Qingqing Long

Wei Ju, Zheng Fang, Yiyang Gu et al. · uw

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

Junyu Luo, Weizhi Zhang, Ye Yuan et al. · pku

The era of intelligent agents is upon us, driven by revolutionary advancements in large language models. Large Language Model (LLM) agents, with goal-driven behaviors and dynamic adaptation capabilities, potentially represent a critical pathway toward artificial general intelligence. This survey systematically deconstructs LLM agent systems through a methodology-centered taxonomy, linking architectural foundations, collaboration mechanisms, and evolutionary pathways. We unify fragmented research threads by revealing fundamental connections between agent design principles and their emergent behaviors in complex environments. Our work provides a unified architectural perspective, examining how agents are constructed, how they collaborate, and how they evolve over time, while also addressing evaluation methodologies, tool applications, practical challenges, and diverse application domains. By surveying the latest developments in this rapidly evolving field, we offer researchers a structured taxonomy for understanding LLM agents and identify promising directions for future research. The collection is available at https://github.com/luo-junyu/Awesome-Agent-Papers.

Qingqing Long, Yuchen Yan, Peiyan Zhang et al.

Large-scale "pre-train and prompt learning" paradigms have demonstrated remarkable adaptability, enabling broad applications across diverse domains such as question answering, image recognition, and multimodal retrieval. This approach fully leverages the potential of large-scale pre-trained models, reducing downstream data requirements and computational costs while enhancing model applicability across various tasks. Graphs, as versatile data structures that capture relationships between entities, play pivotal roles in fields such as social network analysis, recommender systems, and biological graphs. Despite the success of pre-train and prompt learning paradigms in Natural Language Processing (NLP) and Computer Vision (CV), their application in graph domains remains nascent. In graph-structured data, not only do the node and edge features often have disparate distributions, but the topological structures also differ significantly. This diversity in graph data can lead to incompatible patterns or gaps between pre-training and fine-tuning on downstream graphs. We aim to bridge this gap by summarizing methods for alleviating these disparities. This includes exploring prompt design methodologies, comparing related techniques, assessing application scenarios and datasets, and identifying unresolved problems and challenges. This survey categorizes over 100 relevant works in this field, summarizing general design principles and the latest applications, including text-attributed graphs, molecules, proteins, and recommendation systems. Through this extensive review, we provide a foundational understanding of graph prompt learning, aiming to impact not only the graph mining community but also the broader Artificial General Intelligence (AGI) community.

Xunxin Cai, Chengrui Wang, Qingqing Long et al.

The rapid advancement of large language models (LLMs) in biological-medical applications has highlighted a gap between their potential and the limited scale and often low quality of available open-source annotated textual datasets. In addition, the inherent complexity of the biomedical knowledge hierarchy significantly hampers efforts to bridge this gap.Can LLMs themselves play a pivotal role in overcoming this limitation? Motivated by this question, we investigate this challenge in the present study.We propose a framework that automates the distillation of high-quality textual training data from the extensive scientific literature. Our approach self-evaluates and generates questions that are more closely aligned with the biomedical domain, guided by the biomedical knowledge hierarchy through medical subject headings (MeSH). This comprehensive framework establishes an automated workflow, thereby eliminating the need for manual intervention. Furthermore, we conducted comprehensive experiments to evaluate the impact of our framework-generated data on downstream language models of varying sizes. Our approach substantially improves question-answering tasks compared to pre-trained models from the life sciences domain and powerful close-source models represented by GPT-4. Notably, the generated AI-Ready dataset enabled the Llama3-70B base model to outperform GPT-4 using MedPrompt with multiple times the number of parameters. Detailed case studies and ablation experiments underscore the significance of each component within our framework

Meng Xiao, Xunxin Cai, Qingqing Long et al.

