both effectiveness and efficiency in structure-aware code understanding.

Shan Shen, Shenglu Hua, Jiajun Zou et al.

Graph representation learning on Analog-Mixed Signal (AMS) circuits is crucial for various downstream tasks, e.g., parasitic estimation. However, the scarcity of design data, the unbalanced distribution of labels, and the inherent diversity of circuit implementations pose significant challenges to learning robust and transferable circuit representations. To address these limitations, we propose CircuitGCL, a novel graph contrastive learning framework that integrates representation scattering and label rebalancing to enhance transferability across heterogeneous circuit graphs. CircuitGCL employs a self-supervised strategy to learn topology-invariant node embeddings through hyperspherical representation scattering, eliminating dependency on large-scale data. Simultaneously, balanced mean squared error (BMSE) and balanced softmax cross-entropy (BSCE) losses are introduced to mitigate label distribution disparities between circuits, enabling robust and transferable parasitic estimation. Evaluated on parasitic capacitance estimation (edge-level task) and ground capacitance classification (node-level task) across TSMC 28nm AMS designs, CircuitGCL outperforms all state-of-the-art (SOTA) methods, with the $R^2$ improvement of $33.64\% \sim 44.20\%$ for edge regression and F1-score gain of $0.9\times \sim 2.1\times$ for node classification. Our code is available at https://github.com/ShenShan123/CircuitGCL.

Ting Bai, Yue Yu, Le Huang et al.

The sparse Mixture-of-Experts (MoE) architecture of large language models (LLMs) confronts an inherent issue of load imbalance arising from the simplistic linear router strategy, which ultimately causes the instability and inefficient learning of LLMs. To address this challenge, we introduce a novel MoE graph-based framework $\textbf{GMoE}$, aimed at enhancing the collaboration among multiple experts. In GMoE, a graph router function is designed to capture the collaboration signals among experts. This enables all experts to dynamically allocate information derived from input data by sharing information with their neighboring experts. Moreover, we put forward two coordination strategies in GMoE: the $\textit{Poisson distribution-based distinction strategy}$ and the $\textit{Normal distribution-based balance strategy}$, to further release the capacity of each expert and increase the model stability in the fine-tuning of LLMs. Specifically, we leverage a parameter-efficient fine-tuning technique, i.e., Low-Rank Adaptation (LoRA), to implement the graph MoE architecture. Extensive experiments on four real-world benchmark datasets demonstrate the effectiveness of GMoE, showing the benefits of facilitating collaborations of multiple experts in LLM fine-tuning. The code of experimental implementation is available at https://github.com/BAI-LAB/GMoE

Cheng Yang, Jiawei Liu, Chuan Shi

Semi-supervised learning on graphs is an important problem in the machine learning area. In recent years, state-of-the-art classification methods based on graph neural networks (GNNs) have shown their superiority over traditional ones such as label propagation. However, the sophisticated architectures of these neural models will lead to a complex prediction mechanism, which could not make full use of valuable prior knowledge lying in the data, e.g., structurally correlated nodes tend to have the same class. In this paper, we propose a framework based on knowledge distillation to address the above issues. Our framework extracts the knowledge of an arbitrary learned GNN model (teacher model), and injects it into a well-designed student model. The student model is built with two simple prediction mechanisms, i.e., label propagation and feature transformation, which naturally preserves structure-based and feature-based prior knowledge, respectively. In specific, we design the student model as a trainable combination of parameterized label propagation and feature transformation modules. As a result, the learned student can benefit from both prior knowledge and the knowledge in GNN teachers for more effective predictions. Moreover, the learned student model has a more interpretable prediction process than GNNs. We conduct experiments on five public benchmark datasets and employ seven GNN models including GCN, GAT, APPNP, SAGE, SGC, GCNII and GLP as the teacher models. Experimental results show that the learned student model can consistently outperform its corresponding teacher model by 1.4% - 4.7% on average. Code and data are available at https://github.com/BUPT-GAMMA/CPF

Xiao Wang, Deyu Bo, Chuan Shi et al.

Heterogeneous graphs (HGs) also known as heterogeneous information networks have become ubiquitous in real-world scenarios; therefore, HG embedding, which aims to learn representations in a lower-dimension space while preserving the heterogeneous structures and semantics for downstream tasks (e.g., node/graph classification, node clustering, link prediction), has drawn considerable attentions in recent years. In this survey, we perform a comprehensive review of the recent development on HG embedding methods and techniques. We first introduce the basic concepts of HG and discuss the unique challenges brought by the heterogeneity for HG embedding in comparison with homogeneous graph representation learning; and then we systemically survey and categorize the state-of-the-art HG embedding methods based on the information they used in the learning process to address the challenges posed by the HG heterogeneity. In particular, for each representative HG embedding method, we provide detailed introduction and further analyze its pros and cons; meanwhile, we also explore the transformativeness and applicability of different types of HG embedding methods in the real-world industrial environments for the first time. In addition, we further present several widely deployed systems that have demonstrated the success of HG embedding techniques in resolving real-world application problems with broader impacts. To facilitate future research and applications in this area, we also summarize the open-source code, existing graph learning platforms and benchmark datasets. Finally, we explore the additional issues and challenges of HG embedding and forecast the future research directions in this field.

