Graph Prompting for Graph Learning Models: Recent Advances and Future Directions

Graph learning models have demonstrated great prowess in learning expressive representations from large-scale graph data in a wide variety of real-world scenarios. As a prevalent strategy for training powerful graph learning models, the "pre-training, adaptation" scheme first pre-trains graph learning models on unlabeled graph data in a self-supervised manner and then adapts them to specific downstream tasks. During the adaptation phase, graph prompting emerges as a promising approach that learns trainable prompts while keeping the pre-trained graph learning models unchanged. In this paper, we present a systematic review of recent advancements in graph prompting. First, we introduce representative graph pre-training methods that serve as the foundation step of graph prompting. Next, we review mainstream techniques in graph prompting and elaborate on how they design learnable prompts for graph prompting. Furthermore, we summarize the real-world applications of graph prompting from different domains. Finally, we discuss several open challenges in existing studies with promising future directions in this field.

Scalable Graph Generative Modeling via Substructure Sequences

Graph neural networks (GNNs) has been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental limitations -- including constrained expressiveness, over-smoothing, over-squashing, and limited capacity to model long-range dependencies. These issues hinder scalability: increasing data size or model size often fails to yield improved performance, limiting the viability of GNNs as backbones for graph foundation models. In this work, we explore pathways beyond message-passing and introduce Generative Graph Pattern Machine (G$^2$PM), a generative Transformer pre-training framework for graphs. G$^2$PM represents graph instances (nodes, edges, or entire graphs) as sequences of substructures, and employs generative pre-training over the sequences to learn generalizable, transferable representations. Empirically, G$^2$PM demonstrates strong scalability: on the ogbn-arxiv benchmark, it continues to improve with model sizes up to 60M parameters, outperforming prior generative approaches that plateau at significantly smaller scales (e.g., 3M). In addition, we systematically analyze the model design space, highlighting key architectural choices that contribute to its scalability and generalization. Across diverse tasks -- including node classification, graph classification, and transfer learning -- G$^2$PM consistently outperforms strong baselines, establishing a compelling foundation for scalable graph learning. The code and dataset are available at https://github.com/Zehong-Wang/G2PM.

AutoData: A Multi-Agent System for Open Web Data Collection

The exponential growth of data-driven systems and AI technologies has intensified the demand for high-quality web-sourced datasets. While existing datasets have proven valuable, conventional web data collection approaches face significant limitations in terms of human effort and scalability. Current data-collecting solutions fall into two categories: wrapper-based methods that struggle with adaptability and reproducibility, and large language model (LLM)-based approaches that incur substantial computational and financial costs. To address these challenges, we propose AutoData, a novel multi-agent system for Automated web Data collection, that requires minimal human intervention, i.e., only necessitating a natural language instruction specifying the desired dataset. In addition, AutoData is designed with a robust multi-agent architecture, featuring a novel oriented message hypergraph coordinated by a central task manager, to efficiently organize agents across research and development squads. Besides, we introduce a novel hypergraph cache system to advance the multi-agent collaboration process that enables efficient automated data collection and mitigates the token cost issues prevalent in existing LLM-based systems. Moreover, we introduce Instruct2DS, a new benchmark dataset supporting live data collection from web sources across three domains: academic, finance, and sports. Comprehensive evaluations over Instruct2DS and three existing benchmark datasets demonstrate AutoData's superior performance compared to baseline methods. Case studies on challenging tasks such as picture book collection and paper extraction from surveys further validate its applicability. Our source code and dataset are available at https://github.com/GraphResearcher/AutoData.

Graph Foundation Models: A Comprehensive Survey

Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.

Neural Graph Pattern Machine

Graph learning tasks require models to comprehend essential substructure patterns relevant to downstream tasks, such as triadic closures in social networks and benzene rings in molecular graphs. Due to the non-Euclidean nature of graphs, existing graph neural networks (GNNs) rely on message passing to iteratively aggregate information from local neighborhoods. Despite their empirical success, message passing struggles to identify fundamental substructures, such as triangles, limiting its expressiveness. To overcome this limitation, we propose the Neural Graph Pattern Machine (GPM), a framework designed to learn directly from graph patterns. GPM efficiently extracts and encodes substructures while identifying the most relevant ones for downstream tasks. We also demonstrate that GPM offers superior expressivity and improved long-range information modeling compared to message passing. Empirical evaluations on node classification, link prediction, graph classification, and regression show the superiority of GPM over state-of-the-art baselines. Further analysis reveals its desirable out-of-distribution robustness, scalability, and interpretability. We consider GPM to be a step toward going beyond message passing.

Learning Cross-Task Generalities Across Graphs via Task-trees

Foundation models aim to create general, cross-task, and cross-domain machine learning models by pretraining on large-scale datasets to capture shared patterns or concepts (generalities), such as contours, colors, textures, and edges in images, or tokens, words, and sentences in text. However, discovering generalities across graphs remains challenging, which has hindered the development of graph foundation models. To tackle this challenge, in this paper, we propose a novel approach to learn generalities across graphs via task-trees. Specifically, we first define the basic learning instances in graphs as task-trees and assume that the generalities shared across graphs are, at least partially, preserved in the task-trees of the given graphs. To validate the assumption, we first perform a theoretical analysis of task-trees in terms of stability, transferability, and generalization. We find that if a graph neural network (GNN) model is pretrained on diverse task-trees through a reconstruction task, it can learn sufficient transferable knowledge for downstream tasks using an appropriate set of fine-tuning samples. To empirically validate the assumption, we further instantiate the theorems by developing a cross-task, cross-domain graph foundation model named Graph generality Identifier on task-Trees (GIT). The extensive experiments over 30 graphs from five domains demonstrate the effectiveness of GIT in fine-tuning, in-context learning, and zero-shot learning scenarios. Particularly, the general GIT model pretrained on large-scale datasets can be quickly adapted to specific domains, matching or even surpassing expert models designed for those domains. Our data and code are available at https://github.com/Zehong-Wang/GIT.