Corpus distillation for biomedical large language models (LLMs) seeks to address the pressing challenge of insufficient quantity and quality in open-source annotated scientific corpora, which remains a bottleneck for effective LLM training in biomedical research. This paper proposes a knowledge-driven, agentic framework for scientific corpus distillation, tailored explicitly for LLM training in the biomedical domain, addressing the challenge posed by the complex hierarchy of biomedical knowledge. Central to our approach is a collaborative multi-agent architecture, where specialized agents, each guided by the Medical Subject Headings (MeSH) hierarchy, work in concert to autonomously extract, synthesize, and self-evaluate high-quality textual data from vast scientific literature. This agentic framework collectively generates and refines domain-specific question-answer pairs, ensuring comprehensive coverage and consistency with biomedical ontologies while minimizing manual involvement. Extensive experimental results show that language models trained on our multi-agent distilled datasets achieve notable improvements in biomedical question-answering tasks, outperforming both strong life sciences LLM baselines and advanced proprietary models. Notably, our AI-Ready dataset enables Llama3-70B to surpass GPT-4 with MedPrompt and Med-PaLM-2, despite their larger scale. Detailed ablation studies and case analyses further validate the effectiveness and synergy of each agent within the framework, highlighting the potential of multi-agent collaboration in biomedical LLM training.

Wei Ju, Yifan Wang, Yifang Qin et al. · pku

In recent years, deep learning on graphs has achieved remarkable success in various domains. However, the reliance on annotated graph data remains a significant bottleneck due to its prohibitive cost and time-intensive nature. To address this challenge, self-supervised learning (SSL) on graphs has gained increasing attention and has made significant progress. SSL enables machine learning models to produce informative representations from unlabeled graph data, reducing the reliance on expensive labeled data. While SSL on graphs has witnessed widespread adoption, one critical component, Graph Contrastive Learning (GCL), has not been thoroughly investigated in the existing literature. Thus, this survey aims to fill this gap by offering a dedicated survey on GCL. We provide a comprehensive overview of the fundamental principles of GCL, including data augmentation strategies, contrastive modes, and contrastive optimization objectives. Furthermore, we explore the extensions of GCL to other aspects of data-efficient graph learning, such as weakly supervised learning, transfer learning, and related scenarios. We also discuss practical applications spanning domains such as drug discovery, genomics analysis, recommender systems, and finally outline the challenges and potential future directions in this field.

Wei Ju, Siyu Yi, Yifan Wang et al. · pku

Graph-structured data, prevalent in domains ranging from social networks to biochemical analysis, serve as the foundation for diverse real-world systems. While graph neural networks demonstrate proficiency in modeling this type of data, their success is often reliant on significant amounts of labeled data, posing a challenge in practical scenarios with limited annotation resources. To tackle this problem, tremendous efforts have been devoted to enhancing graph machine learning performance under low-resource settings by exploring various approaches to minimal supervision. In this paper, we introduce a novel concept of Data-Efficient Graph Learning (DEGL) as a research frontier, and present the first survey that summarizes the current progress of DEGL. We initiate by highlighting the challenges inherent in training models with large labeled data, paving the way for our exploration into DEGL. Next, we systematically review recent advances on this topic from several key aspects, including self-supervised graph learning, semi-supervised graph learning, and few-shot graph learning. Also, we state promising directions for future research, contributing to the evolution of graph machine learning.

Yuchen Yan, Peiyan Zhang, Zheng Fang et al.

The "Graph pre-training and fine-tuning" paradigm has significantly improved Graph Neural Networks(GNNs) by capturing general knowledge without manual annotations for downstream tasks. However, due to the immense gap of data and tasks between the pre-training and fine-tuning stages, the model performance is still limited. Inspired by prompt fine-tuning in Natural Language Processing(NLP), many endeavors have been made to bridge the gap in graph domain. But existing methods simply reformulate the form of fine-tuning tasks to the pre-training ones. With the premise that the pre-training graphs are compatible with the fine-tuning ones, these methods typically operate in transductive setting. In order to generalize graph pre-training to inductive scenario where the fine-tuning graphs might significantly differ from pre-training ones, we propose a novel graph prompt based method called Inductive Graph Alignment Prompt(IGAP). Firstly, we unify the mainstream graph pre-training frameworks and analyze the essence of graph pre-training from graph spectral theory. Then we identify the two sources of the data gap in inductive setting: (i) graph signal gap and (ii) graph structure gap. Based on the insight of graph pre-training, we propose to bridge the graph signal gap and the graph structure gap with learnable prompts in the spectral space. A theoretical analysis ensures the effectiveness of our method. At last, we conduct extensive experiments among nodes classification and graph classification tasks under the transductive, semi-inductive and inductive settings. The results demonstrate that our proposed method can successfully bridge the data gap under different settings.

Cong Li, Qingqing Long, Yuanchun Zhou et al.

