Bayesian unsupervised learning with multiple data types

Abstract

We propose Bayesian generative models for unsupervised learning with two types of data and an assumed dependency of one type of data on the other. We consider two algorithmic ap- proaches, based on a correspondence model where latent variables are shared across datasets. These models indicate the appropriate number of clusters in addition to indicating relevant features in both types of data. We evaluate the model on arti¯cially created data. We then apply the method to a breast cancer dataset consisting of gene expression and microRNA array data derived from the same patients. We assume dependence of gene expression on microRNA expression in this study. The method ranks genes within subtypes which have statistically signi¯cant abnormal expression and ranks associated abnormally expressing mi- croRNA. We report a genetic signature for the basal-like subtype of breast cancer found across a number of previous gene expression array studies. Using the two algorithmic ap- proaches we ¯nd that this signature also arises from clustering on the microRNA expression data and appears derivative from this data.