Yongchao Liu

Boci Peng, Yun Zhu, Yongchao Liu et al.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field. In order to track recent progress in this field, we set up a repository at \url{https://github.com/pengboci/GraphRAG-Survey}.

Xiaotang Wang, Yun Zhu, Haizhou Shi et al.

Graph Transformers (GTs) have recently achieved significant success in the graph domain by effectively capturing both long-range dependencies and graph inductive biases. However, these methods face two primary challenges: (1) multi-view chaos, which results from coupling multi-view information (positional, structural, attribute), thereby impeding flexible usage and the interpretability of the propagation process. (2) local-global chaos, which arises from coupling local message passing with global attention, leading to issues of overfitting and over-globalizing. To address these challenges, we propose a high-level decoupled perspective of GTs, breaking them down into three components and two interaction levels: positional attention, structural attention, and attribute attention, alongside local and global interaction. Based on this decoupled perspective, we design a decoupled graph triple attention network named DeGTA, which separately computes multi-view attentions and adaptively integrates multi-view local and global information. This approach offers three key advantages: enhanced interpretability, flexible design, and adaptive integration of local and global information. Through extensive experiments, DeGTA achieves state-of-the-art performance across various datasets and tasks, including node classification and graph classification. Comprehensive ablation studies demonstrate that decoupling is essential for improving performance and enhancing interpretability. Our code is available at: https://github.com/wangxiaotang0906/DeGTA

Xiaotang Wang, Yun Zhu, Haizhou Shi et al.

In the graph domain, deep graph networks based on Message Passing Neural Networks (MPNNs) or Graph Transformers often cause over-smoothing of node features, limiting their expressive capacity. Many upsampling techniques involving node and edge manipulation have been proposed to mitigate this issue. However, these methods are often heuristic, resulting in extensive manual labor and suboptimal performance and lacking a universal integration strategy. In this study, we introduce UniGAP, a universal and adaptive graph upsampling framework to mitigate over-smoothing in node classification tasks. Specifically, we design an adaptive graph upsampler based on condensed trajectory features, serving as a plug-in component for existing GNNs to mitigate the over-smoothing problem and enhance performance. Moreover, UniGAP serves as a representation-based and fully differentiable framework to inspire further exploration of graph upsampling methods. Through extensive experiments, UniGAP demonstrates significant improvements over heuristic data augmentation methods in various datasets and metrics. We analyze how graph structure evolves with UniGAP, identifying key bottlenecks where over-smoothing occurs, and providing insights into how UniGAP addresses this issue. Lastly, we show the potential of combining UniGAP with large language models (LLMs) to further improve downstream performance. Our code is available at: https://github.com/wangxiaotang0906/UniGAP

Yun Zhu, Haizhou Shi, Xiaotang Wang et al.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

Yang Liu, Chuan Zhou, Peng Zhang et al.

Knowledge graph embedding (KGE) constitutes a foundational task, directed towards learning representations for entities and relations within knowledge graphs (KGs), with the objective of crafting representations comprehensive enough to approximate the logical and symbolic interconnections among entities. In this paper, we define a metric Z-counts to measure the difficulty of training each triple ($<$head entity, relation, tail entity$>$) in KGs with theoretical analysis. Based on this metric, we propose \textbf{CL4KGE}, an efficient \textbf{C}urriculum \textbf{L}earning based training strategy for \textbf{KGE}. This method includes a difficulty measurer and a training scheduler that aids in the training of KGE models. Our approach possesses the flexibility to act as a plugin within a wide range of KGE models, with the added advantage of adaptability to the majority of KGs in existence. The proposed method has been evaluated on popular KGE models, and the results demonstrate that it enhances the state-of-the-art methods. The use of Z-counts as a metric has enabled the identification of challenging triples in KGs, which helps in devising effective training strategies.

Yun Yue, Zhiling Ye, Jiadi Jiang et al.

