Yuannong Ye

Rijie Xi, Weikang Xu, Wei Xiong et al.

Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since GRNs are ideally modeled as signed directed graphs to capture activation/inhibition relationships, the most intuitive and reasonable approach is to design feature extractors based on the topological structure of GRNs to extract structural features, then combine them with biological characteristics for research. However, traditional spectral graph convolution struggles with this representation. Thus, we propose MSGRNLink, a novel framework that explicitly models GRNs as signed directed graphs and employs magnetic signed Laplacian convolution. Experiments across simulated and real datasets demonstrate that MSGRNLink outperforms all baseline models in AUROC. Parameter sensitivity analysis and ablation studies confirmed its robustness and the importance of each module. In a bladder cancer case study, MSGRNLink predicted more known edges and edge signs than benchmark models, further validating its biological relevance.

Xiaofang Liu, Lingling Sun, Xuqing Zhang et al.

Colorectal cancer (CRC) is closely linked to the malignant transformation of colorectal polyps, making early detection essential. However, current models struggle with detecting small lesions, accurately localizing boundaries, and providing interpretable decisions. To address these issues, we propose HGNet, which integrates High-Order Spatial Awareness Hypergraph and Multi-Scale Context Attention. Key innovations include: (1) an Efficient Multi-Scale Context Attention (EMCA) module to enhance lesion feature representation and boundary modeling; (2) the deployment of a spatial hypergraph convolution module before the detection head to capture higher-order spatial relationships between nodes; (3) the application of transfer learning to address the scarcity of medical image data; and (4) Eigen Class Activation Map (Eigen-CAM) for decision visualization. Experimental results show that HGNet achieves 94% accuracy, 90.6% recall, and 90% mAP@0.5, significantly improving small lesion differentiation and clinical interpretability. The source code will be made publicly available upon publication of this paper.