Graph Prompt Learning

Signed graphs arise in trust--distrust networks, financial correlation systems, biological interaction graphs, and many other domains in which edges can be positive or negative and may also be directed. While signed graph neural networks have improved task-specific learning, graph transfer learning on signed graphs remains underdeveloped. In this paper, we introduce TopoSIGN, a pioneer topology-guided graph pre-training and prompt learning framework for signed graphs. TopoSIGN combines a structural encoder built on the magnetic signed Laplacian with a novel persistent-homology branch that summarizes signed topology through Dowker-complex persistence images. The fused embeddings are then transferred to a prompt learning function. Experimental results on synthetic and real-world datasets demonstrate the efficacy of TopoSIGN in extracting useful structural information in signed graphs, as well as the adaptability and flexibility of the proposed general framework.

Graph prompt learning enables parameter-efficient adaptation of frozen Graph Neural Networks to downstream tasks through lightweight prompt parameters. As routing becomes increasingly node-adaptive, however, independently optimized local decisions can collectively concentrate assignment mass on a small subset of a finite shared prompt bank, even when individual node--prompt matches remain locally meaningful. We propose MINT (Measure-INtegrity Transport), an entropically regularized optimal transport framework that formulates node-to-prompt adaptation as a globally coupled allocation problem. The transport cost favors local geometric compatibility, while a prescribed prompt-side marginal explicitly controls graph-wide prompt utilization. We further derive an exact variance decomposition that separates prompt-side geometric variance into retained prompt-update variation and within-node barycentric dispersion, together with a conditional stability bound for the frozen-encoder forward map. Across standard citation networks and additional heterophilic graphs, MINT remains competitive in few-shot adaptation. Controlled and end-to-end experiments further distinguish the roles of routing and topology: fixed-marginal routing controls graph-wide prompt utilization and has measurable end-to-end effects on citation networks, while topology augmentation provides a complementary, graph-dependent mechanism for addressing structural mismatch. Code is available at https://github.com/Ga1axy0051/MINT.

Graph prompt learning is an effective paradigm to adapt pre-trained graph models to downstream tasks in low-resource scenarios. However, existing multi-task graph pre-training frameworks generally use randomly initialized prompts, leading to poor alignment between the prompt space, pretext objectives and graph structural characteristics. This greatly weakens the task relevance, structural awareness and transferability of prompt representations. To address this challenge, we propose TPGC, a dual-prior prompt initialization solution that explicitly models the synergy between task prior and structural prior. Specifically, the Task-Prior Injection Module first conducts a short homologous multi-task pre-training on an auxiliary graph, enabling prompt initialization to inherit optimization preferences associated with multiple pretext tasks. Built on the task-aware representations, the Structure-Prior Injection Module further extracts transferable global structural context from the auxiliary graph, converting it into layer-wise prompt vectors by aggregating structurally informative node embeddings. Extensive experiments on 6 mainstream benchmarks covering node and graph classification show that TPGC achieves consistently better performance under few-shot settings than state-of-the-art baselines, with fewer downstream tunable parameters and lower runtime. The code is available at https://github.com/Virgilqiu/TPGC

Graph Neural Networks (GNNs) have emerged as a cornerstone for representing complex relational dependencies in diverse multimedia tasks, particularly in cross-platform user interest modeling and cross-modal semantic alignment. In the real world, a practical defense against graph adversarial perturbations is needed. However, we observe that the prevailing adversarial purification methods are essentially domain-restricted defenses, which leads to the following shortcomings: (1) single-domain data provides insufficient structural and semantic diversity for learning robust purification criteria; (2) training of domain-specific defense strategies from scratch consumes substantial computational cost. To address the above limitations, we propose a transferable graph purification scheme, named ProGAP, to bridge adversarial defense knowledge via vulnerability-aware graph prompt learning. Firstly, to capture universal adversarial patterns, a perturbation-capture edge detector is pretrained on data-rich graphs by jointly modeling topological and semantic information. Subsequently, to achieve more knowledge transfer w.r.t. robustness, vulnerability-aware prompts are designed that inject targeted purification guidance into biased nodes, during which the pretrained detector adapts to distribution shifts in downstream graphs without parameter-laborious updates. Experimental results demonstrate that compared with state-of-the-art baselines, our ProGAP achieves 1%-9% improvement, and reduces the time consumption by up to 2.2x. The code for ProGAP is available at https://github.com/Lieyoufffff/ProGAP.