Adaptive optimizers, such as Adam, have achieved remarkable success in deep learning. A key component of these optimizers is the so-called preconditioning matrix, providing enhanced gradient information and regulating the step size of each gradient direction. In this paper, we propose a novel approach to designing the preconditioning matrix by utilizing the gradient difference between two successive steps as the diagonal elements. These diagonal elements are closely related to the Hessian and can be perceived as an approximation of the inner product between the Hessian row vectors and difference of the adjacent parameter vectors. Additionally, we introduce an auto-switching function that enables the preconditioning matrix to switch dynamically between Stochastic Gradient Descent (SGD) and the adaptive optimizer. Based on these two techniques, we develop a new optimizer named AGD that enhances the generalization performance. We evaluate AGD on public datasets of Natural Language Processing (NLP), Computer Vision (CV), and Recommendation Systems (RecSys). Our experimental results demonstrate that AGD outperforms the state-of-the-art (SOTA) optimizers, achieving highly competitive or significantly better predictive performance. Furthermore, we analyze how AGD is able to switch automatically between SGD and the adaptive optimizer and its actual effects on various scenarios. The code is available at https://github.com/intelligent-machine-learning/atorch/tree/main/atorch/optimizers.

Yun Yue, Jiadi Jiang, Zhiling Ye et al.

Deep Neural Networks (DNNs) generalization is known to be closely related to the flatness of minima, leading to the development of Sharpness-Aware Minimization (SAM) for seeking flatter minima and better generalization. In this paper, we revisit the loss of SAM and propose a more general method, called WSAM, by incorporating sharpness as a regularization term. We prove its generalization bound through the combination of PAC and Bayes-PAC techniques, and evaluate its performance on various public datasets. The results demonstrate that WSAM achieves improved generalization, or is at least highly competitive, compared to the vanilla optimizer, SAM and its variants. The code is available at https://github.com/intelligent-machine-learning/atorch/tree/main/atorch/optimizers.

Yun Yue, Yongchao Liu, Suo Tong et al.

We develop a novel framework that adds the regularizers of the sparse group lasso to a family of adaptive optimizers in deep learning, such as Momentum, Adagrad, Adam, AMSGrad, AdaHessian, and create a new class of optimizers, which are named Group Momentum, Group Adagrad, Group Adam, Group AMSGrad and Group AdaHessian, etc., accordingly. We establish theoretically proven convergence guarantees in the stochastic convex settings, based on primal-dual methods. We evaluate the regularized effect of our new optimizers on three large-scale real-world ad click datasets with state-of-the-art deep learning models. The experimental results reveal that compared with the original optimizers with the post-processing procedure which uses the magnitude pruning method, the performance of the models can be significantly improved on the same sparsity level. Furthermore, in comparison to the cases without magnitude pruning, our methods can achieve extremely high sparsity with significantly better or highly competitive performance. The code is available at https://github.com/intelligent-machine-learning/tfplus/tree/main/tfplus.

Boci Peng, Yongchao Liu, Xiaohe Bo et al.

Commonsense question answering is a crucial task that requires machines to employ reasoning according to commonsense. Previous studies predominantly employ an extracting-and-modeling paradigm to harness the information in KG, which first extracts relevant subgraphs based on pre-defined rules and then proceeds to design various strategies aiming to improve the representations and fusion of the extracted structural knowledge. Despite their effectiveness, there are still two challenges. On one hand, subgraphs extracted by rule-based methods may have the potential to overlook critical nodes and result in uncontrollable subgraph size. On the other hand, the misalignment between graph and text modalities undermines the effectiveness of knowledge fusion, ultimately impacting the task performance. To deal with the problems above, we propose a novel framework: \textbf{S}ubgraph R\textbf{E}trieval Enhanced by Gra\textbf{P}h-\textbf{T}ext \textbf{A}lignment, named \textbf{SEPTA}. Firstly, we transform the knowledge graph into a database of subgraph vectors and propose a BFS-style subgraph sampling strategy to avoid information loss, leveraging the analogy between BFS and the message-passing mechanism. In addition, we propose a bidirectional contrastive learning approach for graph-text alignment, which effectively enhances both subgraph retrieval and knowledge fusion. Finally, all the retrieved information is combined for reasoning in the prediction module. Extensive experiments on five datasets demonstrate the effectiveness and robustness of our framework.

