NewGOA: Predicting New GO Annotations of Proteins by Bi-Random Walks on a Hybrid Graph.

A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins. To account for structural difference between GO terms subgraph and proteins subgraph, NewGOA applies a bi-random walks algorithm, which executes asynchronous random walks on the hybrid graph, to predict new GO annotations of proteins. Experimental study on archived GO annotations of two model species (H. Sapiens and S. cerevisiae) shows that NewGOA can more accurately and efficiently predict new annotations of proteins than other related methods. Experimental results also indicate the bi-random walks can explore and further exploit the structural difference between GO terms subgraph and proteins subgraph. The supplementary files and codes of NewGOA are available at: https://mlda.swu.edu.cn/codes.php?name=NewGOA.