Gene function prediction based on combining gene ontology hierarchy with multi-instance multi-label learning

Gene function annotation is the main challenge in the post genome era, which is an important part of the genome annotation. The sequencing of the human genome project produces a whole genome data, providing abundant biological information for the study of gene function annotation. However, to obtain useful knowledge from a large amount of data, a potential strategy is to apply machine learning methods to mine these data and predict gene function. In this study, we improved multi-instance hierarchical clustering by using gene ontology hierarchy to annotate gene function, which combines gene ontology hierarchy with multi-instance multi-label learning frame structure. Then, we used multi-label support vector machine (MLSVM) and multi-label k-nearest neighbor (MLKNN) algorithm to predict the function of gene. Finally, we verified our method in four yeast expression datasets. The performance of the simulated experiments proved that our method is efficient.