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life sciences, where vast collections of single-cell omics data from multiple species provide a foundation for training foundational models. However, the challenge lies in the disparity of data scales across different species, hindering the development of a comprehensive model for interpreting genetic data across diverse organisms. In this study, we propose an innovative hybrid approach that integrates the general knowledge capabilities of LLMs with domain-specific representation models for single-cell omics data interpretation. We begin by focusing on genes as the fundamental unit of representation. Gene representations are initialized using functional descriptions, leveraging the strengths of mature language models such as LLaMA-2. By inputting single-cell gene-level expression data with prompts, we effectively model cellular representations based on the differential expression levels of genes across various species and cell types. In the experiments, we constructed developmental cells from humans and mice, specifically targeting cells that are challenging to annotate. We evaluated our methodology through basic tasks such as cell annotation and visualization analysis. The results demonstrate the efficacy of our approach compared to other methods using LLMs, highlighting significant improvements in accuracy and interoperability. Our hybrid approach enhances the representation of single-cell data and offers a robust framework for future research in cross-species genetic analysis.

Wentao Cui, Shoubo Li, Chen Fang et al.

Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital for efficient and scalable gene-disease association prediction. Graph-based learning models, which leverage node features and network relationships, are commonly employed for biomolecular predictions. However, existing methods often struggle to effectively integrate node features, heterogeneous structures, and semantic information. To address these challenges, we propose COmprehensive MEtapath-based heterogeneous graph Transformer(COMET) for predicting gene-disease associations. COMET integrates diverse datasets to construct comprehensive heterogeneous networks, initializing node features with BioGPT. We define seven Metapaths and utilize a transformer framework to aggregate Metapath instances, capturing global contexts and long-distance dependencies. Through intra- and inter-metapath aggregation using attention mechanisms, COMET fuses latent vectors from multiple Metapaths to enhance GDA prediction accuracy. Our method demonstrates superior robustness compared to state-of-the-art approaches. Ablation studies and visualizations validate COMET's effectiveness, providing valuable insights for advancing human health research.

Xiaohan Huang, Dongjie Wang, Zhiyuan Ning et al.

Tabular data optimization methods aim to automatically find an optimal feature transformation process that generates high-value features and improves the performance of downstream machine learning tasks. Current frameworks for automated feature transformation rely on iterative sequence generation tasks, optimizing decision strategies through performance feedback from downstream tasks. However, these approaches fail to effectively utilize historical decision-making experiences and overlook potential relationships among generated features, thus limiting the depth of knowledge extraction. Moreover, the granularity of the decision-making process lacks dynamic backtracking capabilities for individual features, leading to insufficient adaptability when encountering inefficient pathways, adversely affecting overall robustness and exploration efficiency. To address the limitations observed in current automatic feature engineering frameworks, we introduce a novel method that utilizes a feature-state transformation graph to effectively preserve the entire feature transformation journey, where each node represents a specific transformation state. During exploration, three cascading agents iteratively select nodes and idea mathematical operations to generate new transformation states. This strategy leverages the inherent properties of the graph structure, allowing for the preservation and reuse of valuable transformations. It also enables backtracking capabilities through graph pruning techniques, which can rectify inefficient transformation paths. To validate the efficacy and flexibility of our approach, we conducted comprehensive experiments and detailed case studies, demonstrating superior performance in diverse scenarios.

Zheng Fang, Qingqing Long, Guojie Song et al.

Spatial-temporal forecasting has attracted tremendous attention in a wide range of applications, and traffic flow prediction is a canonical and typical example. The complex and long-range spatial-temporal correlations of traffic flow bring it to a most intractable challenge. Existing works typically utilize shallow graph convolution networks (GNNs) and temporal extracting modules to model spatial and temporal dependencies respectively. However, the representation ability of such models is limited due to: (1) shallow GNNs are incapable to capture long-range spatial correlations, (2) only spatial connections are considered and a mass of semantic connections are ignored, which are of great importance for a comprehensive understanding of traffic networks. To this end, we propose Spatial-Temporal Graph Ordinary Differential Equation Networks (STGODE). Specifically, we capture spatial-temporal dynamics through a tensor-based ordinary differential equation (ODE), as a result, deeper networks can be constructed and spatial-temporal features are utilized synchronously. To understand the network more comprehensively, semantical adjacency matrix is considered in our model, and a well-design temporal dialated convolution structure is used to capture long term temporal dependencies. We evaluate our model on multiple real-world traffic datasets and superior performance is achieved over state-of-the-art baselines.

