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Graph level anomaly detection (GLAD) aims to spot anomalous graphs that structure pattern and feature information are different from most normal graphs in a graph set, which is rarely studied by other researchers but has significant application value. For instance, GLAD can be used to distinguish some different characteristic molecules in drug discovery and chemical analysis. However, GLAD mainly faces the following three challenges: (1) learning more comprehensive graph level representations to differ normal graphs and abnormal graphs, (2) designing an effective graph anomaly evaluation paradigm to capture graph anomalies from the local and global graph perspectives, (3) overcoming the number imbalance problem of normal and abnormal graphs. In this paper, we combine graph neural networks and contrastive learning to build an end-to-end GLAD framework for solving the three challenges above. We aim to design a new graph level anomaly evaluation way, which first utilizes the contrastive learning strategy to enhance different level representations of normal graphs from node and graph levels by a graph convolution autoencoder with perturbed graph encoder. Then, we evaluate the error of them with corresponding representations of the generated reconstruction graph to detect anomalous graphs. Extensive experiments on ten real-world datasets from three areas, such as molecular, protein and social network anomaly graphs, show that our model can effectively detect graph level anomaly from the majority and outperform existing advanced methods.
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http://dx.doi.org/10.1038/s41598-022-22086-3 | DOI Listing |
iScience
September 2025
Max Planck Institute of Psychiatry, 80804 Munich, Germany.
Isoform-specific expression patterns have been linked to stress-related psychiatric disorders such as major depressive disorder (MDD). To further explore their involvement, we constructed co-expression networks using total gene expression (TE) and isoform ratio (IR) data from affected ( = 210, 81% with depressive symptoms) and unaffected ( = 95) individuals. Networks were validated using advanced graph generation methods.
View Article and Find Full Text PDFFront Hum Neurosci
August 2025
Baptist Medical Center, Department of Behavioral Health, Jacksonville, FL, United States.
Introduction: This study investigates four subdomains of executive functioning-initiation, cognitive inhibition, mental shifting, and working memory-using task-based functional magnetic resonance imaging (fMRI) data and graph analysis.
Methods: We used healthy adults' functional magnetic resonance imaging (fMRI) data to construct brain connectomes and network graphs for each task and analyzed global and node-level graph metrics.
Results: The bilateral precuneus and right medial prefrontal cortex emerged as pivotal hubs and influencers, emphasizing their crucial regulatory role in all four subdomains of executive function.
Metabolomics
September 2025
Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.
Introduction: Initially developed for transcriptomics data, pathway analysis (PA) methods can introduce biases when applied to metabolomics data, especially if input parameters are not chosen with care. This is particularly true for exometabolomics data, where there can be many metabolic steps between the measured exported metabolites in the profile and internal disruptions in the organism. However, evaluating PA methods experimentally is practically impossible when the sample's "true" metabolic disruption is unknown.
View Article and Find Full Text PDFPLoS One
September 2025
School of Mechanical and Automotive Engineering, Qingdao University of Technology, Qingdao, Shandong, China.
Drug-target interaction (DTI) prediction is essential for the development of novel drugs and the repurposing of existing ones. However, when the features of drug and target are applied to biological networks, there is a lack of capturing the relational features of drug-target interactions. And the corresponding multimodal models mainly depend on shallow fusion strategies, which results in suboptimal performance when trying to capture complex interaction relationships.
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.
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