We have collected Graph Prompt Papers from recent years and sorted them by year, it can be used to build a knowledge base for efficient retrieval.
NOTE: Since they were collected and exported using a crawler, a few entries may be missing abstracts.
Other Paper List:
Graph Learning in the LLM Era: A Paper List
| Title | Year | Venue | Abstract |
|---|---|---|---|
| Boundary Prompting: Elastic Urban Region Representation via Graph-based Spatial Tokenization | 2025 | arXiv | Urban region representation is essential for various applications such as urban planning, resource allocation, and policy development. Traditional methods rely on fixed, predefined region boundaries, which fail to capture the dynamic and complex nature of real-world urban areas. In this paper, we propose the Boundary Prompting Urban Region Representation Framework (BPURF), a novel approach that allows for elastic urban region definitions. BPURF comprises two key components: (1) A spatial token dictionary, where urban entities are treated as tokens and integrated into a unified token graph, and (2) a region token set representation model which utilize token aggregation and a multi-channel model to embed token sets corresponding to region boundaries. Additionally, we propose fast token set extraction strategy to enable online token set extraction during training and prompting. This framework enables the definition of urban regions through boundary prompting, supporting varying region boundaries and adapting to different tasks. Extensive experiments demonstrate the effectiveness of BPURF in capturing the complex characteristics of urban regions. |
| Does Graph Prompt Work? A Data Operation Perspective with Theoretical Analysis. | 2025 | ICML 2025 | In recent years, graph prompting has emerged as a promising research direction, enabling the learning of additional tokens or subgraphs appended to the original graphs without requiring retraining of pre-trained graph models across various applications. This novel paradigm, shifting from the traditional pretraining and finetuning to pretraining and prompting has shown significant empirical success in simulating graph data operations, with applications ranging from recommendation systems to biological networks and graph transferring. However, despite its potential, the theoretical underpinnings of graph prompting remain underexplored, raising critical questions about its fundamental effectiveness. The lack of rigorous theoretical proof of why and how much it works is more like a dark cloud over the graph prompt area to go further. To fill this gap, this paper introduces a theoretical framework that rigorously analyzes graph prompting from a data operation perspective. Our contributions are threefold: First, we provide a formal guarantee theorem, demonstrating graph prompts capacity to approximate graph transformation operators, effectively linking upstream and downstream tasks. Second, we derive upper bounds on the error of these data operations by graph prompts for a single graph and extend this discussion to batches of graphs, which are common in graph model training. Third, we analyze the distribution of data operation errors, extending our theoretical findings from linear graph models (e.g., GCN) to non-linear graph models (e.g., GAT). Extensive experiments support our theoretical results and confirm the practical implications of these guarantees. |
| Urban Region Pre-training and Prompting: A Graph-based Approach | 2025 | KDD'2025 | Urban region representation is crucial for various urban downstream tasks. However, despite the proliferation of methods and their success, acquiring general urban region knowledge and adapting to different tasks remains challenging. Existing work pays limited attention to the fine-grained functional layout semantics in urban regions, limiting their ability to capture transferable knowledge across regions. Further, inadequate handling of the unique features and relationships required for different downstream tasks may also hinder effective task adaptation. In this paper, we propose a $\textbf{G}$raph-based $\textbf{U}$rban $\textbf{R}$egion $\textbf{P}$re-training and $\textbf{P}$rompting framework ( |
| PT4Rec: A Universal Prompt-tuning Framework for Graph Contrastive Learning-based Recommendations | 2025 | Machine Learning Journal'2025 | None |
| Adaptive Coordinators and Prompts on Heterogeneous Graphs for Cross-Domain Recommendations | 2025 | SIGIR 2025 | In the digital era, users typically interact with diverse items across multiple domains (e.g., e-commerce, streaming platforms, and social networks), generating intricate heterogeneous interaction graphs. Leveraging multi-domain data can improve recommendation systems by enriching user insights and mitigating data sparsity in individual domains. However, integrating such multi-domain knowledge for cross-domain recommendation remains challenging due to inherent disparities in user behavior and item characteristics and the risk of negative transfer, where irrelevant or conflicting information from the source domains adversely impacts the target domain's performance. To tackle these challenges, we propose HAGO, a novel framework with \textbf{H}eterogeneous \textbf{A}daptive \textbf{G}raph co\textbf{O}rdinators, which dynamically integrates multi-domain graphs into a cohesive structure. HAGO adaptively adjusts the connections between coordinators and multi-domain graph nodes to enhance beneficial inter-domain interactions while alleviating negative transfer. Furthermore, we introduce a universal multi-domain graph pre-training strategy alongside HAGO to collaboratively learn high-quality node representations across domains. Being compatible with various graph-based models and pre-training techniques, HAGO demonstrates broad applicability and effectiveness. Extensive experiments show that our framework outperforms state-of-the-art methods in cross-domain recommendation scenarios, underscoring its potential for real-world applications. The source code is available at https://github.com/zhy99426/HAGO. |
| ProG: A Graph Prompt Learning Benchmark | 2024 | None | Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG. |
| Graph Neural Prompting with Large Language Models | 2024 | AAAI'2024 | Large language models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs (KGs) to enhance language modeling via joint training and customized model architectures, applying this to LLMs is problematic owing to their large number of parameters and high computational cost. Therefore, how to enhance pre-trained LLMs using grounded knowledge, e.g., retrieval-augmented generation, remains an open question. In this work, we propose Graph Neural Prompting (GNP), a novel plug-and-play method to assist pre-trained LLMs in learning beneficial knowledge from KGs. GNP encompasses various designs, including a standard graph neural network encoder, a cross-modality pooling module, a domain projector, and a self-supervised link prediction objective. Extensive experiments on multiple datasets demonstrate the superiority of GNP on both commonsense and biomedical reasoning tasks across different LLM sizes and settings. Code is available at https://github.com/meettyj/GNP. |
| HGPROMPT: Bridging Homogeneous and Heterogeneous Graphs for Few-shot Prompt Learning | 2024 | AAAI'2024 | Graph neural networks (GNNs) and heterogeneous graph neural networks (HGNNs) are prominent techniques for homogeneous and heterogeneous graph representation learning, yet their performance in an end-to-end supervised framework greatly depends on the availability of task-specific supervision. To reduce the labeling cost, pre-training on self-supervised pretext tasks has become a popular paradigm,but there is often a gap between the pre-trained model and downstream tasks, stemming from the divergence in their objectives. To bridge the gap, prompt learning has risen as a promising direction especially in few-shot settings, without the need to fully fine-tune the pre-trained model. While there has been some early exploration of prompt-based learning on graphs, they primarily deal with homogeneous graphs, ignoring the heterogeneous graphs that are prevalent in downstream applications. In this paper, we propose HGPROMPT, a novel pre-training and prompting framework to unify not only pre-training and downstream tasks but also homogeneous and heterogeneous graphs via a dual-template design. Moreover, we propose dual-prompt in HGPROMPT to assist a downstream task in locating the most relevant prior to bridge the gaps caused by not only feature variations but also heterogeneity differences across tasks. Finally, we thoroughly evaluate and analyze HGPROMPT through extensive experiments on three public datasets. |
| A Unified Graph Selective Prompt Learning for Graph Neural Networks | 2024 | arXiv | In recent years, graph prompt learning/tuning has garnered increasing attention in adapting pre-trained models for graph representation learning. As a kind of universal graph prompt learning method, Graph Prompt Feature (GPF) has achieved remarkable success in adapting pre-trained models for Graph Neural Networks (GNNs). By fixing the parameters of a pre-trained GNN model, the aim of GPF is to modify the input graph data by adding some (learnable) prompt vectors into graph node features to better align with the downstream tasks on the smaller dataset. However, existing GPFs generally suffer from two main limitations. First, GPFs generally focus on node prompt learning which ignore the prompting for graph edges. Second, existing GPFs generally conduct the prompt learning on all nodes equally which fails to capture the importances of different nodes and may perform sensitively w.r.t noisy nodes in aligning with the downstream tasks. To address these issues, in this paper, we propose a new unified Graph Selective Prompt Feature learning (GSPF) for GNN fine-tuning. The proposed GSPF integrates the prompt learning on both graph node and edge together, which thus provides a unified prompt model for the graph data. Moreover, it conducts prompt learning selectively on nodes and edges by concentrating on the important nodes and edges for prompting which thus make our model be more reliable and compact. Experimental results on many benchmark datasets demonstrate the effectiveness and advantages of the proposed GSPF method. |
| DyGPrompt: Learning Feature and Time Prompts on Dynamic Graphs | 2024 | arXiv | Dynamic graphs capture evolving interactions between entities, such as in social networks, online learning platforms, and crowdsourcing projects. For dynamic graph modeling, dynamic graph neural networks (DGNNs) have emerged as a mainstream technique. However, they are generally pre-trained on the link prediction task, leaving a significant gap from the objectives of downstream tasks such as node classification. To bridge the gap, prompt-based learning has gained traction on graphs, but most existing efforts focus on static graphs, neglecting the evolution of dynamic graphs. In this paper, we propose DYGPROMPT, a novel pre-training and prompt learning framework for dynamic graph modeling. First, we design dual prompts to address the gap in both task objectives and temporal variations across pre-training and downstream tasks. Second, we recognize that node and time features mutually characterize each other, and propose dual condition-nets to model the evolving node-time patterns in downstream tasks. Finally, we thoroughly evaluate and analyze DYGPROMPT through extensive experiments on four public datasets. |
