Recent Advances in Variational Autoencoders With Representation Learning for Biomedical Informatics: A Survey

Variational autoencoders (VAEs) are deep latent space generative models that have been immensely successful in multiple exciting applications in biomedical informatics such as molecular design, protein design, medical image classification and segmentation, integrated multi-omics data analyses, and large-scale biological sequence analyses, among others. The fundamental idea in VAEs is to learn the distribution of data in such a way that new meaningful data with more intra-class variations can be generated from the encoded distribution. The ability of VAEs to synthesize new data with more representation variance at state-of-art levels provides hope that the chronic scarcity of labeled data in the biomedical field can be resolved. Furthermore, VAEs have made nonlinear latent variable models tractable for modeling complex distributions. This has allowed for efficient extraction of relevant biomedical information from learned features for biological data sets, referred to as unsupervised feature representation learning. In this article, we review the various recent advancements in the development and application of VAEs for biomedical informatics. We discuss challenges and future opportunities for biomedical research with respect to VAEs.