NGQA: A Nutritional Graph Question Answering Benchmark for Personalized Health-aware Nutritional Reasoning

Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand, the absence of datasets involving user-specific medical information severely limits \textit{personalization}. This challenge is further compounded by the wide variability in individual health needs. On the other hand, while large language models (LLMs), a popular solution for this task, demonstrate strong reasoning abilities, they struggle with the domain-specific complexities of personalized healthy dietary reasoning, and existing benchmarks fail to capture these challenges. To address these gaps, we introduce the Nutritional Graph Question Answering (NGQA) benchmark, the first graph question answering dataset designed for personalized nutritional health reasoning. NGQA leverages data from the National Health and Nutrition Examination Survey (NHANES) and the Food and Nutrient Database for Dietary Studies (FNDDS) to evaluate whether a food is healthy for a specific user, supported by explanations of the key contributing nutrients. The benchmark incorporates three question complexity settings and evaluates reasoning across three downstream tasks. Extensive experiments with LLM backbones and baseline models demonstrate that the NGQA benchmark effectively challenges existing models. In sum, NGQA addresses a critical real-world problem while advancing GraphQA research with a novel domain-specific benchmark.

Can LLMs Convert Graphs to Text-Attributed Graphs?

Graphs are ubiquitous data structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. Graph neural networks (GNNs) have become a popular tool to learn node embeddings through message passing on these structures. However, a significant challenge arises when applying GNNs to multiple graphs with different feature spaces, as existing GNN architectures are not designed for cross-graph feature alignment. To address this, recent approaches introduce text-attributed graphs, where each node is associated with a textual description, enabling the use of a shared textual encoder to project nodes from different graphs into a unified feature space. While promising, this method relies heavily on the availability of text-attributed data, which can be difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), which leverages large language models (LLMs) to automatically convert existing graphs into text-attributed graphs. The key idea is to integrate topological information with each node's properties, enhancing the LLMs' ability to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating that it enables a single GNN to operate across diverse graphs. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data, even in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

MOPI-HFRS: A Multi-objective Personalized Health-aware Food Recommendation System with LLM-enhanced Interpretation

The prevalence of unhealthy eating habits has become an increasingly concerning issue in the United States. However, major food recommendation platforms (e.g., Yelp) continue to prioritize users' dietary preferences over the healthiness of their choices. Although efforts have been made to develop health-aware food recommendation systems, the personalization of such systems based on users' specific health conditions remains under-explored. In addition, few research focus on the interpretability of these systems, which hinders users from assessing the reliability of recommendations and impedes the practical deployment of these systems. In response to this gap, we first establish two large-scale personalized health-aware food recommendation benchmarks at the first attempt. We then develop a novel framework, Multi-Objective Personalized Interpretable Health-aware Food Recommendation System (MOPI-HFRS), which provides food recommendations by jointly optimizing the three objectives: user preference, personalized healthiness and nutritional diversity, along with an large language model (LLM)-enhanced reasoning module to promote healthy dietary knowledge through the interpretation of recommended results. Specifically, this holistic graph learning framework first utilizes two structure learning and a structure pooling modules to leverage both descriptive features and health data. Then it employs Pareto optimization to achieve designed multi-facet objectives. Finally, to further promote the healthy dietary knowledge and awareness, we exploit an LLM by utilizing knowledge-infusion, prompting the LLMs with knowledge obtained from the recommendation model for interpretation.

Training MLPs on Graphs without Supervision

Graph Neural Networks (GNNs) have demonstrated their effectiveness in various graph learning tasks, yet their reliance on neighborhood aggregation during inference poses challenges for deployment in latency-sensitive applications, such as real-time financial fraud detection. To address this limitation, recent studies have proposed distilling knowledge from teacher GNNs into student Multi-Layer Perceptrons (MLPs) trained on node content, aiming to accelerate inference. However, these approaches often inadequately explore structural information when inferring unseen nodes. To this end, we introduce SimMLP, a Self-supervised framework for learning MLPs on graphs, designed to fully integrate rich structural information into MLPs. Notably, SimMLP is the first MLP-learning method that can achieve equivalence to GNNs in the optimal case. The key idea is to employ self-supervised learning to align the representations encoded by graph context-aware GNNs and neighborhood dependency-free MLPs, thereby fully integrating the structural information into MLPs. We provide a comprehensive theoretical analysis, demonstrating the equivalence between SimMLP and GNNs based on mutual information and inductive bias, highlighting SimMLP's advanced structural learning capabilities. Additionally, we conduct extensive experiments on 20 benchmark datasets, covering node classification, link prediction, and graph classification, to showcase SimMLP's superiority over state-of-the-art baselines, particularly in scenarios involving unseen nodes (e.g., inductive and cold-start node classification) where structural insights are crucial. Our codes are available at: https://github.com/Zehong-Wang/SimMLP.