QWENDY: Gene Regulatory Network Inference Enhanced by Large Language Model and Transformer

Abstract: Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based on a linear gene expression model, it solves the transformation for the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. Then we enhance QWENDY by the transformer neural networks and LLMs to obtain two variants: TEQWENDY and LEQWENDY. We test the performance of these methods on two experimental data sets and two synthetic data sets. TEQWENDY has the best overall performance, while QWENDY ranks the first on experimental data sets.