Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and exhaustive wet lab experiments. Existing methods of automatic function annotation or prediction mainly focus on protein function prediction with sequence, 3D-structures or protein family information. In this study, we propose to tackle the gene function prediction problem by exploring Gene Ontology graph and annotation with BERT (GoBERT) to decipher the underlying relationships among gene functions. Our proposed novel function prediction task utilizes existing functions as inputs and generalizes the function prediction to gene and gene products. Specifically, two pre-train tasks are designed to jointly train GoBERT to capture both explicit and implicit relations of functions. Neighborhood prediction is a self-supervised multi-label classification task that captures the explicit function relations. Specified masking and recovering task helps GoBERT in finding implicit patterns among functions. The pre-trained GoBERT possess the ability to predict novel functions for various gene and gene products based on known functional annotations. Extensive experiments, biological case studies, and ablation studies are conducted to demonstrate the superiority of our proposed GoBERT.

Fox News Flash top headlines are here. Check out what's clicking on Foxnews.com. Donovan Mitchell scored 24 points, Rudy Gobert had 23 points and 20 rebounds, and the Utah Jazz rolled past the short-handed Los Angeles Clippers 114-96 on Wednesday night for their ninth consecutive victory. Jordan Clarkson scored 18 points for the NBA-leading Jazz, who improved to 24-5 with their 20th win in 21 games. After three tight quarters, Utah broke it open in the fourth to win this matchup of Western Conference powerhouses -- although it wasn't a proper showdown with the Clippers missing injured superstars Kawhi Leonard and Paul George.