| Multi-domain Knowledge Graph Collaborative Pre-training and Prompt Tuning for Diverse Downstream Tasks | 2024 | arXiv | Knowledge graphs (KGs) provide reliable external knowledge for a wide variety of AI tasks in the form of structured triples. Knowledge graph pre-training (KGP) aims to pre-train neural networks on large-scale KGs and provide unified interfaces to enhance different downstream tasks, which is a key direction for KG management, maintenance, and applications. Existing works often focus on purely research questions in open domains, or they are not open source due to data security and privacy in real scenarios. Meanwhile, existing studies have not explored the training efficiency and transferability of KGP models in depth. To address these problems, We propose a framework MuDoK to achieve multi-domain collaborative pre-training and efficient prefix prompt tuning to serve diverse downstream tasks like recommendation and text understanding. Our design is a plug-and-play prompt learning approach that can be flexibly adapted to different downstream task backbones. In response to the lack of open-source benchmarks, we constructed a new multi-domain KGP benchmark called KPI with two large-scale KGs and six different sub-domain tasks to evaluate our method and open-sourced it for subsequent research. We evaluated our approach based on constructed KPI benchmarks using diverse backbone models in heterogeneous downstream tasks. The experimental results show that our framework brings significant performance gains, along with its generality, efficiency, and transferability. |
| Prompt Learning on Temporal Interaction Graphs | 2024 | arXiv | Temporal Interaction Graphs (TIGs) are widely utilized to represent real-world systems. To facilitate representation learning on TIGs, researchers have proposed a series of TIG models. However, these models are still facing two tough gaps between the pre-training and downstream predictions in their pre-train, predict'' training paradigm. First, the temporal discrepancy between the pre-training and inference data severely undermines the models' applicability in distant future predictions on the dynamically evolving data. Second, the semantic divergence between pretext and downstream tasks hinders their practical applications, as they struggle to align with their learning and prediction capabilities across application scenarios. Recently, the pre-train, prompt'' paradigm has emerged as a lightweight mechanism for model generalization. Applying this paradigm is a potential solution to solve the aforementioned challenges. However, the adaptation of this paradigm to TIGs is not straightforward. The application of prompting in static graph contexts falls short in temporal settings due to a lack of consideration for time-sensitive dynamics and a deficiency in expressive power. To address this issue, we introduce Temporal Interaction Graph Prompting (TIGPrompt), a versatile framework that seamlessly integrates with TIG models, bridging both the temporal and semantic gaps. In detail, we propose a temporal prompt generator to offer temporally-aware prompts for different tasks. These prompts stand out for their minimalistic design, relying solely on the tuning of the prompt generator with very little supervision data. To cater to varying computational resource demands, we propose an extended ``pre-train, prompt-based fine-tune'' paradigm, offering greater flexibility. Through extensive experiments, the TIGPrompt demonstrates the SOTA performance and remarkable efficiency advantages. |
| Prompt-Enhanced Spatio-Temporal Graph Transfer Learning | 2024 | arXiv | Spatio-temporal graph neural networks have proven efficacy in capturing complex dependencies for urban computing tasks such as forecasting and kriging. Yet, their performance is constrained by the reliance on extensive data for training on a specific task, thereby limiting their adaptability to new urban domains with varied task demands. Although transfer learning has been proposed to remedy this problem by leveraging knowledge across domains, the cross-task generalization still remains under-explored in spatio-temporal graph transfer learning due to the lack of a unified framework. To bridge the gap, we propose Spatio-Temporal Graph Prompting (STGP), a prompt-based framework capable of adapting to multi-diverse tasks in a data-scarce domain. Specifically, we first unify different tasks into a single template and introduce a task-agnostic network architecture that aligns with this template. This approach enables capturing dependencies shared across tasks. Furthermore, we employ learnable prompts to achieve domain and task transfer in a two-stage prompting pipeline, facilitating the prompts to effectively capture domain knowledge and task-specific properties. Our extensive experiments demonstrate that STGP outperforms state-of-the-art baselines in three tasks-forecasting, kriging, and extrapolation-achieving an improvement of up to 10.7%. |
| Subgraph-level Universal Prompt Tuning | 2024 | arXiv | In the evolving landscape of machine learning, the adaptation of pre-trained models through prompt tuning has become increasingly prominent. This trend is particularly observable in the graph domain, where diverse pre-training strategies present unique challenges in developing effective prompt-based tuning methods for graph neural networks. Previous approaches have been limited, focusing on specialized prompting functions tailored to models with edge prediction pre-training tasks. These methods, however, suffer from a lack of generalizability across different pre-training strategies. Recently, a simple prompt tuning method has been designed for any pre-training strategy, functioning within the input graph's feature space. This allows it to theoretically emulate any type of prompting function, thereby significantly increasing its versatility for a range of downstream applications. Nevertheless, the capacity of such simple prompts to fully grasp the complex contexts found in graphs remains an open question, necessitating further investigation. Addressing this challenge, our work introduces the Subgraph-level Universal Prompt Tuning (SUPT) approach, focusing on the detailed context within subgraphs. In SUPT, prompt features are assigned at the subgraph-level, preserving the method's universal capability. This requires extremely fewer tuning parameters than fine-tuning-based methods, outperforming them in 42 out of 45 full-shot scenario experiments with an average improvement of over 2.5%. In few-shot scenarios, it excels in 41 out of 45 experiments, achieving an average performance increase of more than 6.6%. |
| Text-Free Multi-domain Graph Pre-training: Toward Graph Foundation Models | 2024 | arXiv | Given the ubiquity of graph data, it is intriguing to ask: Is it possible to train a graph foundation model on a broad range of graph data across diverse domains? A major hurdle toward this goal lies in the fact that graphs from different domains often exhibit profoundly divergent characteristics. Although there have been some initial efforts in integrating multi-domain graphs for pre-training, they primarily rely on textual descriptions to align the graphs, limiting their application to text-attributed graphs. Moreover, different source domains may conflict or interfere with each other, and their relevance to the target domain can vary significantly. To address these issues, we propose MDGPT, a text free Multi-Domain Graph Pre-Training and adaptation framework designed to exploit multi-domain knowledge for graph learning. First, we propose a set of domain tokens to to align features across source domains for synergistic pre-training. Second, we propose a dual prompts, consisting of a unifying prompt and a mixing prompt, to further adapt the target domain with unified multi-domain knowledge and a tailored mixture of domain-specific knowledge. Finally, we conduct extensive experiments involving six public datasets to evaluate and analyze MDGPT, which outperforms prior art by up to 37.9%. |
| DDIPrompt: Drug-Drug Interaction Event Prediction based on Graph Prompt Learning | 2024 | CIKM'2024 | Drug combinations can cause adverse drug-drug interactions(DDIs). Identifying specific effects is crucial for developing safer therapies. Previous works on DDI event prediction have typically been limited to using labels of specific events as supervision, which renders them insufficient to address two significant challenges: (1) the bias caused by \textbf{highly imbalanced event distribution} where certain interaction types are vastly under-represented. (2) the \textbf{scarcity of labeled data for rare events}, a pervasive issue where rare yet potentially critical interactions are often overlooked or under-explored due to limited available data. In response, we offer ``DDIPrompt'', an innovative solution inspired by the recent advancements in graph prompt learning. Our framework aims to address these issues by leveraging the intrinsic knowledge from pre-trained models, which can be efficiently deployed with minimal downstream data. Specifically, to solve the first challenge, DDIPrompt features a hierarchical pre-training strategy to foster a generalized and comprehensive understanding of drug properties. It captures intra-molecular structures through augmented links based on structural proximity between drugs, further learns inter-molecular interactions emphasizing edge connections rather than concrete catagories. For the second challenge, we implement a prototype-enhanced prompting mechanism during inference. This mechanism, refined by few-shot examples from each category, effectively harnesses the rich pre-training knowledge to enhance prediction accuracy, particularly for these rare but crucial interactions. Extensive experiments on two benchmark datasets demonstrate DDIPrompt's SOTA performance, especially for those rare DDI events. |
| Protein Multimer Structure Prediction via PPI-guided Prompt Learning | 2024 | ICLR'2024 | Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure... |
