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Lei Geng

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5 papers

2 author rows

ICML Conference 2025 Conference Paper

HGOT: Self-supervised Heterogeneous Graph Neural Network with Optimal Transport

Yanbei Liu
Chongxu Wang
Zhitao Xiao
Lei Geng
Yanwei Pang
Xiao Wang 0017

Heterogeneous Graph Neural Networks (HGNNs), have demonstrated excellent capabilities in processing heterogeneous information networks. Self-supervised learning on heterogeneous graphs, especially contrastive self-supervised strategy, shows great potential when there are no labels. However, this approach requires the use of carefully designed graph augmentation strategies and the selection of positive and negative samples. Determining the exact level of similarity between sample pairs is non-trivial. To solve this problem, we propose a novel self-supervised Heterogeneous graph neural network with Optimal Transport (HGOT) method which is designed to facilitate self-supervised learning for heterogeneous graphs without graph augmentation strategies. Different from traditional contrastive self-supervised learning, HGOT employs the optimal transport mechanism to relieve the laborious sampling process of positive and negative samples. Specifically, we design an aggregating view (central view) to integrate the semantic information contained in the views represented by different meta-paths (branch views). Then, we introduce an optimal transport plan to identify the transport relationship between the semantics contained in the branch view and the central view. This allows the optimal transport plan between graphs to align with the representations, forcing the encoder to learn node representations that are more similar to the graph space and of higher quality. Extensive experiments on four real-world datasets demonstrate that our proposed HGOT model can achieve state-of-the-art performance on various downstream tasks. In particular, in the node classification task, HGOT achieves an average of more than 6% improvement in accuracy compared with state-of-the-art methods.

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JBHI Journal 2025 Journal Article

Label-Aware Dual Graph Neural Networks for Multi-Label Fundus Image Classification

Yanbei Liu
Xinwen Peng
Xin Wei
Lei Geng
Fang Zhang
Zhitao Xiao
Jerry Chun-Wei Lin

Fundus disease is a complex and universal disease involving a variety of pathologies. Its early diagnosis using fundus images can effectively prevent further diseases and provide targeted treatment plans for patients. Recent deep learning models for classification of this disease are gradually emerging as a critical research field, which is attracting widespread attention. However, in practice, most of the existing methods only focus on local visual cues of a single image, and ignore the underlying explicit interaction similarity between subjects and correlation information among pathologies in fundus diseases. In this paper, we propose a novel label-aware dual graph neural networks for multi-label fundus image classification that consists of population-based graph representation learning and pathology-based graph representation learning modules. Specifically, we first construct a population-based graph by integrating image features and non-image information to learn patient's representations by incorporating associations between subjects. Then, we represent pathologies as a sparse graph where its nodes are associated with pathology-based feature vectors and the edges correspond to probability of the co-occurrence of labels to generate a set of classifier scores by the propagation of multi-layer graph information. Finally, our model can adaptively recalibrate multi-label outputs. Detailed experiments and analysis of our results show the effectiveness of our method compared with state-of-the-art multi-label fundus image classification methods.

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AAAI Conference 2024 Conference Paper

Direct May Not Be the Best: An Incremental Evolution View of Pose Generation

Yuelong Li
Tengfei Xiao
Lei Geng
Jianming Wang

Pose diversity is an inherent representative characteristic of 2D images. Due to the 3D to 2D projection mechanism, there is evident content discrepancy among distinct pose images. This is the main obstacle bothering pose transformation related researches. To deal with this challenge, we propose a fine-grained incremental evolution centered pose generation framework, rather than traditional direct one-to-one in a rush. Since proposed approach actually bypasses the theoretical difficulty of directly modeling dramatic non-linear variation, the incurred content distortion and blurring could be effectively constrained, at the same time the various individual pose details, especially clothes texture, could be precisely maintained. In order to systematically guide the evolution course, both global and incremental evolution constraints are elaborately designed and merged into the overall framework. And a novel triple-path knowledge fusion structure is worked out to take full advantage of all available valuable knowledge to conduct high-quality pose synthesis. In addition, our framework could generate a series of valuable by-products, namely the various intermediate poses. Extensive experiments have been conducted to verify the effectiveness of the proposed approach. Code is available at https://github.com/Xiaofei-CN/Incremental-Evolution-Pose-Generation.

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ECAI Conference 2024 Conference Paper

TabMedBERT: A Tabular Knowledge Enhanced Biomedical Pretrained Language Model

Xu Yan
Lei Geng
Ziqiang Cao
Juntao Li 0005
Wenjie Li 0002
Sujian Li
Xinjie Zhou
Yang Yang 0074

Most existing biomedical language models are trained on plain text with general learning goals such as random word infilling, failing to capture the knowledge in the biomedical corpus sufficiently. Since biomedical articles usually contain many tables summarising the main entities and their relations, in the paper, we propose a Tabular knowledge enhanced bioMedical pretrained language model, called TabMedBERT. Specifically, we align entities between table cells, and article text spans with pre-defined rules. Then we add two table-related self-supervised tasks to integrate tabular knowledge into the language model: Entity Infilling (EI) and Table Cloze Test (TCT). While EI masks tokens within aligned entities in the article, TCT converts aligned entities in the table layout into a cloze text by erasing one entity and prompts the model to extract the appropriate span to fill in the blank. Experimental results demonstrate that TabMedBERT surpasses all competing language models without adding additional parameters, establishing a new state-of-the-art performance of 85. 59% (+1. 29%) on the BLURB biomedical NLP benchmark and 7 additional information extraction datasets. Moreover, the model architecture for TCT provides a straightforward solution to revise information extraction with paired entities.

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IJCAI Conference 2023 Conference Paper

Multi-Scale Subgraph Contrastive Learning

Yanbei Liu
Yu Zhao
Xiao Wang
Lei Geng
Zhitao Xiao

Graph-level contrastive learning, aiming to learn the representations for each graph by contrasting two augmented graphs, has attracted considerable attention. Previous studies usually simply assume that a graph and its augmented graph as a positive pair, otherwise as a negative pair. However, it is well known that graph structure is always complex and multi-scale, which gives rise to a fundamental question: after graph augmentation, will the previous assumption still hold in reality? By an experimental analysis, we discover the semantic information of an augmented graph structure may be not consistent as original graph structure, and whether two augmented graphs are positive or negative pairs is highly related with the multi-scale structures. Based on this finding, we propose a multi-scale subgraph contrastive learning architecture which is able to characterize the fine-grained semantic information. Specifically, we generate global and local views at different scales based on subgraph sampling, and construct multiple contrastive relationships according to their semantic associations to provide richer self-supervised signals. Extensive experiments and parametric analyzes on eight graph classification real-world datasets well demonstrate the effectiveness of the proposed method.

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