arXiv subjects

Xueying Tian

Publications and source records attributed to Xueying Tian.

2 recordsLinked to original sources

arXiv2025

QWENDY: Gene Regulatory Network Inference by Quadruple Covariance Matrices

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 of the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. We test the performance of QWENDY on three experimental data sets and two synthetic data sets. Compared to previously tested methods on the same data sets, QWENDY ranks the first on experimental data, although it does not perform well on synthetic data.

q-bio.MN↗

arXiv2025

TRENDY: Gene Regulatory Network Inference Enhanced by Transformer

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. 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.

q-bio.MN↗