| All in One and One for All: A Simple yet Effective Method towards Cross-domain Graph Pretraining | 2024 | KDD'2024 | Large Language Models (LLMs) have revolutionized the fields of computer vision (CV) and natural language processing (NLP). One of the most notable advancements of LLMs is that a single model is trained on vast and diverse datasets spanning multiple domains -- a paradigm we term All in One'. This methodology empowers LLMs with super generalization capabilities, facilitating an encompassing comprehension of varied data distributions. Leveraging these capabilities, a single LLM demonstrates remarkable versatility across a variety of domains -- a paradigm we term One for All'. However, applying this idea to the graph field remains a formidable challenge, with cross-domain pretraining often resulting in negative transfer. This issue is particularly important in few-shot learning scenarios, where the paucity of training data necessitates the incorporation of external knowledge sources. In response to this challenge, we propose a novel approach called Graph COordinators for PrEtraining (GCOPE), that harnesses the underlying commonalities across diverse graph datasets to enhance few-shot learning. Our novel methodology involves a unification framework that amalgamates disparate graph datasets during the pretraining phase to distill and transfer meaningful knowledge to target tasks. Extensive experiments across multiple graph datasets demonstrate the superior efficacy of our approach. By successfully leveraging the synergistic potential of multiple graph datasets for pretraining, our work stands as a pioneering contribution to the realm of graph foundational model. |
| Cross-Context Backdoor Attacks against Graph Prompt Learning | 2024 | KDD'2024 | Graph Prompt Learning (GPL) bridges significant disparities between pretraining and downstream applications to alleviate the knowledge transfer bottleneck in real-world graph learning. While GPL offers superior effectiveness in graph knowledge transfer and computational efficiency, the security risks posed by backdoor poisoning effects embedded in pretrained models remain largely unexplored. Our study provides a comprehensive analysis of GPL's vulnerability to backdoor attacks. We introduce \textit{CrossBA}, the first cross-context backdoor attack against GPL, which manipulates only the pretraining phase without requiring knowledge of downstream applications. Our investigation reveals both theoretically and empirically that tuning trigger graphs, combined with prompt transformations, can seamlessly transfer the backdoor threat from pretrained encoders to downstream applications. Through extensive experiments involving 3 representative GPL methods across 5 distinct cross-context scenarios and 5 benchmark datasets of node and graph classification tasks, we demonstrate that \textit{CrossBA} consistently achieves high attack success rates while preserving the functionality of downstream applications over clean input. We also explore potential countermeasures against \textit{CrossBA} and conclude that current defenses are insufficient to mitigate \textit{CrossBA}. Our study highlights the persistent backdoor threats to GPL systems, raising trustworthiness concerns in the practices of GPL techniques. |
| Pre-Training and Prompting for Few-Shot Node Classification on Text-Attributed Graphs | 2024 | KDD'2024 | The text-attributed graph (TAG) is one kind of important real-world graph-structured data with each node associated with raw texts. For TAGs, traditional few-shot node classification methods directly conduct training on the pre-processed node features and do not consider the raw texts. The performance is highly dependent on the choice of the feature pre-processing method. In this paper, we propose P2TAG, a framework designed for few-shot node classification on TAGs with graph pre-training and prompting. P2TAG first pre-trains the language model (LM) and graph neural network (GNN) on TAGs with self-supervised loss. To fully utilize the ability of language models, we adapt the masked language modeling objective for our framework. The pre-trained model is then used for the few-shot node classification with a mixed prompt method, which simultaneously considers both text and graph information. We conduct experiments on six real-world TAGs, including paper citation networks and product co-purchasing networks. Experimental results demonstrate that our proposed framework outperforms existing graph few-shot learning methods on these datasets with +18.98% ~ +35.98% improvements. |
| ProCom: A Few-shot Targeted Community Detection Algorithm | 2024 | KDD'2024 | Targeted community detection aims to distinguish a particular type of community in the network. This is an important task with a lot of real-world applications, e.g., identifying fraud groups in transaction networks. Traditional community detection methods fail to capture the specific features of the targeted community and detect all types of communities indiscriminately. Semi-supervised community detection algorithms, emerged as a feasible alternative, are inherently constrained by their limited adaptability and substantial reliance on a large amount of labeled data, which demands extensive domain knowledge and manual effort. In this paper, we address the aforementioned weaknesses in targeted community detection by focusing on few-shot scenarios. We propose ProCom, a novel framework that extends the ``pre-train, prompt'' paradigm, offering a low-resource, high-efficiency, and transferable solution. Within the framework, we devise a dual-level context-aware pre-training method that fosters a deep understanding of latent communities in the network, establishing a rich knowledge foundation for downstream task. In the prompt learning stage, we reformulate the targeted community detection task into pre-training objectives, allowing the extraction of specific knowledge relevant to the targeted community to facilitate effective and efficient inference. By leveraging both the general community knowledge acquired during pre-training and the specific insights gained from the prompt communities, ProCom exhibits remarkable adaptability across different datasets. We conduct extensive experiments on five benchmarks to evaluate the ProCom framework, demonstrating its SOTA performance under few-shot scenarios, strong efficiency, and transferability across diverse datasets. |
| ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs | 2024 | KDD'2024 | With the development of foundation models such as large language models, zero-shot transfer learning has become increasingly significant. This is highlighted by the generative capabilities of NLP models like GPT-4, and the retrieval-based approaches of CV models like CLIP, both of which effectively bridge the gap between seen and unseen data. In the realm of graph learning, the continuous emergence of new graphs and the challenges of human labeling also amplify the necessity for zero-shot transfer learning, driving the exploration of approaches that can generalize across diverse graph data without necessitating dataset-specific and label-specific fine-tuning. In this study, we extend such paradigms to zero-shot transferability in graphs by introducing ZeroG, a new framework tailored to enable cross-dataset generalization. Addressing the inherent challenges such as feature misalignment, mismatched label spaces, and negative transfer, we leverage a language model to encode both node attributes and class semantics, ensuring consistent feature dimensions across datasets. We also propose a prompt-based subgraph sampling module that enriches the semantic information and structure information of extracted subgraphs using prompting nodes and neighborhood aggregation, respectively. We further adopt a lightweight fine-tuning strategy that reduces the risk of overfitting and maintains the zero-shot learning efficacy of the language model. The results underscore the effectiveness of our model in achieving significant cross-dataset zero-shot transferability, opening pathways for the development of graph foundation models. Codes and data are available at https://github.com/NineAbyss/ZeroG. |
| GPT4Rec: Graph Prompt Tuning for Streaming Recommendation | 2024 | SIGIR'2024 | In the realm of personalized recommender systems, the challenge of adapting to evolving user preferences and the continuous influx of new users and items is paramount. Conventional models, typically reliant on a static training-test approach, struggle to keep pace with these dynamic demands. Streaming recommendation, particularly through continual graph learning, has emerged as a novel solution. However, existing methods in this area either rely on historical data replay, which is increasingly impractical due to stringent data privacy regulations; or are inability to effectively address the over-stability issue; or depend on model-isolation and expansion strategies. To tackle these difficulties, we present GPT4Rec, a Graph Prompt Tuning method for streaming Recommendation. Given the evolving user-item interaction graph, GPT4Rec first disentangles the graph patterns into multiple views. After isolating specific interaction patterns and relationships in different views, GPT4Rec utilizes lightweight graph prompts to efficiently guide the model across varying interaction patterns within the user-item graph. Firstly, node-level prompts are employed to instruct the model to adapt to changes in the attributes or properties of individual nodes within the graph. Secondly, structure-level prompts guide the model in adapting to broader patterns of connectivity and relationships within the graph. Finally, view-level prompts are innovatively designed to facilitate the aggregation of information from multiple disentangled views. These prompt designs allow GPT4Rec to synthesize a comprehensive understanding of the graph, ensuring that all vital aspects of the user-item interactions are considered and effectively integrated. Experiments on four diverse real-world datasets demonstrate the effectiveness and efficiency of our proposal. |
| Instruction-based Hypergraph Pretraining | 2024 | SIGIR'2024 | Pretraining has been widely explored to augment the adaptability of graph learning models to transfer knowledge from large datasets to a downstream task, such as link prediction or classification. However, the gap between training objectives and the discrepancy between data distributions in pretraining and downstream tasks hinders the transfer of the pretrained knowledge. Inspired by instruction-based prompts widely used in pretrained language models, we introduce instructions into graph pretraining. In this paper, we propose a novel pretraining framework named Instruction-based Hypergraph Pretraining. To overcome the discrepancy between pretraining and downstream tasks, text-based instructions are applied to provide explicit guidance on specific tasks for representation learning. Compared to learnable prompts, whose effectiveness depends on the quality and the diversity of training data, text-based instructions intrinsically encapsulate task information and support the model to generalize beyond the structure seen during pretraining. To capture high-order relations with task information in a context-aware manner, a novel prompting hypergraph convolution layer is devised to integrate instructions into information propagation in hypergraphs. Extensive experiments conducted on three public datasets verify the superiority of IHP in various scenarios. |
