MOTIVATION: Integrating multi-omics data provides valuable insights into biological processes by capturing information across multiple molecular layers, enabling a comprehensive understanding of complex diseases and driving advancements in precision medicine. However, existing computational methods for multi-omics integration face significant challenges, such as low reliability and poor generalizability, due to the high dimensionality and low sample size nature of omics data. RESULTS: To address these challenges, we present PEARL (Pearson-Enhanced spectrAl gRaph convoLutional networks), a novel deep graph learning method for biomedical classification and functional important omics features identification. PEARL leverages a simple yet effective learning architecture to achieve superior and robust performance in high-dimensional, low-sample-size multi-omics settings. Our results demonstrate that PEARL significantly outperforms existing state-of-the-art methods on both synthetic and real biomedical datasets. Furthermore, applied to Alzheimer's disease (AD) brain multi-omics data, features prioritized by PEARL lead to functionally important genes that demonstrate significant enrichment in AD-related pathways. These findings highlight PEARL's practical utility in biomedical research and its potential to enhance biological interpretability in multi-omics studies. AVAILABILITY AND IMPLEMENTATION: The source code of our computational framework is available at https://github.com/zqq121017/PEARL.

Drug repositioning presents a compelling strategy to accelerate therapeutic development by uncovering new indications for existing compounds. However, current computational methods are often limited in their ability to integrate heterogeneous biomedical data and model the intricate, multiscale relationships underlying drug-disease associations, while large-scale experimental validation remains prohibitively resource-intensive. Here, we present DREAM-GNN (Dual-Route Embedding-Aware Model for Graph Neural Networks), a multiview deep graph learning framework that incorporates biomedical domain knowledge with two complementary graphs capturing both topological structure and feature similarity to enable accurate and biologically meaningful prediction of drug-disease associations. Extensive experiments on benchmark datasets demonstrate that DREAM-GNN significantly outperforms current state-of-the-art methods in recovering artificially removed repositioning candidates, including in scenarios involving unseen drugs and diseases. These results establish DREAM-GNN as a robust and generalizable computational framework with broad potential to streamline drug discovery and advance precision medicine.

With the advent of the era of big data, people’s lives have undergone earth-shaking changes, not only getting rid of the cumbersome traditional data collection but also collecting and sorting information directly from people’s footprints on social networks. This paper explores and analyzes the privacy issues in current social networks and puts forward the protection strategies of users’ privacy data based on data mining algorithms so as to truly ensure that users’ privacy in social networks will not be illegally infringed in the era of big data. The data mining algorithm proposed in this paper can protect the user’s identity from being identified and the user’s private information from being leaked. Using differential privacy protection methods in social networks can effectively protect users’ privacy information in data publishing and data mining. Therefore, it is of great significance to study data publishing, data mining methods based on differential privacy protection, and their application in social networks.