TY - JOUR T1 - GNE: A deep learning framework for gene network inference by aggregating biological information JF - bioRxiv DO - 10.1101/300996 SP - 300996 AU - KC Kishan AU - Rui Li AU - Feng Cui AU - Anne R. Haake Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/04/13/300996.abstract N2 - Motivation The topological landscape of gene interaction networks provides a rich source of information for inferring functional patterns of genes or proteins. However, it is still a challenging task to aggregate heterogeneous biological information such as gene expression and gene interactions to achieve more accurate inference for prediction and discovery of new gene interactions. In particular, how to generate a unified vector representation to integrate diverse input data is a key challenge addressed here.Results We propose a scalable and robust deep learning framework to learn embedded representations to unify known gene interactions and gene expression for gene interaction predictions. These low-dimensional embeddings derive deeper insights into the structure of rapidly accumulating and diverse gene interaction networks and greatly simplify downstream modeling. We compare the predictive power of our deep embeddings to the state-of-the-art machine learning methods. The results suggest that our deep embeddings achieve significantly more accurate predictions. Moreover, a set of novel gene interaction predictions are validated by up-to-date literature-based database entries.Availability Source code and preprocessed datasets are available at https://github.com/kckishan/GNE under the GNU General Public License.Contact kk3671{at}rit.edu ER -