| Generalized Graph Prompt: Toward a Unification of Pre-Training and Downstream Tasks on Graphs | 2024 | TKDE'2024 | Graph neural networks have emerged as a powerful tool for graph representation learning, but their performance heavily relies on abundant task-specific supervision. To reduce labeling requirement, the "pre-train, prompt" paradigms have become increasingly common. However, existing study of prompting on graphs is limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-trained model in a task-specific manner. To further enhance GraphPrompt in these two stages, we extend it into GraphPrompt+ with two major enhancements. First, we generalize several popular graph pre-training tasks beyond simple link prediction to broaden the compatibility with our task template. Second, we propose a more generalized prompt design that incorporates a series of prompt vectors within every layer of the pre-trained graph encoder, in order to capitalize on the hierarchical information across different layers beyond just the readout layer. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt and GraphPrompt+. |
| MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning | 2024 | WSDM'2024 | Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often scarce and expensive to obtain, it is a great challenge for GNNs to generalize in the extensive molecular space. Recently, the training paradigm of "pre-train, fine-tune" has been leveraged to improve the generalization capabilities of GNNs. It uses self-supervised information to pre-train the GNN, and then performs fine-tuning to optimize the downstream task with just a few labels. However, pre-training does not always yield statistically significant improvement, especially for self-supervised learning with random structural masking. In fact, the molecular structure is characterized by motif subgraphs, which are frequently occurring and influence molecular properties. To leverage the task-related motifs, we propose a novel paradigm of "pre-train, prompt, fine-tune" for molecular representation learning, named molecule continuous prompt tuning (MolCPT). MolCPT defines a motif prompting function that uses the pre-trained model to project the standalone input into an expressive prompt. The prompt effectively augments the molecular graph with meaningful motifs in the continuous representation space; this provides more structural patterns to aid the downstream classifier in identifying molecular properties. Extensive experiments on several benchmark datasets show that MolCPT efficiently generalizes pre-trained GNNs for molecular property prediction, with or without a few fine-tuning steps. |
| Motif-Based Prompt Learning for Universal Cross-Domain Recommendation | 2024 | WSDM'2024 | Cross-Domain Recommendation (CDR) stands as a pivotal technology addressing issues of data sparsity and cold start by transferring general knowledge from the source to the target domain. However, existing CDR models suffer limitations in adaptability across various scenarios due to their inherent complexity. To tackle this challenge, recent advancements introduce universal CDR models that leverage shared embeddings to capture general knowledge across domains and transfer it through "Multi-task Learning" or "Pre-train, Fine-tune" paradigms. However, these models often overlook the broader structural topology that spans domains and fail to align training objectives, potentially leading to negative transfer. To address these issues, we propose a motif-based prompt learning framework, MOP, which introduces motif-based shared embeddings to encapsulate generalized domain knowledge, catering to both intra-domain and inter-domain CDR tasks. Specifically, we devise three typical motifs: butterfly, triangle, and random walk, and encode them through a Motif-based Encoder to obtain motif-based shared embeddings. Moreover, we train MOP under the "Pre-training & Prompt Tuning" paradigm. By unifying pre-training and recommendation tasks as a common motif-based similarity learning task and integrating adaptable prompt parameters to guide the model in downstream recommendation tasks, MOP excels in transferring domain knowledge effectively. Experimental results on four distinct CDR tasks demonstrate the effectiveness of MOP than the state-of-the-art models. |
| GraphControl: Adding Conditional Control to Universal Graph Pre-trained Models for Graph Domain Transfer Learning | 2024 | WWW'2024 | Graph-structured data is ubiquitous in the world which models complex relationships between objects, enabling various Web applications. Daily influxes of unlabeled graph data on the Web offer immense potential for these applications. Graph self-supervised algorithms have achieved significant success in acquiring generic knowledge from abundant unlabeled graph data. These pre-trained models can be applied to various downstream Web applications, saving training time and improving downstream (target) performance. However, different graphs, even across seemingly similar domains, can differ significantly in terms of attribute semantics, posing difficulties, if not infeasibility, for transferring the pre-trained models to downstream tasks. Concretely speaking, for example, the additional task-specific node information in downstream tasks (specificity) is usually deliberately omitted so that the pre-trained representation (transferability) can be leveraged. The trade-off as such is termed as "transferability-specificity dilemma" in this work. To address this challenge, we introduce an innovative deployment module coined as GraphControl, motivated by ControlNet, to realize better graph domain transfer learning. Specifically, by leveraging universal structural pre-trained models and GraphControl, we align the input space across various graphs and incorporate unique characteristics of target data as conditional inputs. These conditions will be progressively integrated into the model during fine-tuning or prompt tuning through ControlNet, facilitating personalized deployment. Extensive experiments show that our method significantly enhances the adaptability of pre-trained models on target attributed datasets, achieving 1.4-3x performance gain. Furthermore, it outperforms training-from-scratch methods on target data with a comparable margin and exhibits faster convergence. |
| GraphPro: Graph Pre-training and Prompt Learning for Recommendation | 2024 | WWW'2024 | GNN-based recommenders have excelled in modeling intricate user-item interactions through multi-hop message passing. However, existing methods often overlook the dynamic nature of evolving user-item interactions, which impedes the adaption to changing user preferences and distribution shifts in newly arriving data. Thus, their scalability and performances in real-world dynamic environments are limited. In this study, we propose GraphPro, a framework that incorporates parameter-efficient and dynamic graph pre-training with prompt learning. This novel combination empowers GNNs to effectively capture both long-term user preferences and short-term behavior dynamics, enabling the delivery of accurate and timely recommendations. Our GraphPro framework addresses the challenge of evolving user preferences by seamlessly integrating a temporal prompt mechanism and a graph-structural prompt learning mechanism into the pre-trained GNN model. The temporal prompt mechanism encodes time information on user-item interaction, allowing the model to naturally capture temporal context, while the graph-structural prompt learning mechanism enables the transfer of pre-trained knowledge to adapt to behavior dynamics without the need for continuous incremental training. We further bring in a dynamic evaluation setting for recommendation to mimic real-world dynamic scenarios and bridge the offline-online gap to a better level. Our extensive experiments including a large-scale industrial deployment showcases the lightweight plug-in scalability of our GraphPro when integrated with various state-of-the-art recommenders, emphasizing the advantages of GraphPro in terms of effectiveness, robustness and efficiency. The implementation details and source code of our GraphPro are available in the repository at https://github.com/HKUDS/GraphPro |
| HetGPT: Harnessing the Power of Prompt Tuning in Pre-Trained Heterogeneous Graph Neural Networks | 2024 | WWW'2024 | Graphs have emerged as a natural choice to represent and analyze the intricate patterns and rich information of the Web, enabling applications such as online page classification and social recommendation. The prevailing "pre-train, fine-tune" paradigm has been widely adopted in graph machine learning tasks, particularly in scenarios with limited labeled nodes. However, this approach often exhibits a misalignment between the training objectives of pretext tasks and those of downstream tasks. This gap can result in the "negative transfer" problem, wherein the knowledge gained from pre-training adversely affects performance in the downstream tasks. The surge in prompt-based learning within Natural Language Processing (NLP) suggests the potential of adapting a "pre-train, prompt" paradigm to graphs as an alternative. However, existing graph prompting techniques are tailored to homogeneous graphs, neglecting the inherent heterogeneity of Web graphs. To bridge this gap, we propose HetGPT, a general post-training prompting framework to improve the predictive performance of pre-trained heterogeneous graph neural networks (HGNNs). The key is the design of a novel prompting function that integrates a virtual class prompt and a heterogeneous feature prompt, with the aim to reformulate downstream tasks to mirror pretext tasks. Moreover, HetGPT introduces a multi-view neighborhood aggregation mechanism, capturing the complex neighborhood structure in heterogeneous graphs. Extensive experiments on three benchmark datasets demonstrate HetGPT's capability to enhance the performance of state-of-the-art HGNNs on semi-supervised node classification. |
| Inductive Graph Alignment Prompt: Bridging the Gap between Graph Pre-training and Inductive Fine-tuning From Spectral Perspective | 2024 | WWW'2024 | 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. |
