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Graph machine learning has been extensively studied in both academia and industry. Although booming with a vast number of emerging methods and techniques, most of the literature is built on the in-distribution hypothesis, i.e., testing and training graph data are identically distributed. However, this in-distribution hypothesis can hardly be satisfied in many real-world graph scenarios where the model performance substantially degrades when there exist distribution shifts between testing and training graph data. To solve this critical problem, out-of-distribution (OOD) generalization on graphs, which goes beyond the in-distribution hypothesis, has made great progress and attracted ever-increasing attention from the research community. In this paper, we comprehensively survey OOD generalization on graphs and present a detailed review of recent advances in this area. First, we provide a formal problem definition of OOD generalization on graphs. Second, we categorize existing methods into three classes from conceptually different perspectives, i.e., data, model, and learning strategy, based on their positions in the graph machine learning pipeline, followed by detailed discussions for each category. We also review the theories related to OOD generalization on graphs and introduce the commonly used graph datasets for thorough evaluations. Finally, we share our insights on future research directions.
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http://dx.doi.org/10.1109/TPAMI.2025.3593897 | DOI Listing |
Brief Bioinform
August 2025
State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China.
The systematic identification of human-virus protein-protein interactions (PPIs) is a critical step toward elucidating the underlying mechanisms of viral infection, directly informing the development of targeted interventions against existing and emerging viral threats. In this work, we presented DeepGNHV, an end-to-end framework that integrated a pretrained protein language model with structural features derived from AlphaFold2 and leveraged graph attention networks to predict human-virus PPIs. In comparison to other state-of-the-art approaches, DeepGNHV exhibited superior predictive performance, especially when applied to viral proteins absent from the training process, indicating its strong generalization capability for detecting newly emerging virus-related PPIs.
View Article and Find Full Text PDFBrief Bioinform
August 2025
College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, P. R. China.
Drug-induced hepatotoxicity (DIH), characterized by diverse phenotypes and complex mechanisms, remains a critical challenge in drug discovery. To systematically decode this diversity and complexity, we propose a multi-dimensional computational framework integrating molecular structure analysis with disease pathogenesis exploration, focusing on drug-induced intrahepatic cholestasis (DIIC) as a representative DIH subtype. First, a graph-based modularity maximization algorithm identified DIIC risk genes, forming a DIIC module and eight disease pathogenesis clusters.
View Article and Find Full Text PDFJ Pharm Anal
August 2025
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
P-glycoprotein (P-gp) is a transmembrane protein widely involved in the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs within the human body. Accurate prediction of P-gp inhibitors and substrates is crucial for drug discovery and toxicological assessment. However, existing models rely on limited molecular information, leading to suboptimal model performance for predicting P-gp inhibitors and substrates.
View Article and Find Full Text PDFRSC Med Chem
August 2025
Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University 4.5 Km the Ring Road Ismailia 41522 Egypt.
Protein kinases are central regulators of cell signaling and play pivotal roles in a wide array of diseases, most notably cancer and autoimmune disorders. The clinical success of kinase inhibitors-such as imatinib and osimertinib-has firmly established kinases as valuable drug targets. However, the development of selective, potent inhibitors remains challenging due to the conserved nature of the ATP-binding site, off-target effects, resistance mutations, and patient-specific variability.
View Article and Find Full Text PDFAuton Agent Multi Agent Syst
September 2025
University of Groningen, Groningen, The Netherlands.
Unlabelled: The popularity of an opinion in one's direct circles is not necessarily a good indicator of its popularity in one's entire community. Network structures make local information about global properties of the group potentially inaccurate, and the way a social network is wired constrains what kind of information distortion can actually occur. In this paper, we discuss which classes of networks allow for a large enough proportion of the population to get a wrong enough impression about the overall distribution of opinions.
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