Yuwei Hu, Xinyi Huang, Zhewei Wei et al.

Large Language Models (LLMs) for Graph Reasoning have been extensively studied over the past two years, involving enabling LLMs to understand graph structures and reason on graphs to solve various graph problems, with graph algorithm problems being the most prevalent. Recent studies underscore the potential of LLMs in handling graph reasoning tasks, but their performance is underwhelming. In this work, we point out issues with existing methods and benchmarks, and rethink the direction that LLMs for graph reasoning should strive toward. We find that base models, e.g., GPT-4o-mini, are largely underestimated due to improper reasoning focus. Base models with reasoning focus redirected from replicating graph algorithms to designing them can easily solve most graph reasoning tasks in existing benchmarks. To truly evaluate the graph reasoning capabilities of LLMs, we construct a more challenging GraphAlgorithm benchmark, comprising 239 different graph problems and 3,041 test instances collected from 4 competition platforms. Finally, we introduce a simple and strong baseline Simple-Reasoning-Then-Coding (Simple-RTC)-which guides LLMs to design graph algorithms first and then code to address graph reasoning tasks. Simple-RTC achieves near-perfect accuracy on existing benchmarks and significantly outperforms GPT-4o-mini and all prior methods on the GraphAlgorithm benchmark. This strong baseline encourages further advancements in LLMs for Graph Reasoning in the future.

Jie Peng, Jiarui Ji, Runlin Lei et al.

Dynamic Text-Attributed Graphs (DyTAGs), which intricately integrate structural, temporal, and textual attributes, are crucial for modeling complex real-world systems. However, most of the existing DyTAG datasets exhibit poor textual quality, which severely limits their utility for DyTAG generation tasks requiring semantically rich inputs. Additionally, prior work mainly focuses on discriminative tasks on DyTAGs, resulting in a lack of standardized task formulations and evaluation protocols tailored for DyTAG generation. To address these critical issues, we propose Generative DyTAG Benchmark (GDGB), which comprises eight meticulously curated DyTAG datasets with high-quality textual features for both nodes and edges, overcoming limitations of prior datasets. Building on GDGB, we define two novel DyTAG generation tasks: Transductive Dynamic Graph Generation (TDGG) and Inductive Dynamic Graph Generation (IDGG). TDGG transductively generates a target DyTAG based on the given source and destination node sets, while the more challenging IDGG introduces new node generation to inductively model the dynamic expansion of real-world graph data. To enable holistic evaluation, we design multifaceted metrics that assess the structural, temporal, and textual quality of the generated DyTAGs. We further propose GAG-General, an LLM-based multi-agent generative framework tailored for reproducible and robust benchmarking of DyTAG generation. Experimental results demonstrate that GDGB enables rigorous evaluation of TDGG and IDGG, with key insights revealing the critical interplay of structural and textual features in DyTAG generation. These findings establish GDGB as a foundational resource for advancing generative DyTAG research and unlocking further practical applications in DyTAG generation. GDGB datasets, source codes, and leaderboards are available at \href{https://gdgb-algo.github.io/}{here}.

Runlin Lei, Jiarui Ji, Haipeng Ding et al.

With the rise of large language models (LLMs), there has been growing interest in Graph Foundation Models (GFMs) for graph-based tasks. By leveraging LLMs as predictors, GFMs have demonstrated impressive generalizability across various tasks and datasets. However, existing research on LLMs as predictors has predominantly focused on static graphs, leaving their potential in dynamic graph prediction unexplored. In this work, we pioneer using LLMs for predictive tasks on dynamic graphs. We identify two key challenges: the constraints imposed by context length when processing large-scale historical data and the significant variability in domain characteristics, both of which complicate the development of a unified predictor. To address these challenges, we propose the GraphAgent-Dynamic (GAD) Framework, a multi-agent system that leverages collaborative LLMs. In contrast to using a single LLM as the predictor, GAD incorporates global and local summary agents to generate domain-specific knowledge, enhancing its transferability across domains. Additionally, knowledge reflection agents enable adaptive updates to GAD's knowledge, maintaining a unified and self-consistent architecture. In experiments, GAD demonstrates performance comparable to or even exceeds that of full-supervised graph neural networks without dataset-specific training. Finally, to enhance the task-specific performance of LLM-based predictors, we discuss potential improvements, such as dataset-specific fine-tuning to LLMs. By developing tailored strategies for different tasks, we provide new insights for the future design of LLM-based predictors.