| MultiGPrompt for Multi-Task Pre-Training and Prompting on Graphs | 2024 | WWW'2024 | Graphs can inherently model interconnected objects on the Web, thereby facilitating a series of Web applications, such as web analyzing and content recommendation. Recently, Graph Neural Networks (GNNs) have emerged as a mainstream technique for graph representation learning. However, their efficacy within an end-to-end supervised framework is significantly tied to the availabilityof task-specific labels. To mitigate labeling costs and enhance robustness in few-shot settings, pre-training on self-supervised tasks has emerged as a promising method, while prompting has been proposed to further narrow the objective gap between pretext and downstream tasks. Although there has been some initial exploration of prompt-based learning on graphs, they primarily leverage a single pretext task, resulting in a limited subset of general knowledge that could be learned from the pre-training data. Hence, in this paper, we propose MultiGPrompt, a novel multi-task pre-training and prompting framework to exploit multiple pretext tasks for more comprehensive pre-trained knowledge. First, in pre-training, we design a set of pretext tokens to synergize multiple pretext tasks. Second, we propose a dual-prompt mechanism consisting of composed and open prompts to leverage task-specific and global pre-training knowledge, to guide downstream tasks in few-shot settings. Finally, we conduct extensive experiments on six public datasets to evaluate and analyze MultiGPrompt. |
| Can Large Language Models Empower Molecular Property Prediction? | 2023 | arXiv | Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at \url{https://github.com/ChnQ/LLM4Mol}. |
| Deep Prompt Tuning for Graph Transformers | 2023 | arXiv | Graph transformers have gained popularity in various graph-based tasks by addressing challenges faced by traditional Graph Neural Networks. However, the quadratic complexity of self-attention operations and the extensive layering in graph transformer architectures present challenges when applying them to graph based prediction tasks. Fine-tuning, a common approach, is resource-intensive and requires storing multiple copies of large models. We propose a novel approach called deep graph prompt tuning as an alternative to fine-tuning for leveraging large graph transformer models in downstream graph based prediction tasks. Our method introduces trainable feature nodes to the graph and pre-pends task-specific tokens to the graph transformer, enhancing the model's expressive power. By freezing the pre-trained parameters and only updating the added tokens, our approach reduces the number of free parameters and eliminates the need for multiple model copies, making it suitable for small datasets and scalable to large graphs. Through extensive experiments on various-sized datasets, we demonstrate that deep graph prompt tuning achieves comparable or even superior performance to fine-tuning, despite utilizing significantly fewer task-specific parameters. Our contributions include the introduction of prompt tuning for graph transformers, its application to both graph transformers and message passing graph neural networks, improved efficiency and resource utilization, and compelling experimental results. This work brings attention to a promising approach to leverage pre-trained models in graph based prediction tasks and offers new opportunities for exploring and advancing graph representation learning. |
| Enhancing Graph Neural Networks with Structure-Based Prompt | 2023 | arXiv | Graph Neural Networks (GNNs) are powerful in learning semantics of graph data. Recently, a new paradigm "pre-train and prompt" has shown promising results in adapting GNNs to various tasks with less supervised data. The success of such paradigm can be attributed to the more consistent objectives of pre-training and task-oriented prompt tuning, where the pre-trained knowledge can be effectively transferred to downstream tasks. Most existing methods are based on the class prototype vector framework. However, in the few-shot scenarios, given few labeled data, class prototype vectors are difficult to be accurately constructed or learned. Meanwhile, the structure information of graph is usually exploited during pre-training for learning node representations, while neglected in the prompt tuning stage for learning more accurate prototype vectors. In addition, they generally ignore the impact of heterophilous neighborhoods on node representation and are not suitable for heterophilous graphs. To bridge these gaps, we propose a novel pre-training and structure prompt tuning framework for GNNs, namely PSP, which consistently exploits structure information in both pre-training and prompt tuning stages. In particular, PSP 1) employs a dual-view contrastive learning to align the latent semantic spaces of node attributes and graph structure, and 2) incorporates structure information in prompted graph to construct more accurate prototype vectors and elicit more pre-trained knowledge in prompt tuning. We conduct extensive experiments on node classification and graph classification tasks to evaluate the effectiveness of PSP. We show that PSP can lead to superior performance in few-shot scenarios on both homophilous and heterophilous graphs. The implemented code is available at https://github.com/gqq1210/PSP. |
| Knowledge Graph Prompting for Multi-Document Question Answering | 2023 | arXiv | The `pre-train, prompt, predict' paradigm of large language models (LLMs) has achieved remarkable success in open-domain question answering (OD-QA). However, few works explore this paradigm in the scenario of multi-document question answering (MD-QA), a task demanding a thorough understanding of the logical associations among the contents and structures of different documents. To fill this crucial gap, we propose a Knowledge Graph Prompting (KGP) method to formulate the right context in prompting LLMs for MD-QA, which consists of a graph construction module and a graph traversal module. For graph construction, we create a knowledge graph (KG) over multiple documents with nodes symbolizing passages or document structures (e.g., pages/tables), and edges denoting the semantic/lexical similarity between passages or intra-document structural relations. For graph traversal, we design an LLM-based graph traversal agent that navigates across nodes and gathers supporting passages assisting LLMs in MD-QA. The constructed graph serves as the global ruler that regulates the transitional space among passages and reduces retrieval latency. Concurrently, the graph traversal agent acts as a local navigator that gathers pertinent context to progressively approach the question and guarantee retrieval quality. Extensive experiments underscore the efficacy of KGP for MD-QA, signifying the potential of leveraging graphs in enhancing the prompt design for LLMs. Our code: https://github.com/YuWVandy/KG-LLM-MDQA. |
| Large Language Models as Topological Structure Enhancers for Text-Attributed Graphs | 2023 | arXiv | The latest advancements in large language models (LLMs) have revolutionized the field of natural language processing (NLP). Inspired by the success of LLMs in NLP tasks, some recent work has begun investigating the potential of applying LLMs in graph learning tasks. However, most of the existing work focuses on utilizing LLMs as powerful node feature augmenters, leaving employing LLMs to enhance graph topological structures an understudied problem. In this work, we explore how to leverage the information retrieval and text generation capabilities of LLMs to refine/enhance the topological structure of text-attributed graphs (TAGs) under the node classification setting. First, we propose using LLMs to help remove unreliable edges and add reliable ones in the TAG. Specifically, we first let the LLM output the semantic similarity between node attributes through delicate prompt designs, and then perform edge deletion and edge addition based on the similarity. Second, we propose using pseudo-labels generated by the LLM to improve graph topology, that is, we introduce the pseudo-label propagation as a regularization to guide the graph neural network (GNN) in learning proper edge weights. Finally, we incorporate the two aforementioned LLM-based methods for graph topological refinement into the process of GNN training, and perform extensive experiments on four real-world datasets. The experimental results demonstrate the effectiveness of LLM-based graph topology refinement (achieving a 0.15%--2.47% performance gain on public benchmarks). |
| MMGPL: Multimodal Medical Data Analysis with Graph Prompt Learning | 2023 | arXiv | Prompt learning has demonstrated impressive efficacy in the fine-tuning of multimodal large models to a wide range of downstream tasks. Nonetheless, applying existing prompt learning methods for the diagnosis of neurological disorder still suffers from two issues: (i) existing methods typically treat all patches equally, despite the fact that only a small number of patches in neuroimaging are relevant to the disease, and (ii) they ignore the structural information inherent in the brain connection network which is crucial for understanding and diagnosing neurological disorders. To tackle these issues, we introduce a novel prompt learning model by learning graph prompts during the fine-tuning process of multimodal large models for diagnosing neurological disorders. Specifically, we first leverage GPT-4 to obtain relevant disease concepts and compute semantic similarity between these concepts and all patches. Secondly, we reduce the weight of irrelevant patches according to the semantic similarity between each patch and disease-related concepts. Moreover, we construct a graph among tokens based on these concepts and employ a graph convolutional network layer to extract the structural information of the graph, which is used to prompt the pre-trained multimodal large models for diagnosing neurological disorders. Extensive experiments demonstrate that our method achieves superior performance for neurological disorder diagnosis compared with state-of-the-art methods and validated by clinicians. |
| Prompt Tuning for Multi-View Graph Contrastive Learning | 2023 | arXiv | Graphs have become an important modeling tool for web applications, and Graph Neural Networks (GNNs) have achieved great success in graph representation learning. However, the performance of traditional GNNs heavily relies on a large amount of supervision. Recently, pre-train, fine-tune'' has become the paradigm to address the issues of label dependency and poor generalization. However, the pre-training strategies vary for graphs with homophily and heterophily, and the objectives for various downstream tasks also differ. This leads to a gap between pretexts and downstream tasks, resulting in negative transfer'' and poor performance. Inspired by prompt learning in Natural Language Processing (NLP), many studies turn to bridge the gap and fully leverage the pre-trained model. However, existing methods for graph prompting are tailored to homophily, neglecting inherent heterophily on graphs. Meanwhile, most of them rely on the randomly initialized prompts, which negatively impact on the stability. Therefore, we propose Self-Prompt, a prompting framework for graphs based on the model and data itself. We first introduce asymmetric graph contrastive learning for pretext to address heterophily and align the objectives of pretext and downstream tasks. Then we reuse the component from pre-training phase as the self adapter and introduce self-prompts based on graph itself for task adaptation. Finally, we conduct extensive experiments on 11 benchmark datasets to demonstrate its superiority. We provide our codes at https://github.com/gongchenghua/Self-Pro. |
