Universal graph pre-training has emerged as a key paradigm in graph representation learning, offering a promising way to train encoders to learn transferable representations from unlabeled graphs and to effectively generalize across a wide range of downstream tasks. However, recent explorations in universal graph pre-training primarily focus on homogeneous graphs and it remains unexplored for heterogeneous graphs, which exhibit greater structural and semantic complexity. This heterogeneity makes it highly challenging to train a universal encoder for diverse heterogeneous graphs: (i) the diverse types with dataset-specific semantics hinder the construction of a unified representation space; (ii) the number and semantics of meta-paths vary across datasets, making encoding and aggregation patterns learned from one dataset difficult to apply to others. To address these challenges, we propose a novel Meta-path-aware Universal heterogeneous Graph pre-training (MUG) approach. Specifically, for challenge (i), MUG introduces a input unification module that integrates information from multiple node and relation types within each heterogeneous graph into a unified representation. This representation is then projected into a shared space by a dimension-aware encoder, enabling alignment across graphs with diverse schemas. Furthermore, for challenge (ii), MUG trains a shared encoder to capture consistent structural patterns across diverse meta-path views rather than relying on dataset-specific aggregation strategies, while a global objective encourages discriminability and reduces dataset-specific biases. Extensive experiments demonstrate the effectiveness of MUG on some real datasets.

Recent advances in generic large models, such as GPT and DeepSeek, have motivated the introduction of universality to graph pre-training, aiming to learn rich and generalizable knowledge across diverse domains using graph representations to improve performance in various downstream applications. However, most existing methods face challenges in learning effective knowledge from generic graphs, primarily due to simplistic data alignment and limited training guidance. The issue of simplistic data alignment arises from the use of a straightforward unification for highly diverse graph data, which fails to align semantics and misleads pre-training models. The problem with limited training guidance lies in the arbitrary application of in-domain pre-training paradigms to cross-domain scenarios. While it is effective in enhancing discriminative representation in one data space, it struggles to capture effective knowledge from many graphs. To address these challenges, we propose a novel Latent sEmantic Distribution Alignment (LEDA) model for universal graph pre-training. Specifically, we first introduce a dimension projection unit to adaptively align diverse domain features into a shared semantic space with minimal information loss. Furthermore, we design a variational semantic inference module to obtain the shared latent distribution. The distribution is then adopted to guide the domain projection, aligning it with shared semantics across domains and ensuring cross-domain semantic learning. LEDA exhibits strong performance across a broad range of graphs and downstream tasks. Remarkably, in few-shot cross-domain settings, it significantly outperforms in-domain baselines and advanced universal pre-training models.

Recently, Graph Foundation Models (GFMs) have emerged as a central focus in the field of graph learning due to their strong generalizability to various unseen graphs. However, existing GFMs typically work under the homophily assumption, and the exploration of universality on heterophilic graphs is still in its early stages. In fact, even in homophilic graphs, there exists limited yet informative heterophilic information that is not fully exploited by current GFMs. Moreover, due to the requirement for universality, the heterophily issue faced by GFMs is more challenging than in classical graph learning, as it requires training a single model to adapt to varying structures, features, and tasks. Classic heterophilic graph learning methods primarily based on the node-level homophily or heterophily. However, we highlight that homophily and heterophily exist not only at the node semantic level, but also at a finer granularity across individual feature dimensions. This finding enables GFMs to adapt to heterophilic graphs and better utilize the small amount of heterophilic information in homophilic graphs. Based on this, we propose Topology-aware Feature Sorting Graph Foundation Model (TFSGFM), which employs a feature-level topology-aware sorting strategy and a dual-channel graph neural network framework, enabling unified modeling of both feature and structure. Extensive experiments demonstrate the strong generalizability of TFSGFM. The source code is available at https://github.com/hedongxiao-tju/TFSGFM.

