Yufei He

Zhenyu Hou, Yufei He, Yukuo Cen et al. · tsinghua

Graph self-supervised learning (SSL), including contrastive and generative approaches, offers great potential to address the fundamental challenge of label scarcity in real-world graph data. Among both sets of graph SSL techniques, the masked graph autoencoders (e.g., GraphMAE)--one type of generative method--have recently produced promising results. The idea behind this is to reconstruct the node features (or structures)--that are randomly masked from the input--with the autoencoder architecture. However, the performance of masked feature reconstruction naturally relies on the discriminability of the input features and is usually vulnerable to disturbance in the features. In this paper, we present a masked self-supervised learning framework GraphMAE2 with the goal of overcoming this issue. The idea is to impose regularization on feature reconstruction for graph SSL. Specifically, we design the strategies of multi-view random re-mask decoding and latent representation prediction to regularize the feature reconstruction. The multi-view random re-mask decoding is to introduce randomness into reconstruction in the feature space, while the latent representation prediction is to enforce the reconstruction in the embedding space. Extensive experiments show that GraphMAE2 can consistently generate top results on various public datasets, including at least 2.45% improvements over state-of-the-art baselines on ogbn-Papers100M with 111M nodes and 1.6B edges.

Yufei He, Zhenyu Hou, Yukuo Cen et al. · tsinghua

Graph pre-training has been concentrated on graph-level tasks involving small graphs (e.g., molecular graphs) or learning node representations on a fixed graph. Extending graph pre-trained models to web-scale graphs with billions of nodes in industrial scenarios, while avoiding negative transfer across graphs or tasks, remains a challenge. We aim to develop a general graph pre-trained model with inductive ability that can make predictions for unseen new nodes and even new graphs. In this work, we introduce a scalable transformer-based graph pre-training framework called PGT (Pre-trained Graph Transformer). Based on the masked autoencoder architecture, we design two pre-training tasks: one for reconstructing node features and the other for reconstructing local structures. Unlike the original autoencoder architecture where the pre-trained decoder is discarded, we propose a novel strategy that utilizes the decoder for feature augmentation. Our framework, tested on the publicly available ogbn-papers100M dataset with 111 million nodes and 1.6 billion edges, achieves state-of-the-art performance, showcasing scalability and efficiency. We have deployed our framework on Tencent's online game data, confirming its capability to pre-train on real-world graphs with over 540 million nodes and 12 billion edges and to generalize effectively across diverse static and dynamic downstream tasks.

Yue Liu, Jiaying Wu, Yufei He et al. · pku, tsinghua

Large Reasoning Models (LRMs) significantly improve the reasoning ability of Large Language Models (LLMs) by learning to reason, exhibiting promising performance in solving complex tasks. However, their deliberative reasoning process leads to inefficiencies in token usage, memory consumption, and inference time. Thus, this survey provides a review of efficient inference methods designed specifically for LRMs, focusing on mitigating token inefficiency while preserving the reasoning quality. The overview structure of this paper is shown in Figure~\ref{fig:paper_structure}. First, we introduce a taxonomy to group the recent methods into two main categories: (a) explicit compact Chain-of-Thought (CoT), which reduces tokens while keeping the explicit reasoning structure, and (b) implicit latent CoT, which encodes reasoning steps within hidden representations instead of explicit tokens. Meanwhile, we discuss their strengths and weaknesses. Then, we conduct empirical analyses on existing methods from reasoning scenarios, object functions, and performance \& efficiency aspects. Besides, we present open challenges in this field, including human-centric controllable reasoning, trade-off between interpretability and efficiency of reasoning, ensuring the safety of efficient reasoning, and broader applications of efficient reasoning. In addition, we highlight key insights for enhancing LRMs' inference efficiency via techniques such as model merging, new architectures, and agent routers. We hope this work serves as a valuable guide, helping researchers overcome challenges in this vibrant field. A collection of efficient reasoning methods for LRMs (papers and codes) is provided at this link: https://github.com/yueliu1999/Awesome-Efficient-Inference-for-LRMs.

Jun Hu, Shangheng Chen, Yufei He et al.

Heterogeneous Graph Neural Networks (HGNNs) are widely used for deep learning on heterogeneous graphs. Typical end-to-end HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Pre-computation-based HGNNs address this by performing message passing only once during preprocessing, collecting neighbor information into regular-shaped tensors, which enables efficient mini-batch training. Label-based pre-computation methods collect neighbors' label information but suffer from training label leakage, where a node's own label information propagates back to itself during multi-hop message passing - the echo effect. Existing mitigation strategies are memory-inefficient on large graphs or suffer from compatibility issues with advanced message passing methods. We propose Echoless Label-based Pre-computation (Echoless-LP), which eliminates training label leakage with Partition-Focused Echoless Propagation (PFEP). PFEP partitions target nodes and performs echoless propagation, where nodes in each partition collect label information only from neighbors in other partitions, avoiding echo while remaining memory-efficient and compatible with any message passing method. We also introduce an Asymmetric Partitioning Scheme (APS) and a PostAdjust mechanism to address information loss from partitioning and distributional shifts across partitions. Experiments on public datasets demonstrate that Echoless-LP achieves superior performance and maintains memory efficiency compared to baselines.

Yufei He, Yuan Sui, Xiaoxin He et al.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

Jun Hu, Yufei He, Yuan Li et al.

Isolated cold-start node classification on multimodal graphs is challenging because such nodes have no edges and often have missing modalities (e.g., absent text or image features). Existing methods address structural isolation by degrading graph learning models to multilayer perceptrons (MLPs) for isolated cold-start inference, using a teacher model (with graph access) to guide the MLP. However, this results in limited model capacity in the student, which is further challenged when modalities are missing. In this paper, we propose Neighbor-to-Self Graph Transformer (NTSFormer), a unified Graph Transformer framework that jointly tackles the isolation and missing-modality issues via a self-teaching paradigm. Specifically, NTSFormer uses a cold-start attention mask to simultaneously make two predictions for each node: a "student" prediction based only on self information (i.e., the node's own features), and a "teacher" prediction incorporating both self and neighbor information. This enables the model to supervise itself without degrading to an MLP, thereby fully leveraging the Transformer's capacity to handle missing modalities. To handle diverse graph information and missing modalities, NTSFormer performs a one-time multimodal graph pre-computation that converts structural and feature data into token sequences, which are then processed by Mixture-of-Experts (MoE) Input Projection and Transformer layers for effective fusion. Experiments on public datasets show that NTSFormer achieves superior performance for multimodal isolated cold-start node classification.

Chenhui Zhang, Yufei He, Yukuo Cen et al.

We present the SCR framework for enhancing the training of graph neural networks (GNNs) with consistency regularization. Regularization is a set of strategies used in Machine Learning to reduce overfitting and improve the generalization ability. However, it is unclear how to best design the generalization strategies in GNNs, as it works in a semi-supervised setting for graph data. The major challenge lies in how to efficiently balance the trade-off between the error from the labeled data and that from the unlabeled data. SCR is a simple yet general framework in which we introduce two strategies of consistency regularization to address the challenge above. One is to minimize the disagreements among the perturbed predictions by different versions of a GNN model. The other is to leverage the Mean Teacher paradigm to estimate a consistency loss between teacher and student models instead of the disagreement of the predictions. We conducted experiments on three large-scale node classification datasets in the Open Graph Benchmark (OGB). Experimental results demonstrate that the proposed SCR framework is a general one that can enhance various GNNs to achieve better performance. Finally, SCR has been the top-1 entry on all three OGB leaderboards as of this submission.