| Prompt Tuning on Graph-augmented Low-resource Text Classification | 2023 | arXiv | Text classification is a fundamental problem in information retrieval with many real-world applications, such as predicting the topics of online articles and the categories of e-commerce product descriptions. However, low-resource text classification, with no or few labeled samples, presents a serious concern for supervised learning. Meanwhile, many text data are inherently grounded on a network structure, such as a hyperlink/citation network for online articles, and a user-item purchase network for e-commerce products. These graph structures capture rich semantic relationships, which can potentially augment low-resource text classification. In this paper, we propose a novel model called Graph-Grounded Pre-training and Prompting (G2P2) to address low-resource text classification in a two-pronged approach. During pre-training, we propose three graph interaction-based contrastive strategies to jointly pre-train a graph-text model; during downstream classification, we explore handcrafted discrete prompts and continuous prompt tuning for the jointly pre-trained model to achieve zero- and few-shot classification, respectively. Moreover, we explore the possibility of employing continuous prompt tuning for zero-shot inference. Specifically, we aim to generalize continuous prompts to unseen classes while leveraging a set of base classes. To this end, we extend G2P2 into G2P2$^$, hinging on a new architecture of conditional prompt tuning. Extensive experiments on four real-world datasets demonstrate the strength of G2P2 in zero- and few-shot low-resource text classification tasks, and illustrate the advantage of G2P2$^$ in dealing with unseen classes. |
| Prompt-based Node Feature Extractor for Few-shot Learning on Text-Attributed Graphs | 2023 | arXiv | Text-attributed Graphs (TAGs) are commonly found in the real world, such as social networks and citation networks, and consist of nodes represented by textual descriptions. Currently, mainstream machine learning methods on TAGs involve a two-stage modeling approach: (1) unsupervised node feature extraction with pre-trained language models (PLMs); and (2) supervised learning using Graph Neural Networks (GNNs). However, we observe that these representations, which have undergone large-scale pre-training, do not significantly improve performance with a limited amount of training samples. The main issue is that existing methods have not effectively integrated information from the graph and downstream tasks simultaneously. In this paper, we propose a novel framework called G-Prompt, which combines a graph adapter and task-specific prompts to extract node features. First, G-Prompt introduces a learnable GNN layer (\emph{i.e.,} adaptor) at the end of PLMs, which is fine-tuned to better capture the masked tokens considering graph neighborhood information. After the adapter is trained, G-Prompt incorporates task-specific prompts to obtain \emph{interpretable} node representations for the downstream task. Our experiment results demonstrate that our proposed method outperforms current state-of-the-art (SOTA) methods on few-shot node classification. More importantly, in zero-shot settings, the G-Prompt embeddings can not only provide better task interpretability than vanilla PLMs but also achieve comparable performance with fully-supervised baselines. |
| Prompt-Based Zero- and Few-Shot Node Classification: A Multimodal Approach | 2023 | arXiv | Multimodal data empowers machine learning models to better understand the world from various perspectives. In this work, we study the combination of \emph{text and graph} modalities, a challenging but understudied combination which is prevalent across multiple settings including citation networks, social media, and the web. We focus on the popular task of node classification using limited labels; in particular, under the zero- and few-shot scenarios. In contrast to the standard pipeline which feeds standard precomputed (e.g., bag-of-words) text features into a graph neural network, we propose \textbf{T}ext-\textbf{A}nd-\textbf{G}raph (TAG) learning, a more deeply multimodal approach that integrates the raw texts and graph topology into the model design, and can effectively learn from limited supervised signals without any meta-learning procedure. TAG is a two-stage model with (1) a prompt- and graph-based module which generates prior logits that can be directly used for zero-shot node classification, and (2) a trainable module that further calibrates these prior logits in a few-shot manner. Experiments on two node classification datasets show that TAG outperforms all the baselines by a large margin in both zero- and few-shot settings. |
| SGL-PT: A Strong Graph Learner with Graph Prompt Tuning | 2023 | arXiv | Recently, much exertion has been paid to design graph self-supervised methods to obtain generalized pre-trained models, and adapt pre-trained models onto downstream tasks through fine-tuning. However, there exists an inherent gap between pretext and downstream graph tasks, which insufficiently exerts the ability of pre-trained models and even leads to negative transfer. Meanwhile, prompt tuning has seen emerging success in natural language processing by aligning pre-training and fine-tuning with consistent training objectives. In this paper, we identify the challenges for graph prompt tuning: The first is the lack of a strong and universal pre-training task across sundry pre-training methods in graph domain. The second challenge lies in the difficulty of designing a consistent training objective for both pre-training and downstream tasks. To overcome above obstacles, we propose a novel framework named SGL-PT which follows the learning strategy ``Pre-train, Prompt, and Predict''. Specifically, we raise a strong and universal pre-training task coined as SGL that acquires the complementary merits of generative and contrastive self-supervised graph learning. And aiming for graph classification task, we unify pre-training and fine-tuning by designing a novel verbalizer-free prompting function, which reformulates the downstream task in a similar format as pretext task. Empirical results show that our method surpasses other baselines under unsupervised setting, and our prompt tuning method can greatly facilitate models on biological datasets over fine-tuning methods. |
| SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design | 2023 | arXiv | Predicting synergistic drug combinations can help accelerate discovery of cancer treatments, particularly therapies personalized to a patient's specific tumor via biopsied cells. In this paper, we propose a novel setting and models for in-context drug synergy learning. We are given a small "personalized dataset" of 10-20 drug synergy relationships in the context of specific cancer cell targets. Our goal is to predict additional drug synergy relationships in that context. Inspired by recent work that pre-trains a GPT language model (LM) to "in-context learn" common function classes, we devise novel pre-training schemes that enable a GPT model to in-context learn "drug synergy functions". Our model -- which does not use any textual corpora, molecular fingerprints, protein interaction or any other domain-specific knowledge -- is able to achieve competitive results. We further integrate our in-context approach with a genetic algorithm to optimize model prompts and select synergy candidates to test after conducting a patient biopsy. Finally, we explore a novel task of inverse drug design which can potentially enable the design of drugs that synergize specifically to target a given patient's "personalized dataset". Our findings can potentially have an important impact on precision cancer medicine, and also raise intriguing questions on non-textual pre-training for LMs. |
| ULTRA-DP:Unifying Graph Pre-training with Multi-task Graph Dual Prompt | 2023 | arXiv | Recent research has demonstrated the efficacy of pre-training graph neural networks (GNNs) to capture the transferable graph semantics and enhance the performance of various downstream tasks. However, the semantic knowledge learned from pretext tasks might be unrelated to the downstream task, leading to a semantic gap that limits the application of graph pre-training. To reduce this gap, traditional approaches propose hybrid pre-training to combine various pretext tasks together in a multi-task learning fashion and learn multi-grained knowledge, which, however, cannot distinguish tasks and results in some transferable task-specific knowledge distortion by each other. Moreover, most GNNs cannot distinguish nodes located in different parts of the graph, making them fail to learn position-specific knowledge and lead to suboptimal performance. In this work, inspired by the prompt-based tuning in natural language processing, we propose a unified framework for graph hybrid pre-training which injects the task identification and position identification into GNNs through a prompt mechanism, namely multi-task graph dual prompt (ULTRA-DP). Based on this framework, we propose a prompt-based transferability test to find the most relevant pretext task in order to reduce the semantic gap. To implement the hybrid pre-training tasks, beyond the classical edge prediction task (node-node level), we further propose a novel pre-training paradigm based on a group of |
| Which Modality should I use - Text, Motif, or Image? Understanding Graphs with Large Language Models | 2023 | arXiv | Our research integrates graph data with Large Language Models (LLMs), which, despite their advancements in various fields using large text corpora, face limitations in encoding entire graphs due to context size constraints. This paper introduces a new approach to encoding a graph with diverse modalities, such as text, image, and motif, coupled with prompts to approximate a graph's global connectivity, thereby enhancing LLMs' efficiency in processing complex graph structures. The study also presents GraphTMI, a novel benchmark for evaluating LLMs in graph structure analysis, focusing on homophily, motif presence, and graph difficulty. Key findings indicate that the image modality, especially with vision-language models like GPT-4V, is superior to text in balancing token limits and preserving essential information and outperforms prior graph neural net (GNN) encoders. Furthermore, the research assesses how various factors affect the performance of each encoding modality and outlines the existing challenges and potential future developments for LLMs in graph understanding and reasoning tasks. All data will be publicly available upon acceptance. |
