Detecting anomalies for dynamic graphs has drawn increasing attention due to their wide applications in social networks, e-commerce, and cybersecurity. Recent deep learning-based approaches have shown promising results over shallow methods. However, they fail to address two core challenges of anomaly detection in dynamic graphs: the lack of informative encoding for unattributed nodes and the difficulty of learning discriminate knowledge from coupled spatial-temporal dynamic graphs. To overcome these challenges, in this paper, we present a novel T ransformer-based A nomaly D etection framework for DY namic graphs ( TADDY ). Our framework constructs a comprehensive node encoding strategy to better represent each node’s structural and temporal roles in an evolving graphs stream. Meanwhile, TADDY captures informative representation from dynamic graphs with coupled spatial-temporal patterns via a dynamic graph transformer model. The extensive experimental results demonstrate that our proposed TADDY framework outperforms the state-of-the-art methods by a large margin on six real-world datasets.

Deep learning-based multi-omics data integration methods have the capability to reveal the mechanisms of cancer development, discover cancer biomarkers and identify pathogenic targets. However, current methods ignore the potential correlations between samples in integrating multi-omics data. In addition, providing accurate biological explanations still poses significant challenges due to the complexity of deep learning models. Therefore, there is an urgent need for a deep learning-based multi-omics integration method to explore the potential correlations between samples and provide model interpretability. Herein, we propose a novel interpretable multi-omics data integration method (DeepKEGG) for cancer recurrence prediction and biomarker discovery. In DeepKEGG, a biological hierarchical module is designed for local connections of neuron nodes and model interpretability based on the biological relationship between genes/miRNAs and pathways. In addition, a pathway self-attention module is constructed to explore the correlation between different samples and generate the potential pathway feature representation for enhancing the prediction performance of the model. Lastly, an attribution-based feature importance calculation method is utilized to discover biomarkers related to cancer recurrence and provide a biological interpretation of the model. Experimental results demonstrate that DeepKEGG outperforms other state-of-the-art methods in 5-fold cross validation. Furthermore, case studies also indicate that DeepKEGG serves as an effective tool for biomarker discovery. The code is available at https://github.com/lanbiolab/DeepKEGG.

Multiview subspace clustering (MVSC) has been used to explore the internal structure of multiview datasets by revealing unique information from different views. Most existing methods ignore the consistent information and angular information of different views. In this article, we propose a novel MVSC via low-rank symmetric affinity graph (LSGMC) to tackle these problems. Specifically, considering the consistent information, we pursue a consistent low-rank structure across views by decomposing the coefficient matrix into three factors. Then, the symmetry constraint is utilized to guarantee weight consistency for each pair of data samples. In addition, considering the angular information, we utilize the fusion mechanism to capture the inherent structure of data. Furthermore, to alleviate the effect brought by the noise and the high redundant data, the Schatten p-norm is employed to obtain a low-rank coefficient matrix. Finally, an adaptive information reduction strategy is designed to generate a high-quality similarity matrix for spectral clustering. Experimental results on 11 datasets demonstrate the superiority of LSGMC in clustering performance compared with ten state-of-the-art multiview clustering methods.

Increasing evidences have proved that circRNA plays a significant role in the development of many diseases. In addition, many researches have shown that circRNA can be considered as the potential biomarker for clinical diagnosis and treatment of disease. Some computational methods have been proposed to predict circRNA-disease associations. However, the performance of these methods is limited as the sparsity of low-order interaction information. In this paper, we propose a new computational method (KGANCDA) to predict circRNA-disease associations based on knowledge graph attention network. The circRNA-disease knowledge graphs are constructed by collecting multiple relationship data among circRNA, disease, miRNA and lncRNA. Then, the knowledge graph attention network is designed to obtain embeddings of each entity by distinguishing the importance of information from neighbors. Besides the low-order neighbor information, it can also capture high-order neighbor information from multisource associations, which alleviates the problem of data sparsity. Finally, the multilayer perceptron is applied to predict the affinity score of circRNA-disease associations based on the embeddings of circRNA and disease. The experiment results show that KGANCDA outperforms than other state-of-the-art methods in 5-fold cross validation. Furthermore, the case study demonstrates that KGANCDA is an effective tool to predict potential circRNA-disease associations.

With the rapid development of Large Language Model (LLM) technology, it has become an indispensable force in biomedical data analysis research. However, biomedical researchers currently have limited knowledge about LLM. Therefore, there is an urgent need for a summary of LLM applications in biomedical data analysis. Herein, we propose this review by summarizing the latest research work on LLM in biomedicine. In this review, LLM techniques are first outlined. We then discuss biomedical datasets and frameworks for biomedical data analysis, followed by a detailed analysis of LLM applications in genomics, proteomics, transcriptomics, radiomics, single-cell analysis, medical texts and drug discovery. Finally, the challenges of LLM in biomedical data analysis are discussed. In summary, this review is intended for researchers interested in LLM technology and aims to help them understand and apply LLM in biomedical data analysis research.