TRENDY: gene regulatory network inference enhanced by transformer.

MOTIVATION: Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and more recent deep learning techniques, the last of which often overlook the underlying gene expression mechanisms. RESULTS: In this work, we introduce TRENDY, a novel GRN inference method that integrates transformer models to enhance the mechanism-based WENDY approach. Through testing on both simulated and experimental datasets, TRENDY demonstrates superior performance compared to existing methods. Furthermore, we apply this transformer-based approach to three additional inference methods, showcasing its broad potential to enhance GRN inference. AVAILABILITY AND IMPLEMENTATION: Code and data files are available at https://github.com/YueWangMathbio/TRENDY, with DOI: 10.6084/m9.figshare.28236074.