Gene regulatory network inference algorithm based on spectral signed directed graph convolution
This work addresses the challenge of GRN inference for computational biology, offering an incremental improvement by adapting spectral methods to signed directed graphs.
The paper tackled the problem of accurately reconstructing Gene Regulatory Networks (GRNs) from single-cell RNA sequencing data by modeling them as signed directed graphs, and the result was that their MSGRNLink framework outperformed all baseline models in AUROC across simulated and real datasets, predicting more known edges and edge signs in a bladder cancer case study.
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.