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Gene Ontology(GO)is a controlled vocabulary of terms that describe molecule function,biological roles and cellular locations of gene products(i.e.,proteins and RNAs),it hierarchically organizes more than 43,000 GO terms via the direct acyclic graph.A gene is generally annotated with several of these GO terms.Therefore,accurately predicting the association between genes and massive terms is a difficult challenge.To combat with this challenge,we propose an matrix factorization based approach called NMFGO.NMFGO stores the available GO annotations of genes in a gene-term association matrix and adopts an ontological structure based taxonomic similarity measure to capture the GO hierarchy.