Generative recommendation commonly represents items using fixed-length semantic identifiers (SIDs) constructed through clustering and quantization. However, these artificial codes may overcompress item semantics, remain misaligned with pretrained LLM vocabularies, and require costly autoregressive decoding. In light of this, we propose VaLiDRec, a generative recommendation framework based on variable-length, LLM-aligned semantic identifiers. VaLiDRec constructs SIDs directly from informative native LLM vocabulary tokens via token importance estimation, semantic-quality-aware pruning, and collision-aware refinement, allowing identifier lengths to adapt to item semantic complexity. To model user preferences, VaLiDRec incorporates graph-aware soft prompts and reformulates recommendation as token-set prediction with token-level item scoring, eliminating autoregressive SID generation and beam search. Experiments on four real-world datasets show that VaLiDRec consistently outperforms strong sequential and generative recommendation baselines across all evaluation metrics. It further achieves superior zero-shot item cold-start performance and 87.49$\times$ faster inference than LC-Rec. These results demonstrate that LLM-native variable-length semantic identifiers provide a more expressive and efficient paradigm for generative recommendation.

Graph Neural Networks have emerged as a powerful tool for the fast and accurate prediction of various crystal properties. These models often encode domain-specific knowledge into their graph encoding modules, which increases their parameter size and makes their performance heavily dependent on domain expertise. Added to this, explicitly incorporating all chemical and structural features, that might influence a specific crystal property into the GNN encoder, is a challenging task. In this work, we propose a soft prompt learning framework that captures latent features essential for property prediction, which are not explicitly provided to the GNN. We introduce a novel multilevel graph prompt learning framework comprising both node-level and graph-level soft prompts. At the node level, we capture the local chemical semantics of different atom types, while at the graph level, we encode the global structural symmetry of the crystal graph. Our proposed prompt learning framework is lightweight and seamlessly integrates with any existing GNN encoder. Extensive experiments on popular benchmark datasets show that incorporating prompt learning significantly improves (3% - 15%) the performance of state-of-the-art GNN models in crystal property prediction tasks. Furthermore, the learned soft prompts enable cross-property knowledge transfer, enhancing prediction performance for properties with limited training data. Code is available at https://github.com/shrimonmuke0202/Prompt.git

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification heads. They mainly rely on generic aggregating methods like concatenation or dot products, which lack biological insight. Motivated by the biological "L3 rule", where multiple length-3 paths between a pair of proteins indicate their interaction likelihood, our study addresses this gap by designing a biologically informed PPI classifier. In this paper, we provide empirical evidence that popular PPI datasets strongly support the L3 rule. We propose an L3-path-regularized graph prompt learning method called L3-PPI, which can generate a prompt graph with virtual L3 paths based on protein representations and controls the number of paths. L3-PPI reformulates the classification of protein embedding pairs into a graph-level classification task over the generated prompt graph. This lightweight module seamlessly integrates with PPI predictors as a plug-and-play component, injecting the interaction prior of complementarity to enhance performance. Extensive experiments show that L3-PPI achieves superior performance enhancements over advanced competitors.

Graph Data Prompt (GDP), which introduces specific prompts in graph data for efficiently adapting pre-trained GNNs, has become a mainstream approach to graph fine-tuning learning problem. However, existing GDPs have been respectively designed for distinct graph component (e.g., node features, edge features, edge weights) and thus operate within limited prompt spaces for graph data. To the best of our knowledge, it still lacks a unified prompter suitable for targeting all graph components simultaneously. To address this challenge, in this paper, we first propose to reinterpret a wide range of existing GDPs from an aspect of Graph Message Prompt (GMP) paradigm. Based on GMP, we then introduce a novel graph prompt learning approach, termed Low-Rank GMP (LR-GMP), which leverages low-rank prompt representation to achieve an effective and compact graph prompt learning. Unlike traditional GDPs that target distinct graph components separately, LR-GMP concurrently performs prompting on all graph components in a unified manner, thereby achieving significantly superior generalization and robustness on diverse downstream tasks. Extensive experiments on several graph benchmark datasets demonstrate the effectiveness and advantages of our proposed LR-GMP.

Graph Out-of-Distribution (OOD) detection aims to identify whether a test graph deviates from the distribution of graphs observed during training, which is critical for ensuring the reliability of Graph Neural Networks (GNNs) when deployed in open-world scenarios. Recent advances in graph OOD detection have focused on test-time training techniques that facilitate OOD detection without accessing potential supervisory information (e.g., training data). However, most of these methods employ a one-pass inference paradigm, which prevents them from progressively correcting erroneous predictions to amplify OOD signals. To this end, we propose a Self-Improving Graph Out-of-Distribution detector (SIGOOD), which is an unsupervised framework that integrates continuous self-learning with test-time training for effective graph OOD detection. Specifically, SIGOOD generates a prompt to construct a prompt-enhanced graph that amplifies potential OOD signals. To optimize prompts, SIGOOD introduces an Energy Preference Optimization (EPO) loss, which leverages energy variations between the original test graph and the prompt-enhanced graph. By iteratively optimizing the prompt by involving it into the detection model in a self-improving loop, the resulting optimal prompt-enhanced graph is ultimately used for OOD detection. Comprehensive evaluations on 21 real-world datasets confirm the effectiveness and outperformance of our SIGOOD method. The code is at https://github.com/Ee1s/SIGOOD.