| Prompt-and-Align: Prompt-Based Social Alignment for Few-Shot Fake News Detection | 2023 | CIKM'2023 | Despite considerable advances in automated fake news detection, due to the timely nature of news, it remains a critical open question how to effectively predict the veracity of news articles based on limited fact-checks. Existing approaches typically follow a "Train-from-Scratch" paradigm, which is fundamentally bounded by the availability of large-scale annotated data. While expressive pre-trained language models (PLMs) have been adapted in a "Pre-Train-and-Fine-Tune" manner, the inconsistency between pre-training and downstream objectives also requires costly task-specific supervision. In this paper, we propose "Prompt-and-Align" (P&A), a novel prompt-based paradigm for few-shot fake news detection that jointly leverages the pre-trained knowledge in PLMs and the social context topology. Our approach mitigates label scarcity by wrapping the news article in a task-related textual prompt, which is then processed by the PLM to directly elicit task-specific knowledge. To supplement the PLM with social context without inducing additional training overheads, motivated by empirical observation on user veracity consistency (i.e., social users tend to consume news of the same veracity type), we further construct a news proximity graph among news articles to capture the veracity-consistent signals in shared readerships, and align the prompting predictions along the graph edges in a confidence-informed manner. Extensive experiments on three real-world benchmarks demonstrate that P&A sets new states-of-the-art for few-shot fake news detection performance by significant margins. |
| Voucher Abuse Detection with Prompt-based Fine-tuning on Graph Neural Networks | 2023 | CIKM'2023 | Voucher abuse detection is an important anomaly detection problem in E-commerce. While many GNN-based solutions have emerged, the supervised paradigm depends on a large quantity of labeled data. A popular alternative is to adopt self-supervised pre-training using label-free data, and further fine-tune on a downstream task with limited labels. Nevertheless, the "pre-train, fine-tune" paradigm is often plagued by the objective gap between pre-training and downstream tasks. Hence, we propose VPGNN, a prompt-based fine-tuning framework on GNNs for voucher abuse detection. We design a novel graph prompting function to reformulate the downstream task into a similar template as the pretext task in pre-training, thereby narrowing the objective gap. Extensive experiments on both proprietary and public datasets demonstrate the strength of VPGNN in both few-shot and semi-supervised scenarios. Moreover, an online deployment of VPGNN in a production environment shows a 23.4% improvement over two existing deployed models. |
| Deep Graph Reprogramming | 2023 | CVPR'2023 | None |
| MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter | 2023 | EMNLP'2023 | Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA. |
| ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction | 2023 | EMNLP'2023 | Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited by insufficient training data and their inability to utilize textual information, undermining their applicability in real-world applications. In this work, we propose ReLM, a novel framework that leverages the chemical knowledge encoded in language models (LMs) to assist GNNs, thereby enhancing the accuracy of real-world chemical reaction predictions. To further enhance the model's robustness and interpretability, we incorporate the confidence score strategy, enabling the LMs to self-assess the reliability of their predictions. Our experimental results demonstrate that ReLM improves the performance of state-of-the-art GNN-based methods across various chemical reaction datasets, especially in out-of-distribution settings. Codes are available at https://github.com/syr-cn/ReLM. |
| A Data-centric Framework to Endow Graph Neural Networks with Out-Of-Distribution Detection Ability | 2023 | KDD'2023 | None |
| All in One: Multi-Task Prompting for Graph Neural Networks | 2023 | KDD'2023 | Recently, ''pre-training and fine-tuning'' has been adopted as a standard workflow for many graph tasks since it can take general graph knowledge to relieve the lack of graph annotations from each application. However, graph tasks with node level, edge level, and graph level are far diversified, making the pre-training pretext often incompatible with these multiple tasks. This gap may even cause a ''negative transfer'' to the specific application, leading to poor results. Inspired by the prompt learning in natural language processing (NLP), which has presented significant effectiveness in leveraging prior knowledge for various NLP tasks, we study the prompting topic for graphs with the motivation of filling the gap between pre-trained models and various graph tasks. In this paper, we propose a novel multi-task prompting method for graph models. Specifically, we first unify the format of graph prompts and language prompts with the prompt token, token structure, and inserting pattern. In this way, the prompting idea from NLP can be seamlessly introduced to the graph area. Then, to further narrow the gap between various graph tasks and state-of-the-art pre-training strategies, we further study the task space of various graph applications and reformulate downstream problems to the graph-level task. Afterward, we introduce meta-learning to efficiently learn a better initialization for the multi-task prompt of graphs so that our prompting framework can be more reliable and general for different tasks. We conduct extensive experiments, results from which demonstrate the superiority of our method. |
| GraphGLOW: Universal and Generalizable Structure Learning for Graph Neural Networks | 2023 | KDD'2023 | Graph structure learning is a well-established problem that aims at optimizing graph structures adaptive to specific graph datasets to help message passing neural networks (i.e., GNNs) to yield effective and robust node embeddings. However, the common limitation of existing models lies in the underlying \textit{closed-world assumption}: the testing graph is the same as the training graph. This premise requires independently training the structure learning model from scratch for each graph dataset, which leads to prohibitive computation costs and potential risks for serious over-fitting. To mitigate these issues, this paper explores a new direction that moves forward to learn a universal structure learning model that can generalize across graph datasets in an open world. We first introduce the mathematical definition of this novel problem setting, and describe the model formulation from a probabilistic data-generative aspect. Then we devise a general framework that coordinates a single graph-shared structure learner and multiple graph-specific GNNs to capture the generalizable patterns of optimal message-passing topology across datasets. The well-trained structure learner can directly produce adaptive structures for unseen target graphs without any fine-tuning. Across diverse datasets and various challenging cross-graph generalization protocols, our experiments show that even without training on target graphs, the proposed model i) significantly outperforms expressive GNNs trained on input (non-optimized) topology, and ii) surprisingly performs on par with state-of-the-art models that independently optimize adaptive structures for specific target graphs, with notably orders-of-magnitude acceleration for training on the target graph. |
| Virtual Node Tuning for Few-shot Node Classification | 2023 | KDD'2023 | Few-shot Node Classification (FSNC) is a challenge in graph representation learning where only a few labeled nodes per class are available for training. To tackle this issue, meta-learning has been proposed to transfer structural knowledge from base classes with abundant labels to target novel classes. However, existing solutions become ineffective or inapplicable when base classes have no or limited labeled nodes. To address this challenge, we propose an innovative method dubbed Virtual Node Tuning (VNT). Our approach utilizes a pretrained graph transformer as the encoder and injects virtual nodes as soft prompts in the embedding space, which can be optimized with few-shot labels in novel classes to modulate node embeddings for each specific FSNC task. A unique feature of VNT is that, by incorporating a Graph-based Pseudo Prompt Evolution (GPPE) module, VNT-GPPE can handle scenarios with sparse labels in base classes. Experimental results on four datasets demonstrate the superiority of the proposed approach in addressing FSNC with unlabeled or sparsely labeled base classes, outperforming existing state-of-the-art methods and even fully supervised baselines. |
| An Empirical Study Towards Prompt-Tuning for Graph Contrastive Pre-Training in Recommendations | 2023 | NeurIPS'2023 | Graph contrastive learning (GCL) has emerged as a potent technology for numerous graph learning tasks. It has been successfully applied to real-world recommender systems, where the contrastive loss... |
| GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning | 2023 | NeurIPS'2023 | Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for tasks, this study investigates the feasibility of employing natural language instructions to accomplish molecule-related tasks in a zero-shot setting. We discover that existing molecule-text models perform poorly in this setting due to inadequate treatment of instructions and limited capacity for graphs. To overcome these issues, we propose GIMLET, which unifies language models for both graph and text data. By adopting generalized position embedding, our model is extended to encode both graph structures and instruction text without additional graph encoding modules. GIMLET also decouples encoding of the graph from tasks instructions in the attention mechanism, enhancing the generalization of graph features across novel tasks. We construct a dataset consisting of more than two thousand molecule tasks with corresponding instructions derived from task descriptions. We pretrain GIMLET on the molecule tasks along with instructions, enabling the model to transfer effectively to a broad range of tasks. Experimental results demonstrate that GIMLET significantly outperforms molecule-text baselines in instruction-based zero-shot learning, even achieving closed results to supervised GNN models on tasks such as toxcast and muv. |