Chuan He, Yongchao Liu, Qiang Li et al.

Cold-start item recommendation is a significant challenge in recommendation systems, particularly when new items are introduced without any historical interaction data. While existing methods leverage multi-modal content to alleviate the cold-start issue, they often neglect the inherent multi-view structure of modalities, the distinction between shared and modality-specific features. In this paper, we propose Multi-Modal Multi-View Variational AutoEncoder (M^2VAE), a generative model that addresses the challenges of modeling common and unique views in attribute and multi-modal features, as well as user preferences over single-typed item features. Specifically, we generate type-specific latent variables for item IDs, categorical attributes, and image features, and use Product-of-Experts (PoE) to derive a common representation. A disentangled contrastive loss decouples the common view from unique views while preserving feature informativeness. To model user inclinations, we employ a preference-guided Mixture-of-Experts (MoE) to adaptively fuse representations. We further incorporate co-occurrence signals via contrastive learning, eliminating the need for pretraining. Extensive experiments on real-world datasets validate the effectiveness of our approach.

Houyi Li, Zhihong Chen, Chenliang Li et al.

The large-scale recommender system mainly consists of two stages: matching and ranking. The matching stage (also known as the retrieval step) identifies a small fraction of relevant items from billion-scale item corpus in low latency and computational cost. Item-to-item collaborative filter (item-based CF) and embedding-based retrieval (EBR) have been long used in the industrial matching stage owing to its efficiency. However, item-based CF is hard to meet personalization, while EBR has difficulty in satisfying diversity. In this paper, we propose a novel matching architecture, Path-based Deep Network (named PDN), which can incorporate both personalization and diversity to enhance matching performance. Specifically, PDN is comprised of two modules: Trigger Net and Similarity Net. PDN utilizes Trigger Net to capture the user's interest in each of his/her interacted item, and Similarity Net to evaluate the similarity between each interacted item and the target item based on these items' profile and CF information. The final relevance between the user and the target item is calculated by explicitly considering user's diverse interests, \ie aggregating the relevance weights of the related two-hop paths (one hop of a path corresponds to user-item interaction and the other to item-item relevance). Furthermore, we describe the architecture design of a matching system with the proposed PDN in a leading real-world E-Commerce service (Mobile Taobao App). Based on offline evaluations and online A/B test, we show that PDN outperforms the existing solutions for the same task. The online results also demonstrate that PDN can retrieve more personalized and more diverse relevant items to significantly improve user engagement. Currently, PDN system has been successfully deployed at Mobile Taobao App and handling major online traffic.

Qinkai Zheng, Houyi Li, Peng Zhang et al.

Graph neural networks (GNNs) have been popularly used in analyzing graph-structured data, showing promising results in various applications such as node classification, link prediction and network recommendation. In this paper, we present a new graph attention neural network, namely GIPA, for attributed graph data learning. GIPA consists of three key components: attention, feature propagation and aggregation. Specifically, the attention component introduces a new multi-layer perceptron based multi-head to generate better non-linear feature mapping and representation than conventional implementations such as dot-product. The propagation component considers not only node features but also edge features, which differs from existing GNNs that merely consider node features. The aggregation component uses a residual connection to generate the final embedding. We evaluate the performance of GIPA using the Open Graph Benchmark proteins (ogbn-proteins for short) dataset. The experimental results reveal that GIPA can beat the state-of-the-art models in terms of prediction accuracy, e.g., GIPA achieves an average test ROC-AUC of $0.8700\pm 0.0010$ and outperforms all the previous methods listed in the ogbn-proteins leaderboard.

