Abstract

Gene expression microarrays provide a characterisation of the transcriptional activity of a particular biological sample. While extemely informative, their high dimensionality hampers the process of pattern extraction. Several approaches have been proposed for gleaning information about the hidden structure of the data. Among these approaches, deep generative models provide a powerful way for approximating the manifold on which the data reside. In this talk I will introduce a deep learning based framework that provides novel insight into the manifold learning for gene expression data, employing a metabolic model to constrain the learned representation. The proposed framework is evaluated, showing its ability to capture biologically relevant features, and encoding that features in a much simpler latent space. We showed how using a metabolic model to drive the autoencoder learning process helps in achieving better generalisation to unseen data.