MultiCausGRN: directed prior-guided graph attention model for multi-omics gene regulatory network inference

Introduction: Existing methods for gene regulatory network (GRN) inference rely primarily on gene expression data alone or on lower-resolution bulk sequencing data. Despite recent advances in integrating chromatin accessibility and RNA sequencing, inferring GRNs from paired single-cell multi-omics data remains challenging due to noise, sparsity, and complex nonlinear regulatory relationships. Methods: We present MultiCausGRN, a graph attention network (GAT)-based framework for GRN inference from paired scRNA-seq and scATAC-seq data. The model incorporates directed prior-guided graph attention learning to capture biologically grounded regulatory directionality by integrating curated directed regulatory edges into graph representation learning. MultiCausGRN performs supervised transcription factor-target link prediction using integrated multi-omics features within a two-layer graph attention architecture. Results: 0.026 across five independent random seeds. Discussion: These results demonstrate that directed prior-guided graph learning can improve the robustness and biological interpretability of GRN inference in data-limited settings. MultiCausGRN is publicly available at: https://github.com/nrr-90/MultiCausGRN.