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Topological structures of real-world graphs often exhibit heterogeneity involving diverse nodes and relation types. In recent years, heterogeneous graph learning methods utilizing meta-paths to capture composite relations and guide neighbor selection have garnered considerable attention. However, meta-path based approaches may establish connections between nodes of different categories while overlooking relations between nodes of the same category, decreasing the quality of node embeddings. In light of this, this paper proposes a Heterogeneous Graph Neural Network with Adaptive Relation Reconstruction (HGNN-AR) that adaptively adjusts the relations to alleviate connection deficiencies and heteromorphic issues. HGNN-AR is grounded on distinct connections derived from multiple meta-paths. By examining the homomorphic correlations of latent features from each meta-path, we reshape the cross-node connections to explore the pertinent latent relations. Through the relation reconstruction, we unveil unique connections reflected by each meta-path and incorporate them into graph convolutional networks for more comprehensive representations. The proposed model is evaluated on various benchmark heterogeneous graph datasets, demonstrating superior performance compared to state-of-the-art competitors.
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http://dx.doi.org/10.1016/j.neunet.2025.107313 | DOI Listing |
Proc Mach Learn Res
November 2024
Pretraining plays a pivotal role in acquiring generalized knowledge from large-scale data, achieving remarkable successes as evidenced by large models in CV and NLP. However, progress in the graph domain remains limited due to fundamental challenges represented by feature heterogeneity and structural heterogeneity. Recent efforts have been made to address feature heterogeneity via Large Language Models (LLMs) on text-attributed graphs (TAGs) by generating fixed-length text representations as node features.
View Article and Find Full Text PDFCurr Microbiol
September 2025
Department of Health Sciences, Università del Piemonte Orientale UPO, Corso Trieste 15/A, 28100, Novara, Italy.
A Python-scripted software tool has been developed to help study the heterogeneity of gene changes, markedly or moderately expressed, when several experimental conditions are compared. The analysis workflow encloses a scorecard that groups genes based on relative fold-change and statistical significance, providing additional functions that facilitate knowledge extraction. The scorecard reports highlight unique patterns of gene regulation, such as genes whose expression is consistently up- or down-regulated across experiments, all of which are supported by graphs and summaries to characterize the dataset under investigation.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
School of Software, Shandong University, Jinan 250101, Shandong, China.
Spatial transcriptomics (ST) reveals gene expression distributions within tissues. Yet, predicting spatial gene expression from histological images still faces the challenges of limited ST data that lack prior knowledge, and insufficient capturing of inter-slice heterogeneity and intra-slice complexity. To tackle these challenges, we introduce FmH2ST, a foundation model-based method for spatial gene expression prediction.
View Article and Find Full Text PDFJ Affect Disord
September 2025
College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China. Electronic address:
Major Depressive Disorder (MDD) poses a significant global health threat, impairing individual functioning and increasing socioeconomic burden. Accurate diagnosis is crucial for improving treatment outcomes. This study proposes Time-Frequency Text-Attributed DeepWalk (TF-TADW), a framework for MDD classification using resting-state functional MRI data.
View Article and Find Full Text PDFIEEE J Biomed Health Inform
September 2025
Drug-target interaction (DTI) identification is of great significance in drug development in various areas, such as drug repositioning and potential drug side effects. Although a great variety of computational methods have been proposed for DTI prediction, it is still a challenge in the face of sparsely correlated drugs or targets. To address the impact of data sparsity on the model, we propose a multi-view neighborhood-enhanced graph contrastive learning approach (MneGCL), which is based on graph clustering according to the adjacency relationship in various similarity networks between drugs or targets, to fully exploit the information of drugs and targets with few corrections.
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