Feng Li, Bencheng Yan, Qingqing Long et al.

Cross features play an important role in click-through rate (CTR) prediction. Most of the existing methods adopt a DNN-based model to capture the cross features in an implicit manner. These implicit methods may lead to a sub-optimized performance due to the limitation in explicit semantic modeling. Although traditional statistical explicit semantic cross features can address the problem in these implicit methods, it still suffers from some challenges, including lack of generalization and expensive memory cost. Few works focus on tackling these challenges. In this paper, we take the first step in learning the explicit semantic cross features and propose Pre-trained Cross Feature learning Graph Neural Networks (PCF-GNN), a GNN based pre-trained model aiming at generating cross features in an explicit fashion. Extensive experiments are conducted on both public and industrial datasets, where PCF-GNN shows competence in both performance and memory-efficiency in various tasks.

Qingqing Long, Yilun Jin, Yi Wu et al.

Graph neural networks (GNNs) have achieved tremendous success in graph mining. However, the inability of GNNs to model substructures in graphs remains a significant drawback. Specifically, message-passing GNNs (MPGNNs), as the prevailing type of GNNs, have been theoretically shown unable to distinguish, detect or count many graph substructures. While efforts have been paid to complement the inability, existing works either rely on pre-defined substructure sets, thus being less flexible, or are lacking in theoretical insights. In this paper, we propose GSKN, a GNN model with a theoretically stronger ability to distinguish graph structures. Specifically, we design GSKN based on anonymous walks (AWs), flexible substructure units, and derive it upon feature mappings of graph kernels (GKs). We theoretically show that GSKN provably extends the 1-WL test, and hence the maximally powerful MPGNNs from both graph-level and node-level viewpoints. Correspondingly, various experiments are leveraged to evaluate GSKN, where GSKN outperforms a wide range of baselines, endorsing the analysis.

Junshan Wang, Ziyao Li, Qingqing Long et al.

Learning low-dimensional representations on graphs has proved to be effective in various downstream tasks. However, noises prevail in real-world networks, which compromise networks to a large extent in that edges in networks propagate noises through the whole network instead of only the node itself. While existing methods tend to focus on preserving structural properties, the robustness of the learned representations against noises is generally ignored. In this paper, we propose a novel framework to learn noise-free node representations and eliminate noises simultaneously. Since noises are often unknown on real graphs, we design two generators, namely a graph generator and a noise generator, to identify normal structures and noises in an unsupervised setting. On the one hand, the graph generator serves as a unified scheme to incorporate any useful graph prior knowledge to generate normal structures. We illustrate the generative process with community structures and power-law degree distributions as examples. On the other hand, the noise generator generates graph noises not only satisfying some fundamental properties but also in an adaptive way. Thus, real noises with arbitrary distributions can be handled successfully. Finally, in order to eliminate noises and obtain noise-free node representations, two generators need to be optimized jointly, and through maximum likelihood estimation, we equivalently convert the model into imposing different regularization constraints on the true graph and noises respectively. Our model is evaluated on both real-world and synthetic data. It outperforms other strong baselines for node classification and graph reconstruction tasks, demonstrating its ability to eliminate graph noises.

Qingqing Long, Yilun Jin, Guojie Song et al.

Graph Convolutional Networks (GCNs) achieved tremendous success by effectively gathering local features for nodes. However, commonly do GCNs focus more on node features but less on graph structures within the neighborhood, especially higher-order structural patterns. However, such local structural patterns are shown to be indicative of node properties in numerous fields. In addition, it is not just single patterns, but the distribution over all these patterns matter, because networks are complex and the neighborhood of each node consists of a mixture of various nodes and structural patterns. Correspondingly, in this paper, we propose Graph Structural-topic Neural Network, abbreviated GraphSTONE, a GCN model that utilizes topic models of graphs, such that the structural topics capture indicative graph structures broadly from a probabilistic aspect rather than merely a few structures. Specifically, we build topic models upon graphs using anonymous walks and Graph Anchor LDA, an LDA variant that selects significant structural patterns first, so as to alleviate the complexity and generate structural topics efficiently. In addition, we design multi-view GCNs to unify node features and structural topic features and utilize structural topics to guide the aggregation. We evaluate our model through both quantitative and qualitative experiments, where our model exhibits promising performance, high efficiency, and clear interpretability.