A Novel Graph Transformer Framework for Gene Regulatory Network Inference

Abstract: The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction problem. Inference of GRNs via gene coexpression profiling data may not always reflect true biological interactions, as its susceptibility to noise and misrepresenting true biological regulatory relationships. Most GRN inference methods face several challenges in the network reconstruction phase. Therefore, it is important to encode gene expression values, leverege the prior knowledge gained from the available inferred network structures and positional informations of the input network nodes towards inferring a better and more confident GRN network reconstruction. In this paper, we explore the integration of multiple inferred networks to enhance the inference of Gene Regulatory Networks (GRNs). Primarily, we employ autoencoder embeddings to capture gene expression patterns directly from raw data, preserving intricate biological signals. Then, we embed the prior knowledge from GRN structures transforming them into a text-like representation using random walks, which are then encoded with a masked LLM, BERT, to generate global embeddings for each gene across all networks. Additionally, we embed the positional encodings of the input gene networks to better identify the position of each unique gene within the graph. These embeddings are integrated into graph transformer-based model, termed GT-GRN, for GRN inference. The GT-GRN model effectively utilizes the topological structure of the ground truth network while incorporating the enriched encoded information. Experimental results demonstrate that GT-GRN significantly outperforms existing GRN inference methods, achieving superior accuracy and highlighting the robustness of our approach.