Yongchao Liu, Houyi Li, Guowei Zhang et al.

Graph neural networks (GNNs) have been demonstrated as a powerful tool for analyzing non-Euclidean graph data. However, the lack of efficient distributed graph learning systems severely hinders applications of GNNs, especially when graphs are big and GNNs are relatively deep. Herein, we present GraphTheta, the first distributed and scalable graph learning system built upon vertex-centric distributed graph processing with neural network operators implemented as user-defined functions. This system supports multiple training strategies and enables efficient and scalable big-graph learning on distributed (virtual) machines with low memory. To facilitate graph convolutions, GraphTheta puts forward a new graph learning abstraction named NN-TGAR to bridge the gap between graph processing and graph deep learning. A distributed graph engine is proposed to conduct the stochastic gradient descent optimization with a hybrid-parallel execution, and a new cluster-batched training strategy is supported. We evaluate GraphTheta using several datasets with network sizes ranging from small-, modest- to large-scale. Experimental results show that GraphTheta can scale well to 1,024 workers for training an in-house developed GNN on an industry-scale Alipay dataset of 1.4 billion nodes and 4.1 billion attributed edges, with a cluster of CPU virtual machines (dockers) of small memory each (5$\sim$12GB). Moreover, GraphTheta can outperform DistDGL by up to $2.02\times$, with better scalability, and GraphLearn by up to $30.56\times$. As for model accuracy, GraphTheta is capable of learning as good GNNs as existing frameworks. To the best of our knowledge, this work presents the largest edge-attributed GNN learning task in the literature.

Yongchao Liu, Yue Jin, Yong Chen et al.

Accelerating deep model training and inference is crucial in practice. Existing deep learning frameworks usually concentrate on optimizing training speed and pay fewer attentions to inference-specific optimizations. Actually, model inference differs from training in terms of computation, e.g. parameters are refreshed each gradient update step during training, but kept invariant during inference. These special characteristics of model inference open new opportunities for its optimization. In this paper, we propose a hardware-aware optimization framework, namely Woodpecker-DL (WPK), to accelerate inference by taking advantage of multiple joint optimizations from the perspectives of graph optimization, automated searches, domain-specific language (DSL) compiler techniques and system-level exploration. In WPK, we investigated two new automated search approaches based on genetic algorithm and reinforcement learning, respectively, to hunt the best operator code configurations targeting specific hardware. A customized DSL compiler is further attached to these search algorithms to generate efficient codes. To create an optimized inference plan, WPK systematically explores high-speed operator implementations from third-party libraries besides our automatically generated codes and singles out the best implementation per operator for use. Extensive experiments demonstrated that on a Tesla P100 GPU, we can achieve the maximum speedup of 5.40 over cuDNN and 1.63 over TVM on individual convolution operators, and run up to 1.18 times faster than TensorRT for end-to-end model inference.

Yongchao Liu, Tony Pan, Oded Green et al.

Pairwise association measure is an important operation in data analytics. Kendall's tau coefficient is one widely used correlation coefficient identifying non-linear relationships between ordinal variables. In this paper, we investigated a parallel algorithm accelerating all-pairs Kendall's tau coefficient computation via single instruction multiple data (SIMD) vectorized sorting on Intel Xeon Phis by taking advantage of many processing cores and 512-bit SIMD vector instructions. To facilitate workload balancing and overcome on-chip memory limitation, we proposed a generic framework for symmetric all-pairs computation by building provable bijective functions between job identifier and coordinate space. Performance evaluation demonstrated that our algorithm on one 5110P Phi achieves two orders-of-magnitude speedups over 16-threaded MATLAB and three orders-of-magnitude speedups over sequential R, both running on high-end CPUs. Besides, our algorithm exhibited rather good distributed computing scalability with respect to number of Phis. Source code and datasets are publicly available at http://lightpcc.sourceforge.net.