Graph Contrastive Learning (GCL) aims to self-supervised learn low-dimensional graph representations, primarily through instance discrimination, which involves manually mining positive and negative pairs from graphs, increasing the similarity of positive pairs while decreasing negative pairs. Drawing from the success of Contrastive Learning (CL) in other domains, a consensus has been reached that the effectiveness of GCLs depends on a large number of negative pairs. As a result, despite the significant computational overhead, GCLs typically leverage as many negative node pairs as possible to improve model performance. However, given that nodes within a graph are interconnected, we argue that nodes cannot be treated as independent instances. Therefore, we challenge this consensus: Does employing more negative nodes lead to a more effective GCL model? To answer this, we explore the role of negative nodes in the commonly used InfoNCE loss for GCL and observe that: (1) Counterintuitively, a large number of negative nodes can actually hinder the model's ability to distinguish between nodes with different semantics. (2) A smaller number of high-quality and non-topologically coupled negative nodes are sufficient to enhance the discriminability of representations. Based on these findings, we propose a new method called GCL with Effective and Efficient Negative samples, E2Neg, which learns discriminative representations using only a very small set of representative negative samples. E2Neg significantly reduces computational overhead and speeds up model training. We demonstrate the effectiveness and efficiency of E2Neg across multiple datasets compared to other GCL methods.

Graph Prompt Learning (GPL) has emerged as a promising paradigm that bridges graph pretraining models and downstream scenarios, mitigating label dependency and the misalignment between upstream pretraining and downstream tasks. Although existing GPL studies explore various prompt strategies, their effectiveness and underlying principles remain unclear. We identify two critical limitations: (1) Lack of consensus on underlying mechanisms: Despite current GPLs have advanced the field, there is no consensus on how prompts interact with pretrained models, as different strategies intervene at varying spaces within the model, i.e., input-level, layer-wise, and representation-level prompts. (2) Limited scenario adaptability: Most methods fail to generalize across diverse downstream scenarios, especially under data distribution shifts (e.g., homophilic-to-heterophilic graphs). To address these issues, we theoretically analyze existing GPL approaches and reveal that representation-level prompts essentially function as fine-tuning a simple downstream classifier, proposing that graph prompt learning should focus on unleashing the capability of pretrained models, and the classifier should adapt to downstream scenarios. Based on our findings, we propose UniPrompt, a novel GPL method that adapts any pretrained models, unleashing the capability of pretrained models while preserving the input graph. Extensive experiments demonstrate that our method can effectively integrate with various pretrained models and achieve strong performance across in-domain and cross-domain scenarios.

Graph Contrastive Learning (GCL) is a widely adopted approach in self-supervised graph representation learning, applying contrastive objectives to produce effective representations. However, current GCL methods primarily focus on capturing implicit semantic relationships, often overlooking the structural commonsense embedded within the graph's structure and attributes, which contains underlying knowledge crucial for effective representation learning. Due to the lack of explicit information and clear guidance in general graph, identifying and integrating such structural commonsense in GCL poses a significant challenge. To address this gap, we propose a novel framework called Structural Commonsense Unveiling in Graph Contrastive Learning (Str-GCL). Str-GCL leverages first-order logic rules to represent structural commonsense and explicitly integrates them into the GCL framework. It introduces topological and attribute-based rules without altering the original graph and employs a representation alignment mechanism to guide the encoder in effectively capturing this commonsense. To the best of our knowledge, this is the first attempt to directly incorporate structural commonsense into GCL. Extensive experiments demonstrate that Str-GCL outperforms existing GCL methods, providing a new perspective on leveraging structural commonsense in graph representation learning.

Contrastive Learning (CL) has emerged as a popular self-supervised representation learning paradigm that has been shown in many applications to perform similarly to traditional supervised learning methods. A key component of CL is mining the latent discriminative relationships between positive and negative samples and using them as self-supervised labels. We argue that this discriminative contrastive task is, in essence, similar to a classification task, and the “either positive or negative” hard label sampling strategies are arbitrary. To solve this problem, we explore ideas from data distillation, which considers probabilistic logit vectors as soft labels to transfer model knowledge. We attempt to abandon the classical hard sampling labels in CL and instead explore self-supervised soft labels. We adopt soft sampling labels that are extracted, without supervision, from the inherent relationships in data pairs to retain more information. We propose a new self-supervised graph learning method, Distill and Contrast (D&C), for learning representations that closely approximate natural data relationships. D&C extracts node similarities from the features and structures to derive soft sampling labels, which also eliminate noise in the data to increase robustness. Extensive experimental results on real-world datasets demonstrate the effectiveness of the proposed method.