Zhongjian Zhang, Yue Yu, Mengmei Zhang et al.

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph tasks. As a widely recognized paradigm, Graph-Tokenizing LLMs (GTokenLLMs) compress complex graph data into graph tokens and treat them as prefix tokens for querying LLMs, leading many to believe that LLMs can understand graphs more effectively and efficiently. In this paper, we challenge this belief: \textit{Do GTokenLLMs fully understand graph tokens in the natural-language embedding space?} Motivated by this question, we formalize a unified framework for GTokenLLMs and propose an evaluation pipeline, \textbf{GTEval}, to assess graph-token understanding via instruction transformations at the format and content levels. We conduct extensive experiments on 6 representative GTokenLLMs with GTEval. The primary findings are as follows: (1) Existing GTokenLLMs do not fully understand graph tokens. They exhibit over-sensitivity or over-insensitivity to instruction changes, and rely heavily on text for reasoning; (2) Although graph tokens preserve task-relevant graph information and receive attention across LLM layers, their utilization varies across models and instruction variants; (3) Additional instruction tuning can improve performance on the original and seen instructions, but it does not fully address the challenge of graph-token understanding, calling for further improvement.

Xiyuan Wang, Yi Hu, Yanbo Wang et al.

With the rapid advancement of large language models (LLMs), classic graph learning tasks have greatly benefited from LLMs, including improved encoding of textual features, more efficient construction of graphs from text, and enhanced reasoning over knowledge graphs. In this paper, we ask a complementary question: How can graphs help LLMs? We address this question from three perspectives: 1) graphs provide an up-to-date knowledge source that helps reduce LLM hallucinations, 2) graph-based prompting techniques-such as Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT)-enhance LLM reasoning capabilities, and 3) integrating graphs into LLMs improves their understanding of structured data, expanding their applicability to domains such as e-commerce, code, and relational databases (RDBs). We further outlook some future directions including designing sparse LLM architectures based on graphs and brain-inspired memory systems.

Tianrui Jia, Haoyang Li, Cheng Yang et al.

Graph neural networks (GNNs) have been demonstrated to perform well in graph representation learning, but always lacking in generalization capability when tackling out-of-distribution (OOD) data. Graph invariant learning methods, backed by the invariance principle among defined multiple environments, have shown effectiveness in dealing with this issue. However, existing methods heavily rely on well-predefined or accurately generated environment partitions, which are hard to be obtained in practice, leading to sub-optimal OOD generalization performances. In this paper, we propose a novel graph invariant learning method based on invariant and variant patterns co-mixup strategy, which is capable of jointly generating mixed multiple environments and capturing invariant patterns from the mixed graph data. Specifically, we first adopt a subgraph extractor to identify invariant subgraphs. Subsequently, we design one novel co-mixup strategy, i.e., jointly conducting environment Mixup and invariant Mixup. For the environment Mixup, we mix the variant environment-related subgraphs so as to generate sufficiently diverse multiple environments, which is important to guarantee the quality of the graph invariant learning. For the invariant Mixup, we mix the invariant subgraphs, further encouraging to capture invariant patterns behind graphs while getting rid of spurious correlations for OOD generalization. We demonstrate that the proposed environment Mixup and invariant Mixup can mutually promote each other. Extensive experiments on both synthetic and real-world datasets demonstrate that our method significantly outperforms state-of-the-art under various distribution shifts.

Yibo Li, Xiao Wang, Hongrui Liu et al.

Recent studies reveal the connection between GNNs and the diffusion process, which motivates many diffusion-based GNNs to be proposed. However, since these two mechanisms are closely related, one fundamental question naturally arises: Is there a general diffusion framework that can formally unify these GNNs? The answer to this question can not only deepen our understanding of the learning process of GNNs, but also may open a new door to design a broad new class of GNNs. In this paper, we propose a general diffusion equation framework with the fidelity term, which formally establishes the relationship between the diffusion process with more GNNs. Meanwhile, with this framework, we identify one characteristic of graph diffusion networks, i.e., the current neural diffusion process only corresponds to the first-order diffusion equation. However, by an experimental investigation, we show that the labels of high-order neighbors actually exhibit monophily property, which induces the similarity based on labels among high-order neighbors without requiring the similarity among first-order neighbors. This discovery motives to design a new high-order neighbor-aware diffusion equation, and derive a new type of graph diffusion network (HiD-Net) based on the framework. With the high-order diffusion equation, HiD-Net is more robust against attacks and works on both homophily and heterophily graphs. We not only theoretically analyze the relation between HiD-Net with high-order random walk, but also provide a theoretical convergence guarantee. Extensive experimental results well demonstrate the effectiveness of HiD-Net over state-of-the-art graph diffusion networks.