Deep autoencoder neural networks for gene ontology annotation predictions

The annotation of genomic information is a major challenge in biology and bioinformatics. Existing databases of known gene functions are incomplete and prone to errors, and the bimolecular experiments needed to improve these databases are slow and costly. While computational methods are not a substitute for experimental verification, they can help in two ways: algorithms can aid in the curation of gene annotations by automatically suggesting inaccuracies, and they can predict previously-unidentified gene functions, accelerating the rate of gene function discovery. In this work, we develop an algorithm that achieves both goals using deep autoencoder neural networks. With experiments on gene annotation data from the Gene Ontology project, we show that deep autoencoder networks achieve better performance than other standard machine learning methods, including the popular truncated singular value decomposition.