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Zejun Li

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5 papers

1 author row

JBHI Journal 2025 Journal Article

Drug Repositioning via Multi-View Representation Learning With Heterogeneous Graph Neural Network

Li Peng
Cheng Yang
Jiahuai Yang
Yuan Tu
Qingchun Yu
Zejun Li
Min Chen
Wei Liang

Exploring simple and efficient computational methods for drug repositioning has emerged as a popular and compelling topic in the realm of comprehensive drug development. The crux of this technology lies in identifying potential drug-disease associations, which can effectively mitigate the burdens caused by the exorbitant costs and lengthy periods of conventional drugs development. However, existing computational drug repositioning methods continue to encounter challenges in accurately predicting associations between drugs and diseases. In this paper, we propose a Multi-view Representation Learning method (MRLHGNN) with Heterogeneous Graph Neural Network for drug repositioning. This method is based on a collection of data from multiple biological entities associated with drugs or diseases. It consists of a view-specific feature aggregation module with meta-paths and auto multi-view fusion encoder. To better utilize local structural and semantic information from specific views in heterogeneous graph, MRLHGNN employs a feature aggregation model with variable-length meta-paths to expand the local receptive field. Additionally, it utilizes a transformer based semantic aggregation module to aggregate semantic features across different view-specific graphs. Finally, potential drug-disease associations are obtained through a multi-view fusion decoder with an attention mechanism. Cross-validation experiments demonstrate the effectiveness and interpretability of the MRLHGNN in comparison to nine state-of-the-art approaches. Case studies further reveal that MRLHGNN can serve as a powerful tool for drug repositioning.

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JBHI Journal 2024 Journal Article

CellDialog: A Computational Framework for Ligand-Receptor-Mediated Cell-Cell Communication Analysis

Lihong Peng
Wei Xiong
Chendi Han
Zejun Li
Xing Chen

Intercellularcommunication significantly influences tumor progression, metastasis, and therapy resistance. An intercellular communication inference method includes two main procedures: ligand-receptor interaction (LRI) curation and LRI-mediated intercellular communication strength measurement. The construction of a comprehensive, high-confident and well-organized LRI database contributes to intercellular communication inference. Here, we developed a computational framework named CellDialog to reconstruct an intercellular connectivity network based on the combined expression of ligands and receptors involved in sender and receiver cells. CellDialog first captures high-confident LRIs through LRI feature extraction, feature selection, and classification. Furthermore, CellDialog uses a three-point estimation approach to measure the LRI-mediated intercellular communication strength by combining LRI filtering and single-cell RNA sequencing data. A comparison analysis of CellDialog and the other tools was conducted, and it was found that CellDialog can efficiently decode intercellular communications. Additionally, CellDialog offers a heatmap view and network view for intercellular communication visualization. In summary, CellDialog provides a tool that allows researchers to analyze intercellular signal transduction.

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AAAI Conference 2021 Conference Paper

An Unsupervised Sampling Approach for Image-Sentence Matching Using Document-level Structural Information

Zejun Li
Zhongyu Wei
Zhihao Fan
Haijun Shan
Xuanjing Huang

In this paper, we focus on the problem of unsupervised image-sentence matching. Existing research explores to utilize document-level structural information to sample positive and negative instances for model training. Although the approach achieves positive results, it introduces a sampling bias and fails to distinguish instances with high semantic similarity. To alleviate the bias, we propose a new sampling strategy to select additional intra-document image-sentence pairs as positive or negative samples. Furthermore, to recognize the complex pattern in intra-document samples, we propose a Transformer based model to capture fine-grained features and implicitly construct a graph for each document, where concepts in a document are introduced to bridge the representation learning of images and sentences in the context of a document. Experimental results show the effectiveness of our approach to alleviate the bias and learn well-aligned multimodal representations.

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IJCAI Conference 2021 Conference Paper

TCIC: Theme Concepts Learning Cross Language and Vision for Image Captioning

Zhihao Fan
Zhongyu Wei
Siyuan Wang
Ruize Wang
Zejun Li
Haijun Shan
Xuanjing Huang

Existing research for image captioning usually represents an image using a scene graph with low-level facts (objects and relations) and fails to capture the high-level semantics. In this paper, we propose a Theme Concepts extended Image Captioning (TCIC) framework that incorporates theme concepts to represent high-level cross-modality semantics. In practice, we model theme concepts as memory vectors and propose Transformer with Theme Nodes (TTN) to incorporate those vectors for image captioning. Considering that theme concepts can be learned from both images and captions, we propose two settings for their representations learning based on TTN. On the vision side, TTN is configured to take both scene graph based features and theme concepts as input for visual representation learning. On the language side, TTN is configured to take both captions and theme concepts as input for text representation re-construction. Both settings aim to generate target captions with the same transformer-based decoder. During the training, we further align representations of theme concepts learned from images and corresponding captions to enforce the cross-modality learning. Experimental results on MS COCO show the effectiveness of our approach compared to some state-of-the-art models.

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JBHI Journal 2017 Journal Article

Predicting Drug–Target Interactions With Multi-Information Fusion

Lihong Peng
Bo Liao
Wen Zhu
Zejun Li
Keqin Li

Identifying potential associations between drugs and targets is a critical prerequisite for modern drug discovery and repurposing. However, predicting these associations is difficult because of the limitations of existing computational methods. Most models only consider chemical structures and protein sequences, and other models are oversimplified. Moreover, datasets used for analysis contain only true-positive interactions, and experimentally validated negative samples are unavailable. To overcome these limitations, we developed a semi-supervised based learning framework called NormMulInf through collaborative filtering theory by using labeled and unlabeled interaction information. The proposed method initially determines similarity measures, such as similarities among samples and local correlations among the labels of the samples, by integrating biological information. The similarity information is then integrated into a robust principal component analysis model, which is solved using augmented Lagrange multipliers. Experimental results on four classes of drug-target interaction networks suggest that the proposed approach can accurately classify and predict drug-target interactions. Part of the predicted interactions are reported in public databases. The proposed method can also predict possible targets for new drugs and can be used to determine whether atropine may interact with alpha1B- and beta1- adrenergic receptors. Furthermore, the developed technique identifies potential drugs for new targets and can be used to assess whether olanzapine and propiomazine may target 5HT2B. Finally, the proposed method can potentially address limitations on studies of multitarget drugs and multidrug targets.

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