Probabilistic Joint and Individual Variation Explained (ProJIVE) for Data Integration

Collecting multiple types of data on the same set of subjects is common in modern scientific applications including genomics, metabolomics, and neuroimaging. Joint and Individual Variation Explained (JIVE) seeks a low-rank approximation of the joint variation between two or more sets of features captured on common subjects and isolates this variation from that unique to each set of features. We develop an expectation-maximization (EM) algorithm to estimate a probabilistic model for the JIVE framework. The model extends probabilistic PCA to multiple datasets. Our maximum likelihood approach simultaneously estimates joint and individual components, which can lead to greater accuracy compared to other methods. We apply ProJIVE to measures of brain morphometry and cognition in Alzheimer’s disease. ProJIVE learns biologically meaningful sources of variation, and the joint morphometry and cognition subject scores are strongly related to more expensive existing biomarkers. Data used in preparation of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. Code to reproduce the analysis is available at https://github.com/thebrisklab/ProJIVE.