| GraphAdapter: Tuning Vision-Language Models With Dual Knowledge Graph | 2023 | NeurIPS'2023 | Adapter-style efficient transfer learning (ETL) has shown excellent performance in the tuning of vision-language models (VLMs) under the low-data regime, where only a few additional parameters are introduced to excavate the task-specific knowledge based on the general and powerful representation of VLMs. However, most adapter-style works face two limitations: (i) modeling task-specific knowledge with a single modality only; and (ii) overlooking the exploitation of the inter-class relationships in downstream tasks, thereby leading to sub-optimal solutions. To mitigate that, we propose an effective adapter-style tuning strategy, dubbed GraphAdapter, which performs the textual adapter by explicitly modeling the dual-modality structure knowledge (i.e., the correlation of different semantics/classes in textual and visual modalities) with a dual knowledge graph. In particular, the dual knowledge graph is established with two sub-graphs, i.e., a textual knowledge sub-graph, and a visual knowledge sub-graph, where the nodes and edges represent the semantics/classes and their correlations in two modalities, respectively. This enables the textual feature of each prompt to leverage the task-specific structure knowledge from both textual and visual modalities, yielding a more effective classifier for downstream tasks. Extensive experimental results on 11 benchmark datasets reveal that our GraphAdapter significantly outperforms previous adapter-based methods. The code will be released at https://github.com/lixinustc/GraphAdapter |
| PRODIGY: Enabling In-context Learning Over Graphs | 2023 | NeurIPS'2023 | In-context learning is the ability of a pretrained model to adapt to novel and diverse downstream tasks by conditioning on prompt examples, without optimizing any parameters. While large language models have demonstrated this ability, how in-context learning could be performed over graphs is unexplored. In this paper, we develop \textbf{Pr}etraining \textbf{O}ver \textbf{D}iverse \textbf{I}n-Context \textbf{G}raph S\textbf{y}stems (PRODIGY), the first pretraining framework that enables in-context learning over graphs. The key idea of our framework is to formulate in-context learning over graphs with a novel \emph{prompt graph} representation, which connects prompt examples and queries. We then propose a graph neural network architecture over the prompt graph and a corresponding family of in-context pretraining objectives. With PRODIGY, the pretrained model can directly perform novel downstream classification tasks on unseen graphs via in-context learning. We provide empirical evidence of the effectiveness of our framework by showcasing its strong in-context learning performance on tasks involving citation networks and knowledge graphs. Our approach outperforms the in-context learning accuracy of contrastive pretraining baselines with hard-coded adaptation by 18% on average across all setups. Moreover, it also outperforms standard finetuning with limited data by 33% on average with in-context learning. |
| Universal Prompt Tuning for Graph Neural Networks | 2023 | NeurIPS'2023 | In recent years, prompt tuning has sparked a research surge in adapting pre-trained models. Unlike the unified pre-training strategy employed in the language field, the graph field exhibits diverse pre-training strategies, posing challenges in designing appropriate prompt-based tuning methods for graph neural networks. While some pioneering work has devised specialized prompting functions for models that employ edge prediction as their pre-training tasks, these methods are limited to specific pre-trained GNN models and lack broader applicability. In this paper, we introduce a universal prompt-based tuning method called Graph Prompt Feature (GPF) for pre-trained GNN models under any pre-training strategy. GPF operates on the input graph's feature space and can theoretically achieve an equivalent effect to any form of prompting function. Consequently, we no longer need to illustrate the prompting function corresponding to each pre-training strategy explicitly. Instead, we employ GPF to obtain the prompted graph for the downstream task in an adaptive manner. We provide rigorous derivations to demonstrate the universality of GPF and make guarantee of its effectiveness. The experimental results under various pre-training strategies indicate that our method performs better than fine-tuning, with an average improvement of about 1.4% in full-shot scenarios and about 3.2% in few-shot scenarios. Moreover, our method significantly outperforms existing specialized prompt-based tuning methods when applied to models utilizing the pre-training strategy they specialize in. These numerous advantages position our method as a compelling alternative to fine-tuning for downstream adaptations. |
| Augmenting Low-Resource Text Classification with Graph-Grounded Pre-training and Prompting | 2023 | SIGIR'2023 | Text classification is a fundamental problem in information retrieval with many real-world applications, such as predicting the topics of online articles and the categories of e-commerce product descriptions. However, low-resource text classification, with few or no labeled samples, poses a serious concern for supervised learning. Meanwhile, many text data are inherently grounded on a network structure, such as a hyperlink/citation network for online articles, and a user-item purchase network for e-commerce products. These graph structures capture rich semantic relationships, which can potentially augment low-resource text classification. In this paper, we propose a novel model called Graph-Grounded Pre-training and Prompting (G2P2) to address low-resource text classification in a two-pronged approach. During pre-training, we propose three graph interaction-based contrastive strategies to jointly pre-train a graph-text model; during downstream classification, we explore prompting for the jointly pre-trained model to achieve low-resource classification. Extensive experiments on four real-world datasets demonstrate the strength of G2P2 in zero- and few-shot low-resource text classification tasks. |
| Contrastive Graph Prompt-tuning for Cross-domain Recommendation | 2023 | TOIS'2023 | Recommender systems are frequently challenged by the data sparsity problem. One approach to mitigate this issue is through cross-domain recommendation techniques. In a cross-domain context, sharing knowledge between domains can enhance the effectiveness in the target domain. Recent cross-domain methods have employed a pre-training approach, but we argue that these methods often result in suboptimal fine-tuning, especially with large neural models. Modern language models utilize prompts for efficient model tuning. Such prompts act as a tunable latent vector, allowing for the freezing of the main model parameters. In our research, we introduce the Personalised Graph Prompt-based Recommendation (PGPRec) framework. This leverages the advantages of prompt-tuning. Within this framework, we formulate personalized graph prompts item-wise, rooted in items that a user has previously engaged with. Specifically, we employ Contrastive Learning (CL) to produce pre-trained embeddings that offer greater generalizability in the pre-training phase, ensuring robust training during the tuning phase. Our evaluation of PGPRec in cross-domain scenarios involves comprehensive testing with the top-k recommendation tasks and a cold-start analysis. Our empirical findings, based on four Amazon Review datasets, reveal that the PGPRec framework can decrease the tuned parameters by as much as 74%, maintaining competitive performance. Remarkably, there's an 11.41% enhancement in performance against the leading baseline in cold-start situations. |
| GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks | 2023 | WWW'2023 | Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks (GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily relies on a large amount of task-specific supervision. To reduce labeling requirement, the “pre-train, fine-tune” and “pre-train, prompt” paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-trained model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt. |
| Structure Pretraining and Prompt Tuning for Knowledge Graph Transfer | 2023 | WWW'2023 | Knowledge graphs (KG) are essential background knowledge providers in many tasks. When designing models for KG-related tasks, one of the key tasks is to devise the Knowledge Representation and Fusion (KRF) module that learns the representation of elements from KGs and fuses them with task representations. While due to the difference of KGs and perspectives to be considered during fusion across tasks, duplicate and ad hoc KRF modules design are conducted among tasks. In this paper, we propose a novel knowledge graph pretraining model KGTransformer that could serve as a uniform KRF module in diverse KG-related tasks. We pretrain KGTransformer with three self-supervised tasks with sampled sub-graphs as input. For utilization, we propose a general prompt-tuning mechanism regarding task data as a triple prompt to allow flexible interactions between task KGs and task data. We evaluate pretrained KGTransformer on three tasks, triple classification, zero-shot image classification, and question answering. KGTransformer consistently achieves better results than specifically designed task models. Through experiments, we justify that the pretrained KGTransformer could be used off the shelf as a general and effective KRF module across KG-related tasks. The code and datasets are available at https://github.com/zjukg/KGTransformer. |
| GPPT: Graph Pre-training and Prompt Tuning to Generalize Graph Neural Networks | 2022 | KDD'2022 | Despite the promising representation learning of graph neural networks (GNNs), the supervised training of GNNs notoriously requires large amounts of labeled data from each application. An effective solution is to apply the transfer learning in graph: using easily accessible information to pre-train GNNs, and fine-tuning them to optimize the downstream task with only a few labels. Recently, many efforts have been paid to design the self-supervised pretext tasks, and encode the universal graph knowledge among the various applications. However, they rarely notice the inherent training objective gap between the pretext and downstream tasks. This significant gap often requires costly fine-tuning for adapting the pre-trained model to downstream problem, which prevents the efficient elicitation of pre-trained knowledge and then results in poor results. Even worse, the naive pre-training strategy usually deteriorates the downstream task, and damages the reliability of transfer learning in graph data. To bridge the task gap, we propose a novel transfer learning paradigm to generalize GNNs, namely graph pre-training and prompt tuning (GPPT). Specifically, we first adopt the masked edge prediction, the most simplest and popular pretext task, to pre-train GNNs. Based on the pre-trained model, we propose the graph prompting function to modify the standalone node into a token pair, and reformulate the downstream node classification looking the same as edge prediction. The token pair is consisted of candidate label class and node entity. Therefore, the pre-trained GNNs could be applied without tedious fine-tuning to evaluate the linking probability of token pair, and produce the node classification decision. The extensive experiments on eight benchmark datasets demonstrate the superiority of GPPT, delivering an average improvement of 4.29% in few-shot graph analysis and accelerating the model convergence up to 4.32X. The code is available in: https://github.com/MingChen-Sun/GPPT. |