Graph contrastive learning (GCL) has attracted considerable attention because it can self-supervisedly extract low-dimensional representation of graph data. InfoNCE-based loss function is widely used in graph contrastive learning, which pulls the representations of positive pairs close to each other and pulls the representations of negative pairs away from each other. Recent works mainly focus on designing new augmentation methods or sampling strategies. However, we argue that the widely used InfoNCE-based methods may contain an implicit conflict which seriously confuses models when learning from negative pairs. This conflict is engendered by the encoder's message-passing mechanism and the InfoNCE loss function. As a result, the learned representations between negative samples cannot be far away from each other, compromising the model performance. To our best knowledge, this is the first time to report and analysis this conflict of GCL. To address this problem, we propose a simple but effective method called Partial ignored Graph Contrastive Learning (PiGCL). Specifically, PiGCL first dynamically captures the conflicts during training by detecting the gradient of representation similarities. It then enables the loss function to ignore the conflict, allowing the encoder to adaptively learn the ignored information without self-supervised samples. Extensive experiments demonstrate the effectiveness of our method.

Graph Contrastive Learning (GCL) has emerged as a powerful approach for generating graph representations without the need for manual annotation. Most advanced GCL methods fall into three main frameworks: node discrimination, group discrimination, and bootstrapping schemes, all of which achieve comparable performance. However, the underlying mechanisms and factors that contribute to their effectiveness are not yet fully understood. In this paper, we revisit these frameworks and reveal a common mechanism—representation scattering—that significantly enhances their performance. Our discovery highlights an essential feature of GCL and unifies these seemingly disparate methods under the concept of representation scattering. To leverage this insight, we introduce Scattering Graph Representation Learning (SGRL), a novel framework that incorporates a new representation scattering mechanism designed to enhance representation diversity through a center-away strategy. Additionally, consider the interconnected nature of graphs, we develop a topology-based constraint mechanism that integrates graph structural properties with representation scattering to prevent excessive scattering. We extensively evaluate SGRL across various downstream tasks on benchmark datasets, demonstrating its efficacy and superiority over existing GCL methods. Our findings underscore the significance of representation scattering in GCL and provide a structured framework for harnessing this mechanism to advance graph representation learning. The code of SGRL is at https://github.com/hedongxiao-tju/SGRL.

Graph Neural Networks (GNNs), known for their effective graph encoding, are extensively used across various fields. Graph self-supervised pre-training, which trains GNN encoders without manual labels to generate high-quality graph representations, has garnered widespread attention. However, due to the inherent complex characteristics in graphs, GNNs encoders pre-trained on one dataset struggle to directly adapt to others that have different node feature shapes. This typically necessitates either model rebuilding or data alignment. The former results in non-transferability as each dataset need to rebuild a new model, while the latter brings serious knowledge loss since it forces features into a uniform shape by preprocessing such as Principal Component Analysis (PCA). To address this challenge, we propose a new Feature-Universal Graph contrastive pre-training strategy (FUG) that naturally avoids the need for model rebuilding and data reshaping. Specifically, inspired by discussions in existing work on the relationship between contrastive Learning and PCA, we conducted a theoretical analysis and discovered that PCA's optimization objective is a special case of that in contrastive Learning. We designed an encoder with contrastive constraints to emulate PCA's generation of basis transformation matrix, which is utilized to losslessly adapt features in different datasets. Furthermore, we introduced a global uniformity constraint to replace negative sampling, reducing the time complexity from $O(n^2)$ to $O(n)$, and by explicitly defining positive samples, FUG avoids the substantial memory requirements of data augmentation. In cross domain experiments, FUG has a performance close to the re-trained new models. The source code is available at: https://github.com/hedongxiao-tju/FUG.

Graph Contrastive Learning (GCL) has recently enjoyed great success as an efficient self-supervised representation learning approach. However, the existing methods have focused on designing of contrastive modes and used data augmentation with a rigid and inefficient one-to-one sampling strategy. We adopted node neighborhoods to extend positive samplings and made avoided resorting to data augmentation to create different views. We also considered the homophily problem in Graph Neural Networks (GNNs) between the inter-class node pairs. The key novelty of our method hinged upon analyzing this GNNs problem and integrating the GCL sampling strategy with homophily discrimination, where we solved these two significant problems using one approach. We introduced a new parameterized neighbor sampling component to replace the conventional sub-optimal samplings. By keeping and updating the neighbor sets, both the positive sampling of GCL and the message passing of GNNs can be optimized. Moreover, we theoretically proved that the new method provided a lower bound of mutual information for unsupervised semantic learning, and it can also keep the lower bound with downstream tasks. In essence, our method is a new self-supervised approach, which we refer to as group discrimination, and it can make the downstream fine-tuning efficient. Our extensive empirical results demonstrate that the new method can significantly outperform the existing GCL methods because the former can solve the homophily problem in a self-supervised way with the new group discrimination method used.