AutoOmics: New multimodal approach for multi-omics research

Abstract

Deep learning is very promising in solving problems in omics research, such as genomics, epigenomics, proteomics, and metabolics. The design of neural network architecture is very important in modeling omics data against different scientific problems. Residual fully-connected neural network (RFCN) was proposed to provide better neural network architectures for modeling omics data. The next challenge for omics research is how to integrate information from different omics data using deep learning, so that information from different molecular system levels could be combined to predict the target. In this paper, we present a novel multi-omics integration approach named AutoOmics that could efficiently integrate information from different omics data and achieve better accuracy than previous approaches. We evaluated our method on four different tasks: drug repositioning, target gene prediction, breast cancer subtyping and cancer type prediction, and all